WO2025212750A1 - Biomolecule preparation methods, kits, and systems - Google Patents
Biomolecule preparation methods, kits, and systemsInfo
- Publication number
- WO2025212750A1 WO2025212750A1 PCT/US2025/022713 US2025022713W WO2025212750A1 WO 2025212750 A1 WO2025212750 A1 WO 2025212750A1 US 2025022713 W US2025022713 W US 2025022713W WO 2025212750 A1 WO2025212750 A1 WO 2025212750A1
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- composition
- particle
- biomolecules
- particles
- formula
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Classifications
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
- G01N33/6848—Methods of protein analysis involving mass spectrometry
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- C—CHEMISTRY; METALLURGY
- C08—ORGANIC MACROMOLECULAR COMPOUNDS; THEIR PREPARATION OR CHEMICAL WORKING-UP; COMPOSITIONS BASED THEREON
- C08L—COMPOSITIONS OF MACROMOLECULAR COMPOUNDS
- C08L33/00—Compositions of homopolymers or copolymers of compounds having one or more unsaturated aliphatic radicals, each having only one carbon-to-carbon double bond, and only one being terminated by only one carboxyl radical, or of salts, anhydrides, esters, amides, imides or nitriles thereof; Compositions of derivatives of such polymers
- C08L33/04—Homopolymers or copolymers of esters
- C08L33/06—Homopolymers or copolymers of esters of esters containing only carbon, hydrogen and oxygen, which oxygen atoms are present only as part of the carboxyl radical
- C08L33/10—Homopolymers or copolymers of methacrylic acid esters
- C08L33/12—Homopolymers or copolymers of methyl methacrylate
-
- B—PERFORMING OPERATIONS; TRANSPORTING
- B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
- B01J—CHEMICAL OR PHYSICAL PROCESSES, e.g. CATALYSIS OR COLLOID CHEMISTRY; THEIR RELEVANT APPARATUS
- B01J20/00—Solid sorbent compositions or filter aid compositions; Sorbents for chromatography; Processes for preparing, regenerating or reactivating thereof
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2446/00—Magnetic particle immunoreagent carriers
- G01N2446/80—Magnetic particle immunoreagent carriers characterised by the agent used to coat the magnetic particles, e.g. lipids
- G01N2446/84—Polymer coating, e.g. gelatin
Definitions
- the methods, kits, and systems provided herein rely on the use of a combination of at least two particles (e.g., comprising macromolecule structures) comprising different surface charges for the isolation, purification, and identification of biomolecules (e.g., proteins or peptides).
- the first macromolecule structure may have a neutral to negative surface charge, such as measured by zeta potential.
- the second macromolecule structure may have a highly negative or more negative surface charge compared to that of the first macromolecule structure.
- this first and second macromolecule structure provides a synergistic relationship that allows for increased ability to isolate, purify, and identify biomolecules, such as proteins in comparison to the use of each of the particles (e.g., comprising the macromolecule structures) on their own.
- Increases in ability to isolate and identify biomolecules present advantages over generally used methods such as various forms of chromatography or suspension trapping, since the methods provided herein are widely applicable and lead to high yields of desired biomolecules, high reproducibility in the identification of biomolecules, and significant number of identifiable biomolecules.
- the methods, kits, and systems provided herein provide for the preparation of biomolecules for further identification or analysis.
- compositions comprising two or more particles comprising: (a) a first particle comprising a first macromolecule structure, the first particle comprising a neutral to negative surface charge; and (b) a second particle comprising a second macromolecule structure, the second particle comprising a greater negative surface charge than the first particle.
- the first particle has a surface charge of greater than -20 mV.
- the second macromolecule structure comprises a polymer comprising one or more units represented by Formula (A): Formula (A) wherein, R is hydrogen R 1 is hydrogen or hydroxyl; q is an integer from 1 to 6; R 2 is C1-C8 diamine, N-substituted with one or more R 3 ; WSGR Docket No.53344-792.601 R 3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; or R 1 and R 2 are taken together to form C 2 -C 6 heterocycloalkyl; and R 4 is hydrogen or C 1 -C 6 alkyl.
- the second macromolecule structure comprises a copolymer comprising two or more units represented by Formula (A) and Formula (B): wherein, R is hydrogen R 1 is hydrogen or hydroxyl; q is an integer from 1 to 6; m is an integer from 1 to 6; R 2 is C1-C8 diamine, N-substituted with one or more R 3 ; R 3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C 1 -C 8 alkyl, C 1 -C 8 alkenyl, and C 1 -C 8 alkynyl; or R 1 and R 2 are taken together to form C 2 -C 6 heterocycloalkyl; R 4 is each independently hydrogen or C1-C6 alkyl; is a single bond or a double bond; and * is an attachment point to another unit of Formula (A) or Formula (B) when is a single bond.
- R is hydrogen
- R 1 is hydrogen or hydroxyl
- q is
- R is .
- R 1 is hydroxyl.
- R 2 is a C2 diamine, N-substituted with one or more R 3 .
- At least one R 3 is C 1 -C 8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl. In some embodiments, at least one R 3 is C1-C8 alkyl substituted with at least one of oxo, hydroxyl, and C 1 -C 8 alkenyl. In some embodiments, the structure of Formula (A) is represented by Formula (A-A): Formula (A-A) wherein, R 5 is C 1 -C 10 alkyl, C 1 -C 10 alkenyl, or C 1 -C 10 alkynyl.
- the structure of Formula (A) is represented by Formula (A-B): Formula (A-B) wherein, WSGR Docket No.53344-792.601 R 5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl.
- the structure of Formula (A) is Formula (A-C): Formula (A-C) wherein, R 5 is each independently C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl.
- the structure of Formula (A-C) is: .
- the structure of Formula (A) is represented by Formula (A-D): Formula (A-D)
- q is an integer from 1 to 3.
- q is an integer of 1.
- R 5 is C1-C10 alkenyl.
- R is hydrogen.
- the structure of Formula (A) is: .
- R 1 and R 2 are taken together to form C 2 heterocycloalkyl.
- m is an integer of 1.
- R 4 is C 1 -C 6 alkyl.
- the structure of Formula (B) is: WSGR Docket No.53344-792.601 .
- the copolymer comprises the structure: .
- the first macromolecule structure comprises a copolymer comprising two or more units represented by Formula (D) and Formula (E): wherein, R 4 is each independently hydrogen or C 1 -C 6 alkyl; R 6 is hydrogen or (CH2)pOR 7 ; R 7 is hydrogen or C 1 -C 6 alkyl; m is an integer from 1 to 6; p is an integer from 1 to 6; is a single bond or a double bond; and * is an attachment point to another unit of Formula (D) or Formula (E) when is a single bond.
- R 6 is (CH 2 ) p OR 7 .
- the first macromolecule structure comprises a copolymer comprising three or more units represented by: WSGR Docket No.53344-792.601
- the unit represented by is present in the first macromolecule structure in an amount of less than 5 wt%.
- the two or more particles are nanoparticles.
- the two or more particles are microparticles.
- the two or more particles each individually have a diameter of from about 100 nm to about 750 nm. In some embodiments, the two or more particles each individually have a diameter of from about 100 nm to about 500 nm.
- the two or more particles each individually have a polydispersity index (PDI) of from about 0.01 to about 0.2. In some embodiments, the two or more particles each individually have a PDI of from about 0.1 to about 0.2. In some embodiments, the two or more particles comprises iron oxide. In some embodiments, the two or more particles comprises a superparamagnetic iron oxide nanoparticle. In some embodiments, the two or more particles comprises a core-shell structure. In some embodiments, the core of the core-shell structure is paramagnetic. In some embodiments, the two or more particles comprise an iron oxide core and a silica shell. In some embodiments, the particle comprises iron oxide crystals embedded in a polystyrene core.
- PDI polydispersity index
- the polymer or the copolymer is covalently coupled to a surface of the particle. In some embodiments, the polymer is non-covalently coupled to a surface of the particle. In some embodiments, the polymer or copolymer is covalently coupled to a surface of the particle via a linker.
- the first particle comprises the structure: wherein, is a surface of the first particle; L is a linker; and A is a copolymer described herein.
- the second particle comprises the structure: WSGR Docket No.53344-792.601 wherein, is a surface of the second particle; L is a linker; and B is the polymer or copolymer described herein.
- the linker comprises an alkylene, esteralkylene, or aralkylene.
- the polymer or copolymer is covalently coupled to the surface via a base polymer.
- the composition further comprises a stabilizing agent.
- the stabilizing agent comprises a metal salt.
- the metal salt comprises aluminum chloride.
- the copolymer is a random copolymer.
- the copolymer is a block copolymer.
- the composition comprises at least 1 wt% of the polymer or copolymer. In some embodiments, the composition comprises from about 1 wt% to about 30 wt% of the polymer or copolymer.
- a method of isolating one or more biomolecules from a biological sample comprising: (a) contacting the biological sample comprising one or more biomolecules with a composition provided herein to bind the one or more biomolecules to the at least two particles, thereby forming at least two biomolecule corona; and (b) eluting the one or more biomolecules from the at least two particles, thereby providing one or more isolated biomolecules.
- assaying detects at least 10% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, assaying detects at least 60% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. In some embodiments, the method further comprises separating the one or more biomolecules and the at least two particles from the biological sample. In some embodiments, the method further comprises optionally digesting, alkylating, and/or lysing the one or more biomolecules to provide one or more digested biomolecules. In some embodiments, the one or more biomolecules comprises proteins, peptides, or a combination thereof.
- the biological sample comprises plasma, serum, or blood. In some embodiments, the biological sample comprises biofluid. In some embodiments, the biofluid is a cell-free biofluid. In some embodiments, the method further comprises diluting the one or more biomolecules and at least two particles. In some embodiments, the one or more biomolecules and at least two particles are diluted in a buffer. In some embodiments, the methods further comprise eluting the one or more biomolecules from the two or more particles. In some embodiments, eluting is in the presence of buffer or an aqueous solution. In some embodiments, the contacting is in the presence of a buffer.
- the buffer comprise a pH of from about 7 to about 8 (e.g., pH of about 8.5). In some embodiments, the buffer comprises a pH of from about 7.4 to 7.6 (e.g., pH of about 7.5). In some embodiments, the buffer comprises HEPES. In some embodiments, one of the first particle or second particle is contacted with the one or more biomolecules at a concentration of 0.1 mg/mL to 0.2 mg/mL. In some embodiments, one of the first particle or second particle is contacted with the one or more biomolecules at a concentration of 0.5 mg/mL to 0.6 mg/mL.
- the first particle and second particle are contacted with the one or more biomolecules at a concentration of 0.6 mg/mL to 0.8 mg/mL.
- the method further comprises contacting the one or more biomolecules with the at least two particles in the presence of an organic solvent.
- the method comprises purifying the one or more digested biomolecules.
- purifying the one or more digested biomolecules comprises contacting the one or more digested biomolecules with a third particle in an organic solvent to form a biomolecule WSGR Docket No.53344-792.601 corona.
- the aqueous solution comprises an organic solvent. In some embodiments, the aqueous solution comprises an organic solvent in an amount of no more than 50 wt% (e.g., 40 wt%, 30 wt%, 20 wt%, 10 wt%, or no more than 5 wt%). In some embodiments, the aqueous solution comprises an organic solvent in an amount of no more than 50 wt% (e.g., 40 wt%, 30 wt%, 20 wt%, 10 wt%, or no more than 5 wt%). In some embodiments, the method is capable of isolating from about 100 to about 20,000 biomolecules.
- the method further comprises identifying the one or more biomolecules. In some embodiments, the method further comprises assaying the one or more digested biomolecules to identify the one or more biomolecules. In some embodiments, the assaying or identifying comprises performing mass spectrometry (MS), liquid chromatography- mass spectrometry (LC-MS), protein sequencing, or a combination thereof. In some embodiments, the method is capable of assaying or identifying from about 1 to about 20,000 biomolecules. In some embodiments, when repeated, the assaying yields a percent quantile normalized coefficient (QNCV) of variation of 30% or less. In some embodiments, when repeated, the assaying yields a percent quantile normalized coefficient (QNCV) of variation of 20% or less.
- QNCV percent quantile normalized coefficient
- the reduction agent comprises TCEP, dithiothreitol, beta-mercaptoethanol, glutathione, cysteine, or any combination thereof.
- the alkylating agent comprises iodoacetamide, iodoacetic acid, acrylamide, chloroacetamide, or any combination thereof.
- a system for isolating one or more biomolecules from a biological sample comprising: (a) a composition provided herein; (b) a suspension solution configured to suspend the at least two particles; (c) a biological sample comprising one or more biomolecules; and (d) an automated system comprising a network of units with differentiated functions configured to isolate one or more biomolecules from the biological sample using the at least two particles.
- the network of units comprises: (a) a first unit comprising a multichannel fluid transfer instrument for transferring fluids between units within the system; (b) a second unit comprising a support for storing a plurality of biological samples; and (c) a third unit comprising a support for an array plate possessing partitions that comprise the two or more particles for binding of the one or more biomolecules with the two or more particles.
- the network of units further comprises a fourth unit comprising supports for storing a plurality of reagents.
- the network of units further comprises a fifth unit comprising supports for storing a reagent to be disposed of.
- the network of units further comprises supports for storing consumables used by a multichannel fluid transfer instrument.
- the automated system is configured to perform a method provided herein.
- a kit for isolating one or more biomolecules from a biological sample the kit comprising a composition provided herein.
- a kit for preparing one or more biomolecules from a biological sample for assaying by mass spectrometry the kit comprising a composition provided herein.
- comprises a washing agent configured to wash the one or more biomolecules bound to the at least two particles.
- the kit comprises an elution agent configured to elute the one or more biomolecules from the at least two particles.
- the kit comprises a denaturing agent.
- the kit comprises a reducing agent.
- the kit further comprises an alkylation agent.
- the kit further comprises at least one buffer.
- the at least one buffer comprises a digestion buffer, resuspension buffer, denaturation buffer, digestion buffer, or a lysis buffer.
- the kit further comprises one or more organic solvents.
- the buffer comprises HEPES.
- one or more components of the kit are prepackaged into one or more containers.
- a method of preparing a mixture of at least two particles comprising recurring units of a first monomer and a second monomer or a first monomer and a third monomer, the method comprising: (a) obtaining a first particle comprising a neutral to negative surface charge; (b) obtaining a second particle comprising a greater negative surface charge than the first particles; and (c) forming a mixture comprising the first and second particles.
- the first particle comprises a surface charge of about 0 mV to about -15 mV.
- the second particle comprises a surface charge of about -35 mV to about -60 mV.
- the surface charge is characterized by a zeta potential.
- the first particle is a first particle described herein.
- the second particle is a second particle described herein.
- a method of preparing a macromolecule structure comprising recurring units of a first component and a second component, the method comprising: (a) providing a mixture of monomers in a solvent comprising a first monomer and a second monomer, wherein the first monomer comprises: wherein q is an integer from 1 to 6; and WSGR Docket No.53344-792.601 the second monomer comprises: wherein m is an integer from 1 to 6; (b) contacting a surface and the mixture of monomers, thereby producing a reaction mixture; (c) polymerizing the mixture of monomers to produce a macromolecule immobilized to the surface of a particle; (d) contacting the macromolecule immobilized to the surface and an amine, thereby producing an
- the particle is a nanoparticle. In some embodiments, the particle is a microparticle. In some embodiments, the particle has a diameter of from about 100 nm to about 750 nm. In some embodiments, the particle has a diameter of from about 100 nm to about 500 nm. In some embodiments, the particle has a polydispersity index (PDI) of about 0.01 to about 0.2. In some embodiments, the particle has a PDI of about 0.1 to about 0.2. In some embodiments, the particle comprises iron oxide. In some embodiments, the particle comprises is a superparamagnetic iron oxide nanoparticle. In some embodiments, the particle comprises a core- shell structure.
- the particle comprises an iron oxide core and a silica shell. In some embodiments, the particle comprises iron oxide crystals embedded in a polystyrene core. In some embodiments, (b) comprises contacting in an organic solvent. In some embodiments, (d) comprises contacting in an organic solvent. In some embodiments, the organic solvent comprises an alcohol, acetonitrile, dichloromethane, dimethylformamide (DMF), dimethylsulfoxide (DMSO), ethylacetate, hexamethylphosphoramide (HMPA), or tetrahydrofuran. In some embodiments, the organic solvent comprises acetonitrile. In some embodiments, the organic solvent comprises DMF. In some embodiments, the method further comprises heating.
- the heating comprises heating to a temperature of at least 50°C, 60°C, 70°C, 80°C, or at least 90°C.
- the polymerization comprises free radical polymerization, atom transfer radical polymerization (ATRP), emulsion polymerization, or precipitation polymerization.
- the macromolecule structure comprises a composition described herein. WSGR Docket No.53344-792.601 [0014]
- a use a macromolecule structure comprising 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units for binding proteins in a biological sample.
- provided herein is a use of a particle comprising a macromolecule structure comprising the structure of Formula (A-D) and the structure of Formula (A-A) as recurring units for binding proteins in a biological sample.
- a particle comprising a macromolecule structure comprising the structure of Formula (A-C) and the structure of Formula (A-B) as recurring units for binding proteins in a biological sample is a use of a composition provided herein for binding proteins in a biological sample.
- compositions comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units.
- a composition comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises ethylene glycol dimethacrylate, monomer 6, and at least one of: monomer 7, monomer 8, monomer 9, and glycidyl methacrylate.
- composition obtained by a method comprising polymerizing 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles.
- a method comprising: (a) contacting a plasma or serum sample comprising one or more proteins with a composition provided herein, thereby adsorbing at least a portion of the proteins to the magnetic particles; (b) separating the adsorbed proteins and the magnetic particles from the plasma or serum; WSGR Docket No.53344-792.601 (c) eluting and optionally digesting the adsorbed proteins from the magnetic particles, thereby providing one or more isolated proteins; (d) optionally purifying the isolated proteins using solid phase extraction; and (e) analyzing the isolated proteins using mass spectrometry.
- a method of making polymer-coated magnetic particles comprising polymerizing 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles.
- a method of making polymer-coated magnetic particles comprising: (i) polymerizing glycidyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles to form polymer-coated particles; (ii) reacting the polymer-coated magnetic particles with an alkylene diamine to form amine-modified magnetic particles; and (iii) reacting the amine- modified magnetic particles with an optionally substituted succinic acid anhydride.
- FIG. 1 shows an exemplary preparation scheme for particle (e.g., comprising a macromolecule structure) (A2).
- FIG. 2 shows an exemplary preparation scheme for particle (e.g., comprising a macromolecule structure)(A3).
- FIG.3 shows protein group (PG) counts for particles (e.g., comprising macromolecule structures) (A1), (A2), and (A1)/(A2) multiplexed in various plasmas.
- FIG.4 shows PG counts for particles (e.g., comprising macromolecule structures) (A3), (A4), (A5), and (A6) in 1M Tris (pH 9.5) along with PG counts for multiplexed particles (e.g., comprising macromolecule structures) (A3)&(A4), (A3)&(A5), and (A3)&(A6).
- FIG. 5A shows a scheme for loading of a 96-well plate to perform a method provided herein with 40 samples.
- FIG.5B shows a scheme for loading a 96-well plate to perform a method provided herein with 80 samples.
- FIG.6 shows peptide yield and protein group counts evaluated for varying multiplexed compositions of (A1) and (A2) described herein at various concentrations.
- an alkyl comprises one to five carbon atoms (i.e., C 1 -C 5 alkyl). In other embodiments, an alkyl comprises one to four carbon atoms (i.e., C 1 -C 4 alkyl). In other embodiments, an alkyl comprises one to three carbon atoms (i.e., C1-C3 alkyl). In other embodiments, an alkyl comprises one to two carbon atoms (i.e., C1-C2 alkyl). Whenever it appears herein, a numerical range such as “C1-C3 alkyl” means that the alkyl group consists of 1 carbon atom, 2 carbon atoms, or 3 carbon atoms.
- an alkyl comprises one carbon atom (i.e., C1 alkyl). In other embodiments, an alkyl comprises five to fifteen carbon atoms WSGR Docket No.53344-792.601 (i.e., C5-C15 alkyl). In other embodiments, an alkyl comprises five to eight carbon atoms (i.e., C5- C8 alkyl). In other embodiments, an alkyl comprises two to five carbon atoms (i.e., C2-C5 alkyl). In other embodiments, an alkyl comprises three to five carbon atoms (i.e., C 3 -C 5 alkyl).
- the alkyl group is selected from methyl, ethyl, 1propyl (n-propyl), 1-methylethyl (isopropyl), 1-butyl (nbutyl), 1-methylpropyl (sec-butyl), 2-methylpropyl (iso-butyl), 1,1dimethylethyl (tertbutyl), 1pentyl (n-pentyl).
- examples include, but are not limited to, methyl, ethyl, n-propyl, isopropyl, 2-methyl-1-propyl, 2-methyl-2-propyl, 2- methyl-1-butyl, 3-methyl-1-butyl, 2-methyl-3-butyl, 2,2-dimethyl-1-propyl, 2-methyl-1-pentyl, 3-methyl-1-pentyl, 4-methyl-1-pentyl, 2-methyl-2-pentyl, 3-methyl-2-pentyl, 4-methyl-2-pentyl, 2,2-dimethyl-1-butyl, 3,3-dimethyl-1-butyl, 2-ethyl-1-butyl, n-butyl, isobutyl, sec-butyl, t-butyl, n-pentyl, isopentyl, neopentyl, tert-amyl, and hexyl, and longer alkyl groups, such as heptyl,
- the alkyl is optionally substituted with oxo, halogen, -CN, -CF 3 , OH, or -OMe. In some embodiments, the alkyl is optionally substituted with halogen such as F. In some embodiments, the alkyl is unsubstituted.
- Alkyl groups may be a straight chain or comprise one or more branched chains. [0040] As used herein, C1-Cx (or C1-x) includes C1-C2, C1-C3... C1-Cx. By way of example only, a group designated as “C1-C4” indicates that there are one to four carbon atoms in the moiety, i.e.
- Alkoxy refers to a radical bonded through an oxygen atom of the formula –O-alkyl, where alkyl is an alkyl chain as defined above. Unless stated otherwise specifically in the specification, an alkoxy group can be optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, an alkoxy is optionally substituted with oxo, halogen, -CN, - CF3, OH, -OMe, NH2, or -NO2.
- an alkoxy is optionally substituted with oxo, halogen, -CN, -CF 3 , OH, or -OMe. In some embodiments, the alkoxy is optionally substituted with halogen. In some embodiments, the alkoxy is unsubstituted.
- Alkenyl refers to an optionally substituted straight or branched hydrocarbon chain radical group containing at least one carbon-carbon double bond, and preferably having from two to twelve carbon atoms (i.e., C 2 -C 12 alkenyl).
- an alkenyl comprises two to eight carbon atoms (i.e., C 2 -C 8 alkenyl). In certain embodiments, an alkenyl comprises four to eight carbon atoms (i.e., C4-C6 alkenyl). In other embodiments, an alkenyl comprises six to eight carbon atoms (i.e., C 6 -C 8 alkenyl). In certain embodiments, an alkenyl comprises at least one double bond at the end of a carbon chain. In other embodiments, an alkenyl comprises at least one double bond in the middle of a carbon chain. The group can be in either the cis or trans configuration about the double bond(s) and should be understood to include both isomers.
- an alkenyl group is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like.
- an alkenyl is optionally substituted with oxo, halogen, -CN, -CF 3 , OH, -OMe, NH 2 , or -NO 2 .
- an alkenyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, or -OMe.
- an alkenyl is optionally substituted with oxo, halogen, -CN, -CF 3 , OH, -OMe, NH2, or -NO2. In some embodiments, an alkenyl is optionally substituted with oxo, halogen, -CN, -CF 3 , OH, or -OMe. In some embodiments, the alkenyl is optionally substituted with halogen. In some embodiments, the alkenyl is unsubstituted.
- Alkynyl refers to an optionally substituted straight or branched hydrocarbon chain radical group containing at least one carbon-carbon triple bond, and preferably having from two to twelve carbon atoms (i.e., C 2 -C 12 alkynyl).
- an alkynyl comprises two to eight carbon atoms (i.e., C2-C8 alkynyl).
- an alkynyl comprises two to six carbon atoms (i.e., C2-C6 alkynyl).
- an alkynyl comprises two to four carbon atoms (i.e., C2-C4 alkynyl).
- an alkynyl group is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like.
- an alkynyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, -OMe, NH2, or -NO 2 .
- an alkynyl is optionally substituted with oxo, halogen, -CN, -CF 3 , OH, or -OMe.
- alkynyl is optionally substituted with halogen. In some embodiments, the alkynyl is unsubstituted.
- alkylene or "alkylene chain” refers to an optionally substituted straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group containing no unsaturation, and preferably having from one to twelve carbon atoms, for example, methylene, ethylene, propylene, nbutylene, and the like. The alkylene chain is attached to the rest of the molecule through a single bond and to the radical group through a single bond.
- an alkylene comprises one to ten carbon atoms (i.e., C1-C8 alkylene). In certain embodiments, an alkylene comprises one to eight carbon atoms (i.e., C 1 -C 8 alkylene). In other embodiments, an alkylene comprises one to five carbon atoms (i.e., C1-C5 alkylene). In other embodiments, an alkylene comprises one to four carbon atoms (i.e., C 1 -C 4 alkylene).
- an alkylene group can be optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like.
- an alkylene is optionally substituted with oxo, halogen, -CN, -CF3, OH, -OMe, NH2, or -NO2.
- an alkylene is optionally substituted with oxo, halogen, -CN, -CF3, OH, or - OMe.
- the alkylene is optionally substituted with halogen.
- the alkylene is -CH2-, -CH2CH2-, or -CH2CH2CH2-.
- the alkylene is -CH2-.
- the alkylene is -CH2CH2-.
- the alkylene is -CH2CH2CH2-.
- the alkylene is unsubstituted.
- Aryl refers to a radical derived from a hydrocarbon ring system comprising at least one aromatic ring. In some embodiments, an aryl comprises hydrogens and 5 to 30 carbon atoms.
- the aryl radical can be a monocyclic, bicyclic, tricyclic, or tetracyclic ring system, which can include fused (when fused with a cycloalkyl or heterocycloalkyl ring, the aryl is bonded through an aromatic ring atom) or bridged ring systems.
- the aryl is a 6- to 10- membered aryl.
- the aryl is a 6-membered aryl.
- an aryl can be optionally substituted, for example, with halogen, amino, alkylamino, aminoalkyl, nitrile, nitro, hydroxyl, alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, -S(O)2NH-C1-C6alkyl, and the like.
- an aryl is optionally substituted with halogen, methyl, ethyl, -CN, -CF3, OH, -OMe, NH2, -NO2, -S(O)2NH2, -S(O) 2 NHCH 3, -S(O) 2 NHCH 2 CH 3 , -S(O) 2 NHCH ( CH 3 ) 2 , -S(O) 2 N(CH 3 ) 2 , or -S(O) 2 NHC(CH 3 ) 3 .
- an aryl is optionally substituted with halogen, methyl, ethyl, -CN, -CF3, OH, or -OMe.
- the aryl is optionally substituted with halogen.
- the aryl is substituted with alkyl, alkenyl, alkynyl, haloalkyl, or heteroalkyl, wherein each alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl is independently unsubstituted, or substituted with halogen, methyl, ethyl, -CN, -CF3, OH, -OMe, NH2, or -NO2.
- the aryl is unsubstituted.
- Alkyl refers to a radical of the formula R c aryl where R c is an alkylene chain as defined above, for example, methylene, ethylene, and the like.
- Alkenyl refers to a radical of the formula –R d aryl where R d is an alkenylene chain as defined above.
- Alkynyl refers to a radical of the formula R e aryl, where R e is an alkynylene chain as defined above.
- Carbocycle refers to a saturated, unsaturated, or aromatic rings in which each atom of the ring is carbon.
- an aromatic ring e.g., phenyl
- a saturated or unsaturated ring e.g., cyclohexane, cyclopentane, or cyclohexene.
- a bicyclic carbocycle includes any combination of saturated, unsaturated and aromatic bicyclic rings, as valence permits.
- a bicyclic carbocycle includes any combination of ring sizes such as 4-5 fused ring systems, 5-5 fused ring systems, 5-6 fused ring systems, 6-6 fused WSGR Docket No.53344-792.601 ring systems, 5-7 fused ring systems, 6-5 fused ring systems, 6-7 fused ring systems, 5-8 fused ring systems, and 6-8 fused ring systems.
- Exemplary carbocycles include cyclopentyl, cyclohexyl, cyclohexenyl, adamantyl, phenyl, indanyl, and naphthyl.
- saturated carbocycle refers to carbocycles with at least one degree of unsaturation and excluding aromatic carbocycles.
- unsaturated carbocycles include cyclohexadiene, cyclohexene, and cyclopentene.
- saturated cycloalkyl refers to a saturated carbocycle.
- Exemplary carbocycles include cyclopropyl, cyclopentyl, cyclohexyl, cyclohexenyl, adamantyl, phenyl, indanyl, norbornyl, and naphthyl.
- Carbocycles can be optionally substituted by one or more substituents such as those substituents described herein.
- Cycloalkyl refers to a stable, partially or fully saturated, monocyclic or polycyclic carbocyclic ring, which can include fused (when fused with an aryl or a heteroaryl ring, the cycloalkyl is bonded through a non-aromatic ring atom), bridged, or spiro ring systems.
- Representative cycloalkyls include, but are not limited to, cycloalkyls having from three to fifteen carbon atoms (C3-C15 cycloalkyl), from three to ten carbon atoms (C3-C10 cycloalkyl), from three to eight carbon atoms (C3-C8 cycloalkyl), from three to six carbon atoms (C3-C6 cycloalkyl), from three to five carbon atoms (C3-C5 cycloalkyl), or three to four carbon atoms (C3-C4 cycloalkyl).
- the cycloalkyl is a 3- to 6-membered cycloalkyl.
- the cycloalkyl is a 5- to 6-membered cycloalkyl.
- Monocyclic cycloalkyls include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl.
- Polycyclic cycloalkyls or carbocycles include, for example, adamantyl, norbornyl, decalinyl, bicyclo[3.3.0]octane, bicyclo[4.3.0]nonane, cis-decalin, trans-decalin, bicyclo[2.1.1]hexane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, and bicyclo[3.3.2]decane, and 7,7-dimethyl-bicyclo[2.2.1]heptanyl.
- Partially saturated cycloalkyls include, for example, cyclopentenyl, cyclohexenyl, cycloheptenyl, and cyclooctenyl. Unless stated otherwise specifically in the specification, a cycloalkyl is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, alkyl, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like.
- a cycloalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, -CF3, -OH, -OMe, -NH2, or -NO2. In some embodiments, a cycloalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, - CF 3 , -OH, or -OMe. In some embodiments, the cycloalkyl is optionally substituted with halogen. In some embodiments, the cycloalkyl is unsubstituted.
- haloalkyl or “haloalkane” refers to an alkyl radical, as defined above, that is substituted by one or more halogen radicals, for example, trifluoromethyl, dichloromethyl, bromomethyl, 2,2,2-trifluoroethyl, 1-fluoromethyl-2-fluoroethyl, and the like.
- the alkyl part of the fluoroalkyl radical is optionally further substituted.
- the alkyl is substituted with one hydroxyl. In some embodiments, the alkyl is substituted with one, two, or three hydroxyls. Hydroxyalkyl include, for example, hydroxymethyl, hydroxyethyl, hydroxypropyl, hydroxybutyl, or hydroxypentyl. In some embodiments, the hydroxyalkyl is hydroxymethyl.
- Amoxyalkyl refers to an alkyl radical, as defined above, that is substituted by one or more amines. In some embodiments, the alkyl is substituted with one amine. In some embodiments, the alkyl is substituted with one, two, or three amines.
- C1-Cx alkyl substituted with disulfide as used herein may refer to a disulfide of the structure R-S-S-R’, where R and R’ may be identical or different. Each R and R’ may be independently selected from C 1 -C y alkyl, such that the length of R and R’ is the length of the C1-Cx alkyl.
- heteroalkyl refers to an alkyl group in which one or more skeletal atoms of the alkyl are selected from an atom other than carbon, e.g., oxygen, nitrogen (e.g., -NH-, -N(alkyl)- ), sulfur, or combinations thereof.
- a heteroalkyl is attached to the rest of the molecule at a carbon atom of the heteroalkyl.
- a heteroalkyl is a C 1 -C 6 heteroalkyl wherein the heteroalkyl is comprised of 1 to 6 carbon atoms and one or more atoms other than carbon, e.g., oxygen, nitrogen (e.g.
- heteroalkyl is attached to the rest of the molecule at a carbon atom of the heteroalkyl.
- heteroalkyl examples include, for example, -CH2OCH3, -CH2CH2OCH3, -CH2CH2OCH2CH2OCH3, or - CH(CH3)OCH3.
- a heteroalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, -CF3, OH, or -OMe. In some embodiments, the heteroalkyl is optionally substituted with halogen. In some embodiments, the heteroalkyl is unsubstituted.
- “Heterocycloalkyl” refers to a stable 3 to 24membered partially or fully saturated ring radical comprising 2 to 23 carbon atoms and at least one ring heteroatoms. In some embodiments, a heterocycloalkyl contains from one to 8 heteroatoms selected from the group consisting of nitrogen, oxygen, phosphorous, and sulfur.
- the heterocycloalkyl radical can be a monocyclic, bicyclic, tricyclic, or tetracyclic ring system, which can include fused (when fused with an aryl or a heteroaryl ring, the heterocycloalkyl is bonded through a non-aromatic ring atom) or bridged ring systems; and the nitrogen, carbon, or sulfur atoms in the heterocycloalkyl radical can be optionally oxidized; the nitrogen atom can be optionally quaternized.
- heterocycloalkyls include, but are not limited to, heterocycloalkyls having from two to fifteen carbon atoms (C 2 -C 15 heterocycloalkyl), from two to ten carbon atoms (C 2 -C 10 heterocycloalkyl), from two to eight carbon atoms (C 2 -C 8 heterocycloalkyl), from two to six carbon atoms (C2-C6 heterocycloalkyl), from two to five carbon atoms (C2-C5 heterocycloalkyl), or two to four carbon atoms (C2-C4 heterocycloalkyl).
- the heterocycloalkyl is a 3- to 6-membered heterocycloalkyl.
- heterocycloalkyl also includes all ring forms of the carbohydrates, including but not limited to, the monosaccharides, the disaccharides, and the oligosaccharides. It is understood that when referring to the number of carbon atoms in a heterocycloalkyl, the number of carbon atoms in the heterocycloalkyl is not the same as the total number of atoms (including the heteroatoms) that make up the heterocycloalkyl (i.e. skeletal atoms of the heterocycloalkyl ring).
- a heterocycloalkyl is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, alkyl, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like.
- a heterocycloalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, -CF3, OH, -OMe, NH 2 , or -NO 2 .
- Heterocycles include e.g., 3- to 10-membered monocyclic rings and 6- to 12-membered bicyclic rings (such as spiro, fused, or bridged rings).
- the heterocyclyl radical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which optionally includes fused, bridged, or spirocyclic ring systems.
- the heteroatoms in the heterocyclyl radical are optionally oxidized.
- One or more nitrogen atoms, if present, are optionally quaternized.
- the heterocyclyl radical can be partially or fully saturated.
- the heterocyclyl is attached to the rest of the molecule through any atom of the ring(s).
- heterocyclyl radicals include, but are not limited to, dioxolanyl, thienyl[1,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2oxopiperazinyl, 2oxopiperidinyl, 2oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1oxothiomorph
- heterocyclyl is meant to include heterocyclyl radicals as defined above that are optionally substituted by one or more substituents.
- a heterocyclyl can be optionally substituted by one or more substituents selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, oxo, thioxo, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally WSGR Docket No.53344-792.601 substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -R b -OR a , -R b -OC(O
- Heteroaryl or “aromatic heterocycle” refers to a ring system radical comprising carbon atom(s) and one or more ring heteroatoms (e.g., selected from the group consisting of nitrogen, oxygen, phosphorous, silicon, and sulfur), and at least one aromatic ring.
- a heteroaryl is a 5 to 14membered ring system radical comprising one to thirteen carbon atoms, one to six heteroatoms selected from the group consisting of nitrogen, oxygen, phosphorous, and sulfur.
- the heteroaryl radical can be a monocyclic, bicyclic, tricyclic, or tetracyclic ring system, which can include fused (when fused with a cycloalkyl or heterocycloalkyl ring, the heteroaryl is bonded through an aromatic ring atom) or bridged ring systems; and the nitrogen, carbon, or sulfur atoms in the heteroaryl radical can be optionally oxidized; the nitrogen atom can be optionally quaternized.
- the heteroaryl is a 5- to 10-membered heteroaryl.
- the heteroaryl is a 5- to 6-membered heteroaryl.
- a heteroaryl is optionally substituted, for example, with halogen, amino, nitrile, nitro, hydroxyl, alkyl, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like.
- a heteroaryl is optionally substituted with halogen, methyl, ethyl, -CN, -CF 3 , OH, -OMe, NH2, or -NO2.
- a heteroaryl is optionally substituted with halogen, methyl, ethyl, -CN, -CF3, OH, or -OMe. In some embodiments, the heteroaryl is optionally substituted with halogen. In some embodiments, the heteroaryl is unsubstituted. [0063] The term “substituted” refers to moieties having substituents replacing a hydrogen on one or more carbons or substitutable heteroatoms, e.g., NH, of the structure.
- the permissible substituents include acyclic and cyclic, branched, and unbranched, carbocyclic and heterocyclic, aromatic and non-aromatic substituents of organic compounds.
- the permissible substituents can be one or more and the same or different for appropriate organic compounds.
- the heteroatoms such as nitrogen can have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms.
- Ranges provided herein are understood to be shorthand for all of the values within the range.
- a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, WSGR Docket No.53344-792.601 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50, as well as all intervening decimal values between the aforementioned integers such as, for example, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, and 1.9.
- a nested sub-range of an exemplary range of 1 to 50 can comprise 1 to 10, 1 to 20, 1 to 30, and 1 to 40 in one direction, or 50 to 40, 50 to 30, 50 to 20, and 50 to 10 in the other direction.
- the compounds and structures provided herein may be stereoisomeric.
- a compound or structure of the disclosure may form a stereoisomer.
- the stereoisomer may be a diastereomer (e.g., a cis/trans isomer, E/Z isomer, conformer, or rotamer).
- the stereoisomer may be an enantiomer (R,S enantiomers or +/- enantiomers).
- the compound or structure of the disclosure may be enantiopure (e.g., 100% pure).
- the compound or structure may form a racemic mixture of enantiomers (e.g., 50% pure).
- a compound or structure of the disclosure may stabilize as a stereoisomer, where the compound or structure of the disclosure comprises at least about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, about 99.9%, or more of a mixture of the compound or structure and the corresponding stereoisomer.
- the combination of particles (e.g., comprising WSGR Docket No.53344-792.601 macromolecule structures), such as described herein, provide a synergistic relationship that enhances the macromolecule structure’s ability to isolate biomolecules. This increased ability in some instances is compared to the ability of a single macromolecule structure to isolate biomolecules on their own.
- the methods and macromolecules provided herein aid in avoiding the need for alternative isolation/purification methods such as solid phase chromatography (e.g., reverse-phase/ion exchange) or suspension trapping which may be solvent intensive and may lead to poor recovery, reproducibility issues, or insufficient purification.
- the methods, systems, and compositions provided herein allow for the use of a diverse range of biological sample types, including but not limited to plasma, serum, cells, and tissues, and at lower required sample volumes than comparable methods.
- the methods provided herein allow for the preparation of biomolecule samples for analysis by mass spectrometry (MS), such as by selective removal of MS incompatible components from a biological sample.
- MS mass spectrometry
- two particles are used, a first particle with a neutral to negative surface charge, and a second particle, with a highly negative surface charge (e.g., more negative than the first particle).
- two macromolecule structures are used, a first macromolecule structure with a neutral to negative surface charge, and a second macromolecule structure, with a highly negative surface charge (e.g., more negative than the first macromolecule structure).
- the combination of the two differing particles e.g., comprising macromolecule structures
- provides a synergistic relationship enabling the isolation, purification, quantification, or identification of a larger number of biomolecules than the two particles (e.g., comprising macromolecule structures) on their own.
- compositions comprising two or more (e.g., structurally unique) particles (e.g., comprising macromolecule structures).
- the compositions comprise a first particle (e.g., comprising a macromolecule structure) and a second particle (e.g., comprising a macromolecule structure).
- the first particle e.g., comprising a macromolecule structure
- the second particle e.g., comprising a macromolecule structure
- the first particle e.g., comprising a macromolecule structure
- the second particle (e.g., comprising a macromolecule structure) comprises a greater negative (e.g., more negative) surface charge than that of the first particle (e.g., comprising a macromolecule structure).
- surface charge herein is measured by zeta potential.
- zeta potential may be measured by electrophoretic light scattering (ELS).
- ELS electrophoretic light scattering
- zeta potential is measured by DLS in 1.5 mM KCl (pH 7.0).
- zeta potential is measured by DLS in 5% PBS (pH 6.8-7.4).
- the surface charge (e.g., zeta potential) described herein is measured by dispersing about 20 ⁇ g of particles in 5% PBS at a pH of 6.8-7.4.
- an instrument such as a Zetasizer Nano ZS (Malvern Instruments, Worcestershire, UK) may be used.
- Particles for testing in some instances are suspended at 10 mg/mL in water with about 10 min of bath sonication prior to testing. Samples then may be diluted to approximately 0.02 wt%, and DLS performed in water at about 25°C in disposable polystyrene semi-micro cuvettes with about 1 min temperature equilibration time.
- Results from several runs may be averaged in some instances (e.g., 3 runs of about 1 min), with a 633 nm laser in 173° backscatter mode.
- DLS results in some instances are then analyzed using the cumulants method and zeta potential measured in 5% pH 7.4 PBS in disposable folded capillary cells (Malvern Instruments, PN DTS1070) at about 25°C with an about 1 min equilibration time.
- three measurements are performed with automatic measurement duration with a minimum of 10 runs and a maximum of 100 runs, and a 1 min hold between measurements.
- the Smoluchowski model is used to determine the zeta potential from the electrophoretic mobility. Used to determine the zeta potential from the electrophoretic mobility.
- a neutral surface charge is characterized by a zeta potential of from about -5 mV to about 5 mV. In some embodiments, a neutral surface charge is characterized by a zeta potential of at most 5 mV (e.g., at most 4 mV, 3 mV, 2 mV, 1 mV, 0.75 mV, 0.5 mV, 0.25 mV, or at most 0.1 mV).
- a neutral surface charge is characterized by a zeta potential of at least -5 mV (e.g., at least -4 mV, -3 mV, -2 mV, -1.5 mV, -1 mV, -0.75 mV, -0.5 mV, -0.25 mV, or at least -0.1 mV).
- a neutral surface charge is characterized by a zeta potential of about 0 mV.
- a neutral surface charge is characterized by a zeta potential of about -1 mV, 0 mV, or 1 mV.
- the first particle (e.g., comprising the first macromolecule structure) provided herein comprises a surface charge (e.g., characterized by a zeta potential) of from about 10 mV to about -15 mV.
- the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of from about 0 to about -15 mV.
- the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of from about 0 to about -10 mV.
- the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of from about -10 to about -20 mV.
- the first particle (e.g., comprising a macromolecule structure) comprises a WSGR Docket No.53344-792.601 surface charge of at most about 0 mV. In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of at most about -1 mV (e.g., -2 mV, -3 mV, -5 mV, -6 mV, -8 mV, -9 mV, or at most -10 mV).
- -1 mV e.g., -2 mV, -3 mV, -5 mV, -6 mV, -8 mV, -9 mV, or at most -10 mV.
- the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of at least -15 mV (e.g., -12 mV, -10 mV, -8 mV, -6 mV, -5 mV, -4 mV, -3 mV, -2 mV, or -1 mV).
- -15 mV e.g., -12 mV, -10 mV, -8 mV, -6 mV, -5 mV, -4 mV, -3 mV, -2 mV, or -1 mV.
- the first particle (e.g., comprising a macromolecule structure) comprises a zeta potential of about 0 mV, -1 mV, -2 mV, -3 mV, -4 mV, -5 mV, -6 mV, -7 mV, -8 mV, -9 mV, or -10 mV.
- the first particle (e.g., comprising a macromolecule structure) comprises a zeta potential of about -10 mV, -11 mV, -12 mV, -13 mV, -14 mV, -15 mV, -16 mV, -17 mV, -18 mV, -19 mV, or -20 mV.
- a negative surface charge is characterized by a zeta potential of from about 0 mV to about -80 mV.
- a negative surface charge is characterized by a zeta potential of from about 0 mV to about -60 mV.
- a negative surface charge is characterized by a zeta potential of from about -5 mV to about -60 mV (e.g., about -10 mV to about -60 mV, about -20 mV to about -60 mV, about -30 mV to about -60 mV, or about -40 mV to about -60 mV).
- a negative surface charge is characterized by a zeta potential of at least -80 mV (e.g., at least -70 mV, -60 mV, -50 mV, -40 mV, -30 mV, -20 mV, -10 mV, or at least -5 mV).
- a negative surface charge is characterized by a zeta potential of at most 0 mV (e.g., at most -5 mV, -10 mV, -20 mV, -30 mV, -40 mV, -50 mV, or -60 mV). In some embodiments, a negative surface charge is characterized by a zeta potential of about -3 mV, -8 mV, --12 mV, -20 mV, -25 mV, -30 mV, -40 mV, -45 mV, -50 mV, or -55 mV.
- the second particle (e.g., comprising a macromolecule structure) comprises a surface charge (e.g., characterized by a zeta potential) of from about -15 mV to about -60 mV.
- the second particle (e.g., comprising a macromolecule structure) comprises a surface charge of about 0 mV to about -60 mV.
- the second particle (e.g., comprising a macromolecule structure) comprises a surface charge about -35 mV to about -60 mV.
- the second particle (e.g., comprising a macromolecule structure) comprises a surface charge about -40 mV to about -50 mV.
- the second particle (e.g., comprising a macromolecule structure) WSGR Docket No.53344-792.601 comprises a surface charge of about -36 mV (e.g., -38 mV, -40 mV, -42 mV, -44 mV, -46 mV, - 48 mV, -50 mV, -52 mV, -54 mV, -56 mV, -58 mV, or -60 mV).
- -36 mV e.g., -38 mV, -40 mV, -42 mV, -44 mV, -46 mV, - 48 mV, -50 mV, -52 mV, -54 mV, -56 mV, -58 mV, or -60 mV.
- the first particle has a surface charge characterized by a zeta potential of from about -10 mV to -20 mV. In some embodiments, the first particle has a surface charge characterized by a zeta potential of -13 mV.
- the second particle e.g., comprising a macromolecule structure
- the second particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of from about – 40 mV to about -60 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of from about -40 mV to -50 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of about -42 mV.
- a surface charge of the second particle is characterized by a zeta potential of at least 4-fold more negative than the surface charge of the first particle (e.g., comprising a macromolecule structure).
- a surface charge of the second particle is characterized by a zeta potential of at least 8-fold more negative than the surface charge of the first particle (e.g., comprising a macromolecule structure).
- a surface charge of the second particle is characterized by a zeta potential of about 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13- fold, 14-fold, or 15-fold more negative than the surface charge of the first particle (e.g., comprising a macromolecule structure).
- the compositions herein comprise the multiple different particles (e.g., comprising macromolecule structures) in varying relative amounts.
- the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) in varying relative amounts.
- the compositions comprise the first particle (e.g., comprising a macromolecule WSGR Docket No.53344-792.601 structure) and second particle (e.g., comprising a macromolecule structure) at a ratio of about 10:1 to about 1:10.
- the compositions comprise the first particle (e.g., comprising a macromolecule structure) and second particle (e.g., comprising a macromolecule structure) at a ratio of about 5:1 to about 1:5.
- the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) at a ratio of about 1:1 to about 1:10. In some embodiments, the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) at a ratio of 1:1 to about 1:4 (e.g., 1:2, 1:2.5, 1:3, 1:3.5, or 1:3.75).
- the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) at a ratio of about 1:2, 1:1, 1:2, 1:2.5, 1:3, 1:3.5:, 1:3.75, 1:4, 1:4.25, 1:4.5, 1:5, 1:6, 1:7, 1:8, 1:9, or about 1:10.
- the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) at a ratio of about 1:4.
- the ratio is a molar ratio.
- the ratio is a mass ratio.
- the ratio is a surface area ratio.
- the particle e.g., comprising a macromolecule structure
- the particle provided herein comprise a surface and a polymer or co-polymer.
- the polymer or co-polymer is covalently attached to the surface.
- the polymer or co-polymer is non-covalently attached to the surface.
- the co-polymer is a random co-polymer.
- the co-polymers herein comprise 2, 3, 4, 5, 6, or more unique monomers.
- at least a portion of the monomers within the co- polymers act as cross-linkers.
- the surface comprises a base polymer.
- the particles provided herein comprise macromolecule structures comprising a polymer comprising one or more units represented by Formula (A): Formula (A) WSGR Docket No.53344-792.601
- R is hydrogen or .
- R is hydrogen.
- R is .
- when R is hydroxyl the structure of Formula (A) is represented by: .
- R 1 is hydrogen or hydroxyl.
- R 1 is hydrogen.
- R 1 is hydroxyl.
- R 3 is each independently hydrogen or C 1 -C 8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl.
- R3 is hydrogen.
- R3 is optionally substituted C 1 -C 8 alkyl.
- R 3 is C 1 -C 8 alkyl optionally substituted with C 1 -C 8 alkenyl, oxo(s), (in some instances two oxos), and hydroxyl.
- R2 is , wherein p is an integer from 1 to 6.
- R 1 and R 2 are taken together to form C2-C6 heterocyloalkyl. In some embodiments, R 1 and R 2 are taken together, forming the structure: [0090] In some embodiments, R 4 is hydrogen or C 1 -C 6 alkyl. In some embodiments, R 4 is hydrogen. In other embodiments, R 4 is C1-C6 alkyl. In some embodiments, R 4 is C1 alkyl.
- the polymer comprises two or more units represented by Formula (A), wherein the two or more units have a different structure.
- the two or more units comprises a first unit represented by Formula (A), wherein R is and R 2 .
- q is 1 for the first unit.
- the two or more units comprises a second unit represented by Formula (A) having the structure of .
- the two or more units comprises a second unit represented by Formula (A), wherein R 1 and R 2 are taken together having the structure of .
- the two or more units comprises a second unit represented by Formula (A), wherein R is and R 2 .
- q is 1 for the second unit.
- the second unit is a crosslinking unit.
- the crosslinking unit is obtained from a monomer having two or more vinyl groups.
- the crosslinking unit may obtained from divinyl benzene, polyethylene glycol dimethacrylate, or ethylene glycol dimethacrylate.
- compositions comprising a macromolecular structure comprising two or more units represented by Formula (A), as described hereinabove, and Formula (B): WSGR Docket No.53344-792.601 [0093]
- R is hydrogen or .
- R is hydrogen.
- R is .
- R 2 is optionally substituted C1-C8 diamine. In some embodiments, R 2 is C 1 -C 8 diamine, N-substituted with one or more R 3 . In some embodiments, R 2 is C 2 diamine, N-substituted with one or more R 3 . [0098] In some embodiments, R 3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C12 alkenyl, and C1-C8 alkynyl.
- R 3 is each independently hydrogen or C 1 -C 8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl. In some embodiments, R 3 is hydrogen. In some embodiments, R 3 is optionally substituted C1-C8 alkyl. In some embodiments, R 3 is C 1 -C 8 alkyl optionally substituted with C 1 -C 8 alkenyl, (e.g., 2) oxo, and hydroxyl.
- R 3 is C 1 -C 8 alkyl optionally substituted with C 1 -C 12 alkenyl, (e.g., 2) oxo, and hydroxyl.
- R2 is , wherein p is an integer from 1 to 6. In some embodiments, p is 1. In some embodiments, p is 2. In some embodiments, p is 3. In some embodiments, p is 4. In some embodiments, p is 5. In some embodiments, p is 6. [00100] In some embodiments, R 1 and R 2 are taken together to form C2-C6 heterocyloalkyl.
- the composition comprises one or more units (e.g., of Formula (A)) represented by Formula (C): Formula (C) [00105]
- R 3 is each independently hydrogen or C 1 -C 8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl.
- R 3 is hydrogen.
- R 3 is optionally substituted C1-C8 alkyl.
- R 3 is C 1 -C 8 alkyl optionally substituted with C 1 -C 8 alkenyl, (e.g., 2) oxo, and hydroxyl. In some embodiments, one hydrogen. In some embodiments, two one of R 3 is hydrogen. [00106] In some embodiments, the composition comprises one or more units (e.g., of Formula (A)) represented by Formula (A-A): Formula (A-A) [00107] In some embodiments, R 5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, R 5 is C1-C10 alkyl. In some embodiments, R 5 is C1-C10 alkenyl.
- the composition comprises one or more units (e.g., of Formula (A)) represented by Formula (A-C): Formula (A-C) [00112]
- R 5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, R 5 is C1-C10 alkyl. In some embodiments, R 5 is C1-C10 alkenyl. In some embodiments, R 5 is C 1 -C 10 alkynyl. In some embodiments, R 5 is C 8 alkenyl. In some embodiments, R 5 is . In some embodiments, R 5 is .
- the structure of Formula (B) is: [00116]
- the structure of Formula (B), such as when Formula (B) acts as a crosslinking monomer is: [00117]
- the particles comprise a macromolecule structure comprising a co-polymer of the structure (A1): WSGR Docket No.53344-792.601
- C5H11 as used herein refers to n-C5H11.
- C 5 H 11 refers to .
- C 5 H 11 is .
- the particle comprises a macromolecule structure further comprising methacrylic acid as a monomer unit.
- the second particle comprises a macromolecule structure comprising the co-polymer of structure (A1). [00122] In some embodiments, the second particle comprises a macromolecule structure comprising a co-polymer comprising any number of units represented in Table 1. WSGR Docket No.53344-792.601 TABLE 1 WSGR Docket No.53344-792.601 [00123] In some embodiments, C 5 H 11 as used herein refers to n-C 5 H 11 . In some embodiments, C5H11 refers [00124] In some embodiments, the copolymer comprises monomer 6 and monomer 3. In some embodiments, the copolymer comprises monomer 6, monomer 3, and monomer 7.
- the copolymer comprises monomer 6, monomer 3, and monomer 8. In some embodiments, the copolymer comprises monomer 6, monomer 3, and monomer 9. In some embodiments, the copolymer comprises monomer 6, monomer 3, and monomer 5. In some embodiments, the copolymer comprises monomer 6, monomer 7, and monomer 8. [00125] Provided herein, in some embodiments, is a particle comprising a macromolecule structure comprising a copolymer comprising two or more units represented by Formula (D) and Formula (E): WSGR Docket No.53344-792.601 [00126] In some embodiments, the particle comprises a macromolecule structure comprising a unit represented by Formula (D).
- the particle comprises a macromolecule structure comprising a unit represented by Formula (E).
- R 4 is each independently hydrogen or C1-C6 alkyl. In some embodiments, R 4 is hydrogen. In some embodiments, R 4 is C1-C6 alkyl. In some embodiments, R 4 is C1-C3 alkyl. In some embodiments, R 4 is C1 alkyl. [00128] In some embodiments, R 6 is C 1 -C 6 alkyl optionally substituted with R 7 . In some embodiments, R 6 is hydrogen or (CH2)pOR 7 . In some embodiments, R 6 is hydrogen. [00129] In some embodiments, R7 is hydrogen or C1-C6 alkyl.
- p is 5. In some embodiments, p is 6. [00132] In some embodiments, is a single bond or a double bond. In some embodiments, is a single bond. In some embodiments, is a double bond. [00133] In some embodiments * is an attachment point to another unit of Formula (D) or Formula (E), such as when is a single bond. When * is an attachment point to another unit of Formula (D), the unit of Formula (B) acts as a crosslinking monomer.
- the macromolecule structure comprises one or more units (e.g., of Formula (E)) represented by the structure of Formula (E-A): WSGR Docket No.53344-792.601 Formula (E-A) [00135]
- R 4 is each independently hydrogen or C 1 - C6 alkyl. In some embodiments, R 4 is hydrogen. In some embodiments, R 4 is C1-C6 alkyl. In some embodiments, R 4 is C 1 -C 3 alkyl. In some embodiments, R 4 is C 1 alkyl.
- R 7 is hydrogen or C 1 -C 6 alkyl. In some embodiments, R 7 is hydrogen.
- R 7 is C1-C6 alkyl. In some embodiments, R 7 is C1-C3 alkyl. In some embodiments, R 7 is C1 alkyl. [00137] In some embodiments, p is an integer from 1 to 6. In some embodiments, p is 1. In some embodiments, p is 2. In some embodiments, p is 3. In some embodiments, p is 4. In some embodiments, p is 5. In some embodiments, p is 6. [00138] In some embodiments, the particle comprises a macromolecule structure comprising one or more units (e.g., of Formula (E)) represented by the structure: .
- the particle comprises a macromolecule structure comprising one or more units (e.g., of Formula (E)) represented by the structure: .
- the particle comprises a macromolecule structure comprising one or more units (e.g., of Formula (D)) represented by the structure: WSGR Docket No.53344-792.601
- the unit of Formula (B) acts as a crosslinking monomer.
- the particle comprises a macromolecule structure comprising three or more units (e.g., of Formula (E)) represented by: [00144]
- the structure of Formula (D), such as when Formula (D) acts as a crosslinking monomer is: .
- the macromolecule structure comprises a macromolecule structure comprising a co-polymer of the structure (A2): .
- the particle comprises a macromolecule structure comprising a co-polymer of the structure (A2’): WSGR Docket No.53344-792.601 [00147]
- the monomers represented by n and m are randomly distributed throughout the polymer.
- the monomers represented by n, m, and p are randomly distributed throughout the polymer.
- the first particle comprises a macromolecule structure comprising the co-polymer of structure (A2).
- the first particle comprises a macromolecule structure comprising the co-polymer of structure (A2’).
- the first particle comprises a macromolecule structure further comprising methacrylic acid as a monomer unit.
- the amount of methacrylic acid monomer units may be, in some embodiments, no more than about 10%, no more than about 5%, or no more than about 1% by weight or number of monomer units.
- the amount of methacrylic acid monomer units may be, in some embodiments, at least 0.1%, at least 0.5%, at least 1% or at least 2% by weight or number of monomer units.
- the copolymer may comprise monomer 14 in an amount of less than 10% (e.g., less than 8%, 6%, or 5%) by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of less than 8% by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of less than 6%. In some embodiments, the copolymer comprises monomer 14 in an amount of less than 5% by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of less than 4% by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of at least 2% by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of at least 3% by weight.
- the polymers or copolymers comprise a molecular weight of at least 0.1 kDa (e.g., WSGR Docket No.53344-792.601 at least 1 kDa, 5 kDa, 10 kDa, 20 kDa, 25 kDa, 50 kDa, 100 kDa, 250 kDa, or at least 500 kDa).
- a molecular weight of at least 0.1 kDa e.g., WSGR Docket No.53344-792.601 at least 1 kDa, 5 kDa, 10 kDa, 20 kDa, 25 kDa, 50 kDa, 100 kDa, 250 kDa, or at least 500 kDa.
- the polymers or copolymers comprise a molecular weight of at most 1000 kDa (e.g., at most 900 kDa, 800 kDa, 750 kDa, 600 kDa, 500 kDa, 250 kDa, 100 kDa, 75 kDa, 50 kDa, 40 kDa, 30 kDa, 25 kDa, 20 kDa, 15 kDa, or at most 10 kDa).
- kDa e.g., at most 900 kDa, 800 kDa, 750 kDa, 600 kDa, 500 kDa, 250 kDa, 100 kDa, 75 kDa, 50 kDa, 40 kDa, 30 kDa, 25 kDa, 20 kDa, 15 kDa, or at most 10 kDa).
- the polymer or copolymer comprises a molecular weight of about 0.1 kDa to about 500 kDa, about 0.5 kDa to about 250 kDa, about 0.5 kDa to about 100 kDa, about 0.5 kDa to about 70 kDa, 0.5 kDa to about 10 kDa, 0.5 kDa to about 15 kDa, or about 1 kDa to about 25 kDa.
- “molecular weight” may refer to number average molecular weight or weight average molecular weight.
- the polymers or copolymers provided herein may comprise any suitable number of recurring units.
- the polymer or copolymer comprises from about 1 to about 250 (e.g., about 1 to about 500, about 1 to about 1,000, about 100 to about 1,000, about 10 to about 500, about 25 to about 750, or about 100 to about 500) recurring units.
- the particles (e.g., comprising macromolecule structures) provided herein comprise a surface.
- the first particle (e.g., comprising a macromolecule structure) comprises a surface.
- the second particle e.g., comprising a macromolecule structure
- the surface of the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) are the same. In some embodiments, the surface of the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) are different.
- the surfaces herein comprise a particle. In some embodiments, the particles comprise a surface. In some embodiments, the particle is a microparticle. In some embodiments, the particle is a nanoparticle. [00155] In some embodiments, the particle is magnetic, for instance comprising any magnetic material suitable according to one of skill in the art.
- the particle is paramagnetic, or comprises a paramagnetic material. In some embodiments, the particle is superparamagnetic or comprises a superparamagnetic material. WSGR Docket No.53344-792.601 [00156] In some embodiments, the particle comprises a metal material, such as but limited to a metal chalcogenide (e.g., metal oxide), metal halide.
- a metal chalcogenide e.g., metal oxide
- metal halide e.g., metal oxide
- the particle comprises a core-shell structure.
- the core of the core-shell structure comprises a paramagnetic material.
- the particle comprises an iron oxide core.
- the iron oxide core comprises magnetite.
- the iron oxide core comprises maghemite.
- the iron oxide core is functionalized with linking (e.g., tethering) moieties and/or polymers or copolymers provided elsewhere herein (e.g., bound covalently or non- covalently).
- the particle comprises a silica shell.
- the silica shell is functionalized with linking (e.g., tethering) moieties and/or polymers or copolymers provided elsewhere herein (e.g., bound covalently or non-covalently).
- the particle comprises iron oxide crystals.
- the particle comprises polystyrene.
- the particle comprises iron oxide crystals embedded in a polystyrene core.
- the particles (e.g., comprising macromolecule structures) (e.g., first particle (e.g., comprising a macromolecule structure)) provided herein comprise the structure: [00159]
- the surface (e.g., of the particle) is at least partially coated with silica.
- the particles (e.g., comprising macromolecule structures) (e.g., first particle (e.g., comprising a macromolecule structure)) provided herein comprises the structure: [00160]
- L is a linker.
- A is a polymer or copolymer comprising (e.g., randomly distributed) monomers of Formulas (D), (E), (E-A), or represented in Table 2.
- A is a copolymer comprising randomly distributed monomers of Formulas (D), (E), (E-A), or represented in Table 2.
- the particles e.g., comprising macromolecule structures
- second particle e.g., comprising a macromolecule structure
- the surface e.g., of the particle
- compositions comprising a combination of: [00169] In some embodiments, L, A, B, and are described elsewhere herein.
- the linkers provided herein comprise optionally substituted alkylene (e.g., C 1 -C 20 alkylene), optionally substituted heteroalkylene (e.g., C 1 -C 20 heteroalkylene), or optionally substituted aralkylene (e.g., C 1 -C 20 aralkylene).
- the linker comprises optionally substituted C1-C20 alkylene (e.g., C1-C12, C1-C10, or C 1 -C 6 ).
- the linker comprises C 1 -C 20 heteroalkylene. In some embodiments, the linker comprises C 1 -C 20 aralkylene. [00171] In some embodiments, provided herein are compositions comprising a combination of: WSGR Docket No.53344-792.601 [00172] In some embodiments, provided herein are compositions comprising a combination of: [00173] In some embodiments, provided herein are compositions comprising a combination of: [00174] In some embodiments, provided herein are compositions comprising a combination of: [00175] In some embodiments, L is a linker.
- compositions comprising a (e.g., first) particle (e.g., comprising a macromolecule structure) comprising one or more units represented by Formulas (A)-(C), (A-A), (A-B), (A-C), (A-D), or represented in Table 1, attached (e.g., covalently) to a surface described elsewhere herein.
- a particle e.g., comprising a macromolecule structure
- Formulas A)-(C), (A-A), (A-B), (A-C), (A-D), or represented in Table 1, attached (e.g., covalently) to a surface described elsewhere herein.
- compositions comprising a (e.g., second) particle (e.g., comprising a macromolecule structure) comprising one or more units represented by Formulas (D), (E), (E-A), or represented in Table 2, attached (e.g., covalently) to a surface described elsewhere herein.
- compositions comprising a (e.g., first) particle (e.g., comprising a macromolecule structure) comprising one or more units represented by Formulas (A)-(C), (A-A), (A-B), (A-C), (A-D), or represented in Table 1, attached (e.g., covalently) to a surface described elsewhere herein, and a (e.g., second) particle (e.g., comprising a macromolecule structure) comprising one or more units represented by Formulas (D), (E), (E-A), or represented in Table 2, attached (e.g., covalently) to a surface described elsewhere herein.
- a (e.g., first) particle e.g., comprising a macromolecule structure) comprising one or more units represented by Formulas (A)-(C), (A-A), (A-B), (A-C), (A-D), or represented in Table 1
- a (e.g., second) particle e.g., comprising
- the particles e.g., comprising macromolecule structures
- the particle size can be measured by dynamic light scattering (DLS) as an indirect measure of size.
- the DLS measurement can be an ‘intensity-weighted’ average, which means the size distribution that the mean is calculated from can be weighted by the sixth power of radius. This can be referred to herein as ‘z-average’ or ‘intensity-mean’.
- the particles (e.g., comprising the macromolecule structures) provided herein comprise a diameter (e.g., particle size) of from about 200 nm to about 1000 nm. In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a diameter (e.g., particle size) of from about 300 nm to about 600 nm.
- the particles comprise a diameter of from about 200 nm to about 800 nm, from about 200 nm to about 600 nm, about 300 nm to about 1000 nm, about 300 nm to about 700 nm, or about 400 nm to about 500 nm.
- the particles (e.g., comprising the macromolecule structures) provided herein comprise a diameter of from about 400 nm to about 500 nm.
- the particles (e.g., comprising the macromolecule structures) provided herein comprise a diameter of from about 410 nm to about 460 nm.
- the particles provided herein have a diameter of about 350 nm to about 460 nm. In some embodiments, the particles provided herein have a diameter of about 370 nm to about 445 nm. In some embodiments, the particles (e.g., WSGR Docket No.53344-792.601 comprising the macromolecule structures) comprise a diameter of at least 100 nm (e.g., at least 200 nm, 300 nm, 400 nm, 410 nm, 420 nm, 430 nm, 440 nm, 450 nm, 460 nm, 470 nm, 480 nm, 500 nm, 600 nm, 700 nm, 750 nm, 800 nm, 900 nm, or at least 1000 nm).
- nm e.g., at least 200 nm, 300 nm, 400 nm, 410 nm, 420 nm, 430 nm
- the particles herein comprise a diameter of about 410 nm, 411 nm, 412 nm, 413 nm, 414 nm, 415 nm, 416 nm, 417 nm, 418 nm, 419 nm, 420 nm, 421 nm, 422 nm, 423 nm, 424 nm, 425 nm, 426 nm, 427 nm, 428 nm, 429 nm, 430 nm, 431 nm, 432 nm, 433 nm, 434 nm, 435 nm, 436 nm, 437 nm, 438 nm, 439 nm, 440 nm, 441 nm, 442 nm, 443 nm, 444 nm, 445 nm, 446 nm, 447 nm,
- the particles described herein are freeze dried. In some instances, the particles are freeze dried before being supplied in the kits described herein.
- the particles comprised in the kits herein may be freeze dried particles which are configured for resuspension by a user.
- the resuspended particles, such as after freeze drying or lyophilization have a diameter that is about 20 nm greater than before freeze drying or lyophilization.
- the resuspended particles have an average diameter of about 390 nm to about 470 nm.
- the resuspended first particles have an average diameter of about 390 nm to about 470 nm.
- the resuspended second particles have an average diameter of about 390 nm to about 470 nm.
- the diameter e.g., as measured by DLS
- the particles (e.g., as measured by DLS) is the average diameter.
- the particles (e.g., comprising the macromolecule structures) provided herein comprise homogenous or heterogenous size distribution.
- the particles (e.g., comprising the macromolecule structures) provided herein comprise a homogenous size distribution.
- polydispersity index (PDI) is used as a measure WSGR Docket No.53344-792.601 for size distribution. PDI may be measured by techniques such as dynamic light scattering (DLS).
- the particles (e.g., comprising the macromolecule structures) provided herein comprise a PDI of at least 0.01 (e.g., at least 0.025, 0.05, 0.075, 0.1, 0.125, 0.15, 0.175, at least 0.2, or at least 0.5). In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a PDI of at most 0.5 (e.g., at most 0.4, 0.35, 0.3, 0.25, 0.2, 0.175, 0.15, 0.125, or 0.1).
- the particles (e.g., comprising the macromolecule structures) provided herein comprise a PDI of from 0.05 to 0.2. In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a PDI of from about 0.1 to about 0.2. In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise a PDI of about 0.07, 0.08, 0.09, 0.1, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.25, or 0.25. In some embodiments, the first macromolecule structure comprises a PDI of about 0.12, such as described in Example 1.
- the second macromolecule structure comprises a PDI of about 0.14, such as described in Example 2. In some embodiments, the particles have a PDI of less than 0.2.
- the particles (e.g., comprising the macromolecule structures) provided herein comprise varying amounts of the polymer or co-polymer, such as any amount suitable according to one of skill in the art. In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise at least 1% w/w of the polymer or co-polymer.
- the particles comprise at least 2.5% w/w (e.g., 3% w/w, 4% w/w, 5% w/w, 6% w/w, 8% w/w, 10% w/w, 12% w/w, 15% w/w, 20% w/w, or at least 25% w/w) of the polymer or copolymer.
- the macromolecule structure comprises about 1% w/w, 2% w/w, 3% w/w, 4% w/w, 5% w/w, 6% w/w, 7% w/w, 8% w/w, 9% w/w, 10% w/w, 11% w/w, 12% w/w, 13% w/w, 14% w/w, 15% w/w, 16% w/w, 17% w/w, 18% w/w, 19% w/w, or 20% w/w.
- the macromolecule structure comprises about 17% w/w of the polymer or copolymer.
- the first monomer comprises the structure: WSGR Docket No.53344-792.601 [00206] In some embodiments, q is an integer from 1 to 6. In some embodiments, q is 1. In some embodiments, q is 2. In some embodiments, q is 3. In some embodiments, q is 4. In some embodiments, q is 5. In some embodiments, q is 6. [00207] In some embodiments, the first monomer is glycidyl methacrylate.
- the second monomer is ethyleneglycol dimethacrylate. In some embodiments, the second monomer comprises a crosslinking monomer. In some embodiments, the crosslinking monomer is a diene. In some embodiments, the cross-linking monomer comprises the structure: [00211] In some embodiments, R 1 is hydrogen or C1-C6 alkyl. In some embodiments, R 1 is hydrogen. In some embodiments, R 1 is C1-C6 alkyl. In some embodiments, R 2 is hydrogen or C1- C 6 alkyl. In some embodiments, R 2 is hydrogen. In some embodiments, R 2 is C 1 -C 6 alkyl.
- R 3 is hydrogen or C1-C6 alkyl. In some embodiments, R 3 is hydrogen. In some embodiments, R 3 is C1-C6 alkyl. In some embodiments, R 3 is methyl. In some embodiments, R 1’ is hydrogen or C 1 -C 6 alkyl. In some embodiments, R 1’ is hydrogen. In some embodiments, R 1’ is C 1 -C 6 alkyl. In some embodiments, R 2’ is hydrogen or C 1 -C 6 alkyl. In some embodiments, R 2’ is WSGR Docket No.53344-792.601 hydrogen. In some embodiments, R 2’ is C1-C6 alkyl.
- R 3’ is hydrogen or C1- C6 alkyl. In some embodiments, R 3’ is hydrogen. In some embodiments, R 3’ is C1-C6 alkyl. In some embodiments, R 3’ is methyl.
- the first and/or second monomers comprise one or more impurities. In some instances, the impurities are polymerized and are comprised within the macromolecule chain. In some embodiments, impurities include impurities within the first monomer and second monomer or non-fully reacted monomers within the polymers or copolymers formed after functionalization.
- the methods comprise contacting a surface and the mixture of monomers (e.g., comprising a first monomer and a second monomer), thereby producing a reaction mixture.
- the surface is a surface as provided elsewhere herein.
- the surface comprises polymerizable olefins that may polymerize with the mixture of monomers, thus covalently attaching the monomers, and the resulting polymer or copolymer, to the surface.
- the surface is reacted with one or more monomers to create a polymer coated surface.
- the polymer coated surface may undergo polymerization with the mixture of monomers provided herein.
- the radical initiator comprises azobisisobutyronitrile (AIBN).
- the method comprises contacting the macromolecule immobilized to the surface and an amine, thereby producing an aminated macromolecule.
- the amine is an alkylamine (e.g., comprising from 1 to 6 carbons (e.g., a C1-C6 alkylamine).
- the amine comprises the structure: [00218] In some embodiments, the amine is an alkylenediamine. In some embodiments, the amine is ethylenediamine.
- any one of the steps in a method provided herein may be completed under inert conditions.
- the inert conditions comprise nitrogen gas (N 2 ).
- any one of the steps in a method provided herein may comprise heating.
- the method comprises heating to multiple (e.g., 2 or more, or 3 or more) different temperatures during the course of the method.
- the method comprises heating to at least 40°C (e.g., 50°C, 60°C, 70°C, 80°C, 90°C, or at least 100°C).
- the alkylene diamine is ethylene glycol.
- the optionally substituted succinic anhydride is an alkenylsuccinic anhydride.
- the optionally substituted succinic anhydride is an C 4 -C 10 alkenylsuccinic anhydride.
- the optionally substituted succinic anhydride is octenylsuccinic anhydride.
- provided herein are compositions obtained by a method comprising polymerizing 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles.
- the particles e.g., comprising the macromolecule structures
- the particles can be used in the methods disclosed in U.S. Patent Nos.10,866,242, 11,428,688, WSGR Docket No.53344-792.601 11,906,526, and PCT App. Nos. PCT/US2021/042254 and PCT/US2023/068457, each of which is incorporated by reference herein in its entirety.
- a biological sample comprises plasma, serum, or blood. In some embodiments, a biological sample comprises blood. In some embodiments, a biological sample comprises plasma. In some embodiments, a biological sample comprises serum. In some embodiments, the biological sample is a biofluid. In some embodiments, the biological sample is a cell-free biofluid. [00234] In some embodiments, the method comprises contacting a biological sample comprising one or more biomolecules with one, two or more particles (e.g., comprising the macromolecule structures) (e.g., such as particles (e.g., comprising the macromolecule structures) provided elsewhere herein).
- particles e.g., comprising the macromolecule structures
- the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of about 0.5 mg/mL, about 0.55 mg/mL, about 0.6 mg/mL, about 0.65 mg/mL, about 0.7 mg/mL, about 0.75 mg/mL, about 0.8 mg/mL, about 0.85 mg/mL, about 0.9 mg/mL, or about 0.95 mg/mL.
- the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of about 0.7 mg/mL.
- the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of about 0.5 mg/mL, 0.51 mg/mL, 0.52 mg/mL, 0.53 mg/mL 0.54 mg/mL, 0.55 mg/mL, 0.56 mg/mL, 0.57 mg/mL, 0.58 mg/mL, 0.59 mg/mL, or 0.6 mg/mL.
- the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of about 0.56 mg/mL.
- the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of about 0.36 mg/mL.
- the method comprises contacting a biological sample (e.g., plasma or serum) comprising one or more biomolecules (e.g., proteins) with the magnetic particles in any one of the compositions provided herein.
- a biological sample e.g., plasma or serum
- biomolecules e.g., proteins
- a “biomolecule corona” refers to one or more biomolecules adsorbed to a surface of a macromolecule structure described herein.
- multiple (e.g., a plurality) of biomolecules may be adsorbed to particles (e.g., comprising the macromolecule structures) provided herein.
- a plurality of unique biomolecules may be adsorbed to a macromolecule structure.
- digestion comprises the use of trypsin, lysin, serine protease, chymotrypsin, pepsin, thermolysin, proteinase K, or a combination thereof.
- the digestion comprises trypsin.
- the digestion comprises lysin.
- the digestion comprises serine protease.
- the digestion comprises chymotrypsin.
- the digestion comprises pepsin.
- the digestion comprises thermolysin.
- the digestion comprises proteinase K.
- the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of about 40 mg/mL to about 45 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of about 40 mg/mL, about 41 mg/mL, about 42 mg/mL, about 43 mg/mL, about 44 mg/mL, about 45 mg/mL, about 46 mg/mL. about 47 mg/mL, about 48 mg/mL, about 49 mg/mL, or about 50 mg/mL.
- a buffer as provided herein comprises a pH of about 6.7. In some embodiments, a buffer as provided herein comprises a pH of about 6.6. In some embodiments, a buffer as provided herein comprises a pH of about 6.5. In some embodiments, a buffer may be any suitable buffer according to one of skill in the art. In some embodiments, the buffer comprises phosphate buffer, Tris, HEPES, MES, MOPS, TES, CAPS, Bicine, or Bis-Tris. In some embodiments, the buffering agent is CAPS. In some embodiments, the buffering agent is HEPES. In some embodiments, the buffering agent does not comprise a primary amine.
- the organic solvent is N,N-dimethylacetamide.
- the organic solvents provided herein comprise a combination of two or more organic solvents.
- the organic solvent comprises an alcohol, acetonitrile, dichloromethane, dimethylformamide (DMF), dimethylsulfoxide (DMSO), ethyl acetate, hexamethylphosphoramide (HMPA), or tetrahydrofuran.
- the organic solvent comprises DMF.
- the organic solvent comprises acetonitrile.
- eluting comprises the use of an elution buffer, such as a buffer described elsewhere herein.
- the methods provided herein are capable of isolating at least 100 (e.g., 250, 500, 750, 1,000, 1,500, 2,000, 2,500, or at least 3000 biomolecules). In some embodiments, the methods provided herein are capable of isolating at least about 1,000 biomolecules. In some embodiments, the methods provided herein are capable of isolating at most 20,000 biomolecules (e.g., at most 15,000, 12,500, 10,000, 8,000, 7,000, 6,000, 5,000, 4,000, 3,000, or at most 2,500) biomolecules.
- the combination of a first macromolecule structure and a second macromolecule structure provides a synergistic relationship allowing for identification, isolation, purification, or quantification of a larger number of biomolecules.
- the combination of the two particles e.g., comprising the macromolecule structures
- the wash solution comprises an aqueous solution.
- the wash solution comprises a buffer.
- the washing may be performed after adsorbing the one or more biomolecules to the particles (e.g., comprising the macromolecule structures), and before eluting the one or more biomolecules.
- the methods provided herein comprise purifying the isolated biomolecules (e.g., proteins), such as by solid phase extraction.
- the solid phase extraction comprises use of a third particle, such as a third particle described elsewhere herein.
- the isolating comprises contacting with the third particle described elsewhere herein.
- the solid phase comprises a polyalkylene glycol (PAG) methacrylate, polyalkylene glycol (PAG) acrylate, polyalkylene glycol (PAG) methacrylamide, polyalkylene glycol (PAG) acrylamide, polyalkylene glycol (PAG) vinyl ether, and combinations thereof.
- the solid phase comprises polyethylene glycol (PEG) methacrylate.
- the methods provided herein comprise removing a surfactant from the biological sample.
- the amount of surfactants in a composition comprising the population of biomolecules is greater than the amount of surfactants in a composition comprising the one or more isolated biomolecules by about 10 wt% to about 100 wt%, 10 wt% to about 90 wt%, 20 wt% to about 100 wt%, 30 wt% to about 100 wt%, 50 wt% to about 100 wt%, 50 wt% to about 80 wt%, or about 80 wt% to about 100 wt%.
- Non-limiting examples of surfactants that may be greater include sodium lauryl sulfate, Triton X-100, TWEEN, NP-40, CHAPS, Octyl glucoside, and decyl maltoside.
- the surfactant is sodium lauryl sulfate.
- the surfactant is CHAPS.
- the surfactant is a synthetic molecule. [00274]
- the methods provided herein comprise removing a buffering agent from the biological sample.
- the methods provided herein comprise removing at least 90% (e.g., at least 95%, at least 97.5%, at least 98%, at least 99%, at least 99.5%) of a buffering agent. In some embodiments, the methods provided herein comprise removing about 90% to about 99.9%, about 90% to about 99%, about 90% to about 98%, about 92% to about 97.5%, or about 93% to about 99% of a buffering agent. In some embodiments, the amount of buffering agent in the composition comprising the population of biomolecules is greater than the amount of buffering agent in a composition comprising the one or more isolated biomolecules.
- the amount of buffering agent in a composition comprising the population of biomolecules is greater than the amount of buffering agent in a composition comprising the one or more isolated biomolecules by at most 100 wt% (e.g., 99 wt%, 95 wt%, 90 wt%, 80 wt%, 70 wt%, 60 wt%).
- the buffering agent is CAPS. In some embodiments, the buffering agent is HEPES. WSGR Docket No.53344-792.601 [00275]
- the methods provided herein comprise removing a chaotrope from the biological sample. In some embodiments, the methods provided herein comprise removing at least 90% (e.g., at least 95%, at least 97.5%, at least 98%, at least 99%, at least 99.5%) of a chaotrope. In some embodiments, the methods provided herein comprise removing about 90% to about 99.9%, about 90% to about 99%, about 90% to about 98%, about 92% to about 97.5%, or about 93% to about 99% of a chaotrope.
- the methods provided herein comprise removing at least 90% (e.g., at least 95%, at least 97.5%, at least 98%, at least 99%, at least 99.5%) of a base. In some embodiments, the methods provided herein comprise removing about 90% to about 99.9%, about 90% to about 99%, about 90% to about 98%, about 92% to about 97.5%, or about 93% to about 99% of a base. In some embodiments, the amount of base in the composition comprising the population of biomolecules is greater than the amount of base in a composition comprising the one or more isolated biomolecules.
- the amount of base in a composition comprising the population of biomolecules is greater than the amount of base in a composition comprising the one or more isolated biomolecules by at least 10 wt% (e.g., at least 20 wt%, 30 wt%, 50 wt%, 80 wt%, 90 wt%, or at least 100 wt%). In some embodiments, the amount of base in a composition comprising the population of biomolecules is greater than the amount of base in a composition comprising the one or more isolated biomolecules by at least 70 wt%.
- the amount of base in a composition comprising the population of biomolecules is greater than the amount of base in a composition comprising the one or more isolated biomolecules by at most 100 wt% (e.g., 99 wt%, 95 wt%, 90 wt%, 80 wt%, 70 wt%, or at most 60 wt%).
- the methods provided herein comprise providing one or more isolated biomolecules that are at least 75% (e.g., at least 80%, 85%, 90%, 93%, 95%, 97%, 98%, 99%, 99.5%, or at least 99.9%) pure. In some embodiments, the methods provided herein comprise providing one or more isolated biomolecules that are at most 99.9% (e.g., at most 99%, 98%, 97%, WSGR Docket No.53344-792.601 96%, 95%, 94%, or at most 92%) pure.
- the methods comprise assaying the purified isolated proteins (e.g., such as purified by solid phase extraction). In some embodiments, the methods comprise analyzing the isolated proteins using mass spectrometry. In some embodiments, such as when the method comprises digestion, the isolated proteins are or comprise peptides. [00280] In some embodiments, the method comprises contacting the biological sample with a composition provided herein to form at least two biomolecule corona. In some embodiments, the method comprises assaying the at least two biomolecule corona to detect one or more biomolecules in the biological sample.
- the assaying detects at least 2% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, the assaying detects at least 5% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, the assaying detects at least 7% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, the assaying detects at least 10% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle.
- the assaying detects at least 60% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. In some embodiments, the assaying detects at least 70% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. [00283] In some embodiments, the method does not comprise pre-selection of the detected biomolecules before assaying. [00284] In some embodiments, the methods herein comprise detecting or identifying the one or more (e.g., isolated biomolecules).
- the (e.g., isolated biomolecules) biomolecules can be identified, measured, and quantified using mass spectrometry, high performance liquid chromatography, LC-MS, LC- MS/MS, Edman degradation, immunoaffinity techniques, and methods disclosed in EP3548652, WO2019083856, WO2019133892, each of which is incorporated herein by reference in its entirety.
- the methods provided herein are capable of identifying at least 50 biomolecules. In some embodiments, the methods provided herein are capable of identifying at least 100 (e.g., 250, 500, 750, 1,000, 1,500, 2,000, 2,500, or at least 3000 biomolecules).
- the methods provided herein are capable of identifying (e.g., isolated) biomolecules over a dynamic range of at least 2 (e.g., at least 3, 4, 5, 6, 7, 8, 9, or at least 10). In some embodiments, the methods herein are capable of identifying (e.g., isolated) biomolecules over a dynamic range of at least 7, at least 8, at least 9, or at least 10.
- the uses and methods provided herein comprise using the structures of Formula (A-D) and Formula (A-A) as recurring units for binding proteins in a biological sample.
- the uses and methods provided herein comprise using the structures of Formula (A-C) and Formula (A-B) as recurring units for binding proteins in a biological sample.
- the uses and methods provided herein comprise the use of any of the compositions provided herein for binding proteins in a biological sample.
- the system comprises a plurality of particles (e.g., comprising the macromolecule structures).
- the system comprises at least two particles (e.g., comprising the macromolecule structures).
- the at least two particles e.g., comprising the macromolecule structures
- the at least two particles comprise a first macromolecule structure with a neutral to negative surface charge.
- the at least two particles e.g., comprising the macromolecule structures
- a first macromolecule structure e.g., such as WSGR Docket No.53344-792.601 a macromolecule structure provided elsewhere herein).
- the at least two particles comprise a second macromolecule structure (e.g., such as a macromolecule structure provided elsewhere herein).
- the system comprise any composition provided elsewhere herein.
- the system is configured to perform any one of the methods provided elsewhere herein.
- the system comprises a suspension solution.
- the suspension solution is configured to suspend the at least two particles (e.g., comprising the macromolecule structures).
- the suspension solution comprises a buffer.
- the suspension solution comprises Tris, EDTA, CHAPS, or HEPES buffer.
- the suspension solution comprises HEPES buffer.
- the suspension solution comprises a buffer at a concentration of about 10 mM, 25 mM, 30 mM, 50 mM, 75 mM, 100 mM, 125 mM, 200 mM, 250 mM, or about 300 mM. In some embodiments, the suspension solution comprises the buffer at an amount of about 300 mM. As an example, a suspension solution may comprise 300 mM HEPES buffer. In another example, the suspension solution may be 10mM Tris HCl pH 7.4, 1 mM EDTA. [00302] In some embodiments, the system comprises a biological sample, such as a biological sample provided elsewhere herein. In some embodiments, the biological sample comprises a plurality of biomolecules.
- the system comprises an automated system comprising a network of units with differentiated functions configured to isolate one or more biomolecules from the biological sample using the at least two particles (e.g., comprising the macromolecule structures).
- the present disclosure provides an automated system comprising a network of units as described in U.S. Patent No. 11,630,112, which is incorporated herein by reference in its entirety.
- the network of units may comprise differentiated functions in distinguishing states of a complex biological sample using two or more particles (e.g., comprising the macromolecule structures) having surfaces with different physicochemical properties.
- the system comprises a first unit comprising a multichannel fluid transfer instrument for transferring fluids between units within the system.
- the first unit comprises a degree of mobility that enables access to all other units within the system.
- the first unit comprises a capacity to perform pipetting functions.
- the system comprises a second unit comprising a support for storing a plurality of biological samples.
- the second unit can facilitate a transfer of the sample for mass spectrometry to a mass spectrometry unit.
- WSGR Docket No.53344-792.601 the second unit can facilitate a transfer of the sample for analysis, such as by any analytical technique described herein.
- the system comprises a third unit comprising a support for an array plate possessing partitions that comprise the one or more macromolecule structure for binding of the one or more biomolecules with the two or more particles (e.g., comprising the macromolecule structures).
- the support of the second and/or third unit comprises support for a single plate, a 6 well plate, a 12 well plate, a 96 well plate, or a rack of microtubes.
- the second and/or unit comprises a thermal unit capable of modulating the temperature of said support and a sample.
- the second and/or third unit comprises a rotational unit capable of physically agitating and/or mixing a sample.
- the two or more particles having surfaces with different physicochemical properties for binding a population of analytes (e.g., biomolecules) within the biological sample are immobilized to a macromolecule WSGR Docket No.53344-792.601 structure within a partition of the sensory array.
- the two or more particles comprise different physicochemical properties for binding a population of analytes (e.g., biomolecules) within the biological sample.
- the system comprises a step wherein the sensor array plate is transferred to an additional seventh unit that comprises a magnetized support and a thermal unit capable of modulating the temperature of said support and a sample and incubated for an additional amount of time.
- incubating the biological sample with at least two particles (e.g., comprising the macromolecule structures) contained within the partition of the sensor array plate comprises an incubation time of at least about 10 seconds (e.g., at least about 15 seconds, 20 seconds, 25 seconds, 30 seconds, 40 seconds, 50 seconds, 60 seconds, 90 seconds, 2 minutes, 4 minutes, 5 minutes, 6 minutes, 8 minutes, 10 minutes, 15 minutes 20 minutes, 30 minutes, 45 minutes, 60 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 8 hours, 10 hours, 12 hours, 14 hours, 16 hours, 18 hours, 20 hours, or at least about 24 hours).
- incubating the biological sample with the at least two particles (e.g., comprising the macromolecule structures) contained within the partition of the substrate comprises an incubation temperature of at least 4°C (e.g., at least 5°C, 10°C, 15°C, 20°C, 25°C, 30°C, 35°C, or at least 40°C). In some embodiments, the incubation temperature is at most 50°C (e.g., at most 45°C, 40°C, 38°C, 35°C, 30°C, 25°C, or 20°C). In some embodiments, the incubation temperature is from about 4°C to about 40°C.
- the automated apparatus comprises a sample preparation unit; a substrate comprising a plurality of channels; a plurality of pipettes; a plurality of solutions; a plurality of particles (e.g., comprising the macromolecule structures) as provided WSGR Docket No.53344-792.601 elsewhere herein.
- the automated apparatus comprises a sample preparation unit.
- the automated apparatus comprises a substrate comprising a plurality of channels.
- the automated apparatus comprises a plurality of pipettes.
- the automated apparatus comprises a plurality of solutions.
- the automated apparatus comprises a plurality of particles (e.g., comprising the macromolecule structures), such as described elsewhere herein.
- the automated apparatus is configured to form a biomolecule corona and digest the biomolecule corona (or two or more biomolecule coronas).
- the automated apparatus is configured for digestion (e.g., by enzymolysis), such as using any digestion agent provided herein (e.g., trypsin) of the biomolecule corona.
- the automated apparatus is configured for BCA, gel, or trypsin digestion of the biomolecule corona.
- the automated apparatus is enclosed.
- the automated apparatus is sterilized before use.
- the automated apparatus is configured to a mass spectrometer.
- the automated apparatus is temperature controlled.
- the automated apparatus comprises a substrate comprising a plurality of partitions, a first unit comprising the biological sample, and a loading unit that is movable across the substrate and is capable of transferring a volume (e.g., a volume of buffer) between different units of the apparatus.
- the substrate is a multi-well plate.
- the plurality of partitions comprises a plurality of sensor elements.
- the plurality of sensor elements may comprise particles (e.g., comprising the macromolecule structures) as provided elsewhere herein.
- a partition from among the plurality of partitions may comprise 4 to 10 types of sensor elements.
- a partition from WSGR Docket No.53344-792.601 among the plurality of partitions may comprise 5 to 12 types of sensor elements.
- a partition from among the plurality of partitions may comprise 6 to 15 types of sensor elements.
- a partition from among the plurality of partitions may comprise 8 to 20 types of sensor elements.
- a partition from among the plurality of partitions may comprise 2 types of sensor elements.
- a partition from among the plurality of partitions may comprise at least 2 types of sensor elements.
- a partition from among the plurality of partitions may comprise 3 types of sensor elements. [00322] Two or more partitions from among the plurality of partitions may comprise different quantities of sensor elements.
- a substrate partition may comprise a solution comprising a high concentration of particles (e.g., comprising the macromolecule structures).
- Partitions from among the plurality of partitions comprise different concentrations or amounts (e.g., by mass/molar amount per unit volume of sample) of sensor elements.
- a partition from among the plurality of partitions may comprise from 1 pM to 100 nM of sensor elements.
- a partition from among the plurality of partitions may comprise from 10 pM to 1 nM of sensor elements.
- a partition from among the plurality of partitions may comprise from 100 pM to 10 nM of sensor elements.
- the loading unit may be configured to move precise volumes (e.g., within 0.1%, 0.01%, 0.001% of the specified volume).
- the loading unit may be configured to collect a volume from the substrate or a compartment or partition within the substrate and dispense the volume back into the substrate or compartment or partition within the substrate, or to dispense the volume or a portion of the volume into a different unit, compartment, or partition.
- the loading unit is configured to move multiple volumes simultaneously, such as 2 to 400 separate volumes.
- the loading unit may comprise a plurality of pipette tips. [00326]
- the loading unit may be configured to move a volume of a liquid.
- the volume may be at least 0.1 ⁇ L (e.g., at least 0.4 ⁇ L, 0.6 ⁇ L 0.8 ⁇ L, 1 ⁇ L, 5 ⁇ L, 10 ⁇ L, 25 ⁇ L, 100 ⁇ L, or at least 250 ⁇ L). In some embodiments, the volume may be at most 5 mL (e.g., at most 2 mL, 1 mL, 750 ⁇ L, 500 ⁇ L, 250 ⁇ L, 200 ⁇ L, 100 ⁇ L, or at most 50 ⁇ L).
- the volume may be about 0.1 ⁇ l, 0.2 ⁇ l, 0.3 ⁇ l, 0.4 ⁇ l, 0.5 ⁇ l, 0.6 ⁇ l, 0.7 ⁇ l, 0.8 ⁇ l, 0.9 ⁇ l, 1 ⁇ l, 2 ⁇ l, 3 ⁇ l, 4 ⁇ l, 5 ⁇ l, 6 ⁇ l, 7 ⁇ l, 8 ⁇ l, 9 ⁇ l, 10 ⁇ l, 12 ⁇ l, 15 ⁇ l, 20 ⁇ l, 25 ⁇ l, 30 ⁇ l, 40 ⁇ l, 50 ⁇ l, 60 ⁇ l, 70 ⁇ l, 80 ⁇ l, 90 ⁇ l, 100 ⁇ l, 120 ⁇ l, 150 ⁇ l, 180 ⁇ l, 200 ⁇ l, 250 ⁇ l, 300 ⁇ l, 400 ⁇ l, 500 ⁇ l, 600 ⁇ l, 800 ⁇ l, 1 ml, or more than 1 ml.
- the solution comprises a wash solution, a resuspension solution, a denaturing solution, a buffer, a reagent (e.g., a reducing reagent), or any combination thereof.
- the solution comprises a biological sample.
- the loading unit can be capable of partitioning a sample. In some embodiments, this comprises dividing a sample into a number of partitions. A sample can be divided into at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 120, 150, 180, 200, 250, 300, 350, 400, 500, or more partitions.
- the volume of biological sample loaded into a partition may be about 0.1 ⁇ l, 0.2 ⁇ l, 0.3 ⁇ l, 0.4 ⁇ l, 0.5 ⁇ l, 0.6 ⁇ l, 0.7 ⁇ l, 0.8 ⁇ l, 0.9 ⁇ l, 1 ⁇ l, 2 ⁇ l, 3 ⁇ l, 4 ⁇ l, 5 ⁇ l, 6 ⁇ l, 7 ⁇ l, 8 ⁇ l, 9 ⁇ l, 10 ⁇ l, 12 ⁇ l, 15 ⁇ l, 20 ⁇ l, 25 ⁇ l, 30 ⁇ l, 40 ⁇ l, 50 ⁇ l, 60 ⁇ l, 70 ⁇ l, 80 ⁇ l, 90 ⁇ l, 100 ⁇ l, 120 ⁇ l, 150 ⁇ l, 180 ⁇ l, 200 ⁇ l, 250 ⁇ l, 300 ⁇ l, 400 ⁇ l, 500 ⁇ l, 600 ⁇ l, 800 ⁇ l, 1 ml, or more than 1 ml.
- the automated apparatus may dilute a sample or sample partition by 2-fold, 3- fold, 4-fold, 5-fold, 6-fold, 8-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 75-fold, 100-fold, 150-fold, 200-fold, 300-fold, 400-fold, 500-fold or greater.
- the automated apparatus may dilute a sample or sample partition by about 2-fold to about 5-fold.
- the automated apparatus may perform different dilutions on two samples or sample partitions.
- the system may perform different dilutions on each partition from among a plurality of partitions. For example, the system may perform different dilutions on each of the 96 sample partitions in a 96 well plate.
- the different dilutions comprise different degrees of dilution (e.g., 2- fold vs. 4-fold). In some cases, the different dilutions comprise dilution with different solutions (e.g., different buffers). In some cases, two sample partitions may be made to differ in one or more chemical properties, such as pH, salinity, or viscosity.
- the system may modify the chemical composition of a sample or sample partition. The system may modify or adjust the pH, salinity, osmolarity, dielectric constant, viscosity, buffer types, salt types, sugar types, detergent types, or any combination thereof for a sample or sample partition.
- the automated apparatus may comprise a unit comprising a resuspension solution.
- the loading unit may be capable of transferring a volume of the resuspension solution to a partition from among the plurality of partitions of the substrate. In some cases, this results in the dilution of a sample present within the partition and can further result in the desorption of a plurality of biomolecules from a biomolecule corona disposed on a sensor element within the partition.
- the transfer of a volume of the resuspension solution into a partition may result in the desorption of 10% to 20% of the biomolecules from a biomolecule corona.
- the transfer of a volume of the resuspension solution into a partition may result in the desorption of 20% to 30% of the biomolecules from a biomolecule corona.
- the transfer of a volume of the resuspension solution into a partition may result in the desorption of 30% to 40% of the biomolecules from a biomolecule corona.
- the transfer of a volume of the resuspension solution into a partition may result in the desorption of 40% to 50% of the biomolecules from a biomolecule corona.
- the transfer of a volume of the resuspension solution into a partition may result in the desorption of 50% to 60% of the biomolecules from a biomolecule corona.
- the transfer of a volume of the resuspension solution into a partition may result in the desorption of 60% to 70% of the biomolecules from a biomolecule corona.
- the transfer of a volume of the resuspension solution into a partition may result in the desorption of 70% to 80% of the biomolecules from a biomolecule corona.
- the transfer of a volume of the resuspension solution into a partition may result in the desorption of 80% to 90% of the biomolecules from a biomolecule corona.
- the transfer of a volume of the resuspension solution into a partition may result in the desorption of more than 90% of the biomolecules from a biomolecule corona.
- multiple rounds of desorption are performed. In each round, the supernatant comprising the desorbed biomolecules may be collected, analyzed, or discarded. The types and abundances of biomolecules in the supernatant may differ between desorption rounds.
- the automated apparatus may perform one or more desorption and discard cycles (i.e., washes), followed by one or more desorption cycles comprising sample collection and/or analysis.
- the resuspension solution may be tailored to optimize enrichment of particular biomarkers.
- the resuspension solution may comprise a buffer, such as Tris-EDTA (TE), CHAPS, PBS, citrate, HEPES, MES, CHES, or another bio buffer.
- the resuspension solution may comprise Tris EDTA (TE) 150mM KCl 0.05% CHAPS buffer.
- the resuspension solution may comprise 10 mM TrisHCl pH 7.4, 1 mM EDTA.
- the resuspension solution may comprise 300 mM HEPES.
- the resuspension solution may also contain or be highly purified water (e.g., distilled or deionized water). Biomolecule desorption may be augmented by heating or agitation by an incubation element.
- the denaturing solution may comprise a chemical denaturant such as guanidine, urea, sodium deoxycholate, acetonitrile, trichloroacetic acid, acetic acid, sulfosalicylic acid, sodium bicarbonate, ethanol, perchlorate, dodecyl sulfate, or any combination thereof.
- the denaturing solution may comprise a reductant, such as 2-mercaptoethanol, dithiothreitol, or tris(2-carboxyethyl)phosphine.
- the protease may be trypsin.
- the denaturing solution may be added to a partition following desorption.
- the denaturing solution may be added to a partition comprising biomolecule coronas.
- the automated apparatus may comprise a magnet or array of magnets.
- the automated apparatus may be capable of moving the substrate onto and off of the magnet or array of magnets.
- the array of magnets may be structured so that a plurality of magnets from the array of magnets can rest directly underneath a plurality of partitions from the substrate.
- the magnet may be capable of immobilizing magnetic sensor elements (e.g., magnetic particles (e.g., comprising the macromolecule structures) provided herein) within a partition on the substrate.
- the magnet may prevent magnetic particles (e.g., comprising the macromolecule structures) from being removed from a partition during a wash step.
- the magnet may also create a pellet from a collection of magnetic particles (e.g., comprising the macromolecule structures).
- the magnet may create a macromolecule structure pellet in less than 10 minutes.
- the magnet may create a particle pellet in less than 5 minutes.
- the macromolecule structure pellet may comprise a particle with a biomolecule corona.
- the automated apparatus may comprise a purification unit.
- the purification unit may comprise a plurality of partitions comprising an adsorbent or resin.
- the purification unit may comprise a solid-phase extraction array or plate.
- the solid-phase extraction array or plate may comprise a polar stationary phase material.
- the solid-phase extraction array or plate may comprise a non-polar stationary phase material.
- the solid-phase extraction array or plate may comprise a C18 stationary phase material (e.g., octadecyl group silica gel).
- the automated apparatus comprises a unit with a conditioning solution for the purification unit (e.g., a conditioning solution for a solid-phase extraction material).
- the automated apparatus may comprise a unit with an elution solution for removing biomolecules from the purification unit.
- the purification unit may comprise a solution comprising the third particles described herein.
- a supernatant is removed from the sensor array plate.
- the automated apparatus may perform a series of wash steps.
- a wash step may remove biomolecules that are not bound to the sensor elements within the partition.
- a wash step may desorb a subset of biomolecules bound to sensor elements within a partition.
- a wash step may result in the desorption and removal of a subset of soft corona analytes, while leaving the majority of hard corona analytes bound to the sensor element.
- WSGR Docket No.53344-792.601 the present disclosure provides an automated apparatus to identify proteins in a biological sample, the automated apparatus comprising: a sample preparation unit; a substrate comprising a plurality of channels; a plurality of pipettes; a plurality of solutions, a plurality of particles (e.g., comprising the macromolecule structures), such as particles (e.g., comprising the macromolecule structures) provided elsewhere herein, and wherein the automated apparatus is configured to form a biomolecule corona and digest the biomolecule corona.
- the automated apparatus comprises a sample preparation unit. In some embodiments, the automated apparatus comprises a substrate comprising a plurality of channels. In some embodiments, the automated apparatus comprises a plurality of pipettes. In some embodiments, the automated apparatus comprises a plurality of solutions. In some embodiments, the automated apparatus comprises a plurality of particles (e.g., comprising the macromolecule structures). In some embodiments, the automated apparatus is configured to form a biomolecule corona and digest the biomolecule corona. [00341] In some embodiments, the automated apparatus or system is enclosed. Kits [00342] Provided herein, in some embodiments, are kits for isolating one or more biomolecules from a biological sample.
- the plurality (e.g., at least two) of particles (e.g., comprising the macromolecule structures) can be packaged together to comprise a combination of particles (e.g., comprising the macromolecule structures) in a single package.
- the particles (e.g., comprising the macromolecule structures) of the kits provided herein may be freeze dried and stored in sealed containers.
- the kits comprise particles (e.g., comprising the macromolecule structures), such as particles (e.g., comprising the macromolecule structures) provided elsewhere herein.
- the kits comprise at least two particles (e.g., comprising the macromolecule structures).
- the particles comprise a first macromolecule structure.
- the first macromolecule structure comprises a neutral to negative surface charge.
- the particles (e.g., comprising the macromolecule structures) comprise a second macromolecule structure.
- the second macromolecule structure comprises a negative surface charge.
- the second macromolecule structure comprises a greater negative surface charge than that of the first macromolecule structure.
- the kits provided herein comprise a buffer.
- Non-limiting examples of buffers that may be greater include Tris, phosphate buffer, HEPES, MES, MOPS, TES, TE, CAPS, Bicine, and Bis-Tris.
- the buffer is CAPS.
- the buffer is HEPES.
- the buffer comprises 200-750, 100- 750, 250-750, 300-7250, 400-750, 400-1000, 500-1000, or 500-750 mM HEPES.
- the buffer is 300 mM HEPES.
- buffers include but are not limited to a digestion buffer, resuspension buffer, dilution buffer, denaturation buffer, or a lysis buffer.
- kits provided herein comprise a washing agent (e.g., a washing solution). In some embodiments, a washing agent comprise a wash solution as described elsewhere herein. [00347] In some embodiments, the kits provided herein comprise an elution agent. In some embodiments, the elution agent is an elution buffer as described elsewhere herein. [00348] In some embodiments, the kits comprise a digestion solution or digestion agent, such as a digestion solution or digestion agent provided elsewhere herein. In some embodiments, the digestion solution comprises Trypsin. In some embodiments, the digestion solution comprises Trypsin/LysC protease.
- kits comprise a denaturing solution or denaturing agent.
- the denaturing agent comprises at least one of: sodium dodecyl sulfate, acetic acid, trichloroacetic acid, sulfosalicylic acid, sodium bicarbonate, ethanol, formaldehyde, glutaraldehyde, urea, guanidium chloride, lithium perchlorate, 2-mercaptoethanol, dithiothreitol, tris(2-carboxyethyl)phosphine (TCEP), or any combination thereof.
- the kit comprises a reducing agent.
- the reducing agent comprises TCEP, dithiothreitol, beta-mercaptoethanol, glutathione, cysteine, or any combination thereof.
- the kit comprises an alkylating agent.
- the alkylating agent comprises iodoacetamide, iodoacetic acid, acrylamide, chloroacetamide, or any combination thereof.
- the kit comprises a solid support for solid phase extraction.
- the kit comprises a polar stationary phase material.
- the kit comprises a non-polar stationary phase material.
- the kit comprises WSGR Docket No.53344-792.601 a C18 stationary phase material (e.g., octadecyl group silica gel).
- the kit comprises conditioning solution for the solid phase extraction material.
- the solid support comprises magnetic particles.
- the kit comprises an organic solvent (e.g., acetonitrile) to precipitate biomolecules onto the magnetic particles.
- the kit comprises cleanup particles.
- the kit comprises a wash solution.
- the kit comprises a multi-well plate. In some embodiments, the multi-well plate is a 4 well plate.
- the multi-well plate is a In some embodiments, the multi-well plate is a 12 well plate. In some embodiments, the multi-well plate is a 24 well plate. In some embodiments, the multi-well plate is a 48 well plate. In some embodiments, the multi-well plate is a 96 well plate. In some embodiments, the multi-well plate is a 384 well plate. In some embodiments, the multi-well plate is a 1536 well plate. [00356] In some embodiments, the kit comprises a diluent. In some embodiments, the diluent is an organic solvent. In some embodiments, the diluent is water. In some embodiments, the diluent is a buffer.
- the diluent is an organic solvent, water, a buffer, or any combination thereof.
- the kit comprises a reconstitution solution.
- the reconstitution solution may be suitable to reconstitute lyophilized particles described herein.
- the kit further comprises an organic solvent, such as an organic solvent described elsewhere herein.
- the kit further comprises a cysteine blocking reagent.
- the cysteine blocking reagent comprises methyl methanethiosulfonate, iodoacetamide, N-ethylmaleimide, methylsulfonyl benzothiazole, or any combination thereof.
- Kits may also, in some embodiments, comprise one or more of outer packaging, lot numbers, and instructions for use of the kit with the methods provided herein.
- Kits may also, in some embodiments, comprise one or more of outer packaging, lot numbers, and instructions for use of the kit with the methods provided herein.
- Example 1 Preparation of a First Particle
- a particle comprising randomly distributed ethyleneglycol dimethacrylate and hydroxyethylmethacrylate were prepared according to FIG. 1.
- Olefin functionalized superparamagnetic iron oxide@silica nanoparticles (12 g) were provided and optionally dispersed in acetonitrile.
- HEMA hydroxyethyl)methacrylate
- EGDMA ethyleneglycol dimethacrylate
- AIBN 1.4 g, 8.8 mmol
- EGDMA 23g, 116 mmol
- GMA glycidylmethacrylate
- the resulting macromolecule structure was washed with ethanol once and at least three times with water. were added and allowed to stir at 60°C overnight (16 hrs). The resulting macromolecule structure was washed with ethanol once and at least three times with water.
- the particle size, zeta potential, and % polymer were dependent on the length of time before quenching with benzoquinone in the first reaction (Table 3 and Table 4). TABLE 3 TABLE 4 Example 3: Performance of Multiplexed Particles [00366]
- the particles (e.g., comprising the macromolecule structures) provided herein were assessed for their performance in isolating protein groups both individually and while multiplexed.
- the particles were exposed to three different plasma samples, both on their own, and as a combination of (A2) and (A1).
- the ratio of (A2):(A1) was about 4:1.
- the total concentration of particles (e.g., comprising the macromolecule structures) in each of the experiments was about 0.31 mg/mL with a particle:plasma volume ratio of about 100 ⁇ L:100 ⁇ L. The results are depicted in FIG.
- Particles (A1) and (A2) were evaluated at varying concentrations in equal volumes of particles and plasma (100 ⁇ L:100 ⁇ L) as shown in FIG. 6. Concentrations of total particles evaluated were 0.45 mg/mL, 0.45 mg/mL, and 0.6 mg/mL.
- Peptide mass ( ⁇ g) and protein group counts were evaluated for samples with a multiplexed composition of (A1) and (A2) in a ratio of 4:1, 1:4, and (A2) alone.
- the ratios are weight ratios, for example, in the 4:1 (A1):(A2) multiplexed samples, 0.36 mg/mL of (A1) and 0.09 mg/mL of (A2) may be combined to arrive at the composition used.
- the results in FIG.6 may indicate that multiplexing of (A1) and (A2) can result in higher peptide mass yields at all concentrations of nanoparticle used.
- FIG. 6 also may indicate that increasing amounts of (A2) relative to (A1) e.g., 1:4 (A1):(A2) may result in increased protein group identification.
- particles e.g., comprising the macromolecule structures
- A3, A4), (A5), and (A6) were similarly assessed for a synergistic relationship when multiplexed.
- (A3), (A4), and (A5) had highly negative surface charges, whereas (A6) had an almost neutral surface charge.
- WSGR Docket No.53344-792.601 [00369] In this instance, the protein group count improvement from multiplexing was assessed, complexing (A3) with other negative particles (e.g., comprising the macromolecule structures) or almost neutral particles (e.g., comprising the macromolecule structures) (A6).
- Biomolecule Assay Protocol Methods of assaying biomolecules may be completed using the following protocol.
- the assay protocol and methods herein may provide high-throughput, unbiased, deep, rapid proteomics analysis of biological samples, such as plasma, serum, and tissue or cell lysates (or other biological samples provided herein).
- the protocol may comprise an assay step, a peptide quantification step, and a peptide reconstitution step, which may be run separately.
- Materials may be used to assay 40 or 80 biomolecules (peptide) samples on a single 96 well plate.
- the estimated time for each step of an exemplary method provided herein is shown in Table 6, such as for an 80 or 40 sample analysis.
- Table 6 WSGR Docket No.53344-792.601
- the assay may require use of an assay kit, such as a kit provided herein (i.e., assay kit). In cases where peptide quantification and peptide reconstitution are desired, an additional kit may be required (i.e., a PQR kit).
- the assay kit for analysis of 40 or 80 samples may contain the following reagents in Table 6.
- the kit may also include a labware box including a binding reservoir, black lid, 2 cleanup plates, clear lid, collection plate, nanoparticle plate, preparation plate, 2 reagents reservoirs, and a sample transfer plate.
- the labware box may not be refrigerated whereas the reagents kit (i.e., Table 7) may be refrigerated.
- the method may also make use of a peptide calibration kit.
- biomolecule (peptide) preparation, quantification, and reconstitution may require the following additional equipment: (1) a centrifuge with plate adapter that can achieve a relative centrifugal force of 500 x g and accommodate a standard 96 well microplate; (2) a fluorometric microplate reader that can measure peptide concentration via fluorescence (Ex. 390, Em.475 nm) in a 96-well plate format; (3) a refrigerated microcentrifuge that can achieve a relative centrifugal force of 5000 x g, maintain a temperature of 4°C, and accommodate sample tubes; and (4) a vacuum concentrator capable of maintaining refrigerated temperature at vacuum and accommodate a standard 96 well microplate.
- process control a pooled plasmas sample that is processed through the entirety of the workflow, including corona formation, trypsin digestion, and peptide cleanup
- digestion control a pooled plasma sample that is processed through workflow steps after the corona formation, including trypsin digestion and peptide cleanup, used for diagnostic and troubleshooting efforts
- user control an available well for the end user to supply their own on plate control sample of interest
- cleanup control a digested peptide sample generated from pooled plasma sample that is only processed through the peptide cleanup steps of the assay, also used for diagnostic and troubleshooting efforts.
- the centrifuge is first set to 4°C. If the biological (e.g., plasma) samples are frozen, they are removed from the freezer and thawed in an ice-water bath. The plasma samples should not be allowed to warm to room temperature and should be kept on ice or at 4°C until they are loaded into the sample prep plate and into the instrument. The labware is removed from the above-mentioned labware box and the Trypsin/LysC tube is placed on ice.
- biological e.g., plasma
- Required materials for the peptide quantification may include the PQR kit, described above, as well as an acid-resistant CentriVap centrifugal vacuum concentrator, a fluorescence intensity microplate reader, 50 ⁇ L nested conductive tips (NCTs), 300 ⁇ L NCTs, aluminum sealing foil 5 x 3 in, a Pierce quantitative fluorometric peptide assay, and pipettes with tips varying from 1-10 mL to 10-1000 ⁇ L.
- the PQR kit may include a black lid, quantification plate, quantification reservoir, reconstitution reservoir, recovery solution, and standards prep plate.
- Peptide reconstitution may be completed, which can reconstitute the dried peptides to the concentration and volume needed for mass spectrometry.
- the peptide reconstitution method may require use of the PQR kit described above as well as 300 ⁇ L NCTs, aluminum sealing foil 5 x 3 in, Axygen AxyMats 96 round well sealing mat for PCR microplates, peptide reconstitution buffer, and pipettes with tips varying from 1-10 mL to 10-1000 ⁇ L.
- an appropriate sized bottle large enough to hold a sufficient volume to make a single batch for the anticipated study size is obtained, assuming 4 mL per plate.
- Embodiment 1 A composition comprising two or more macromolecule structures comprising: (a) a first macromolecule structure comprising a neutral to negative surface charge; and (b) a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure.
- Embodiment 2. The composition of embodiment 1, wherein the first macromolecule structure comprises a surface charge of about 0 mV to about -15 mV.
- Embodiment 3. The composition of any one of the preceding embodiments, wherein the second macromolecule structure comprises a surface charge of about -35 mV to about -60 mV.
- composition of any one of embodiments 1-7, wherein the second macromolecule structure comprises a polymer comprising one or more units represented by Formula (A): WSGR Docket No.53344-792.601 Formula (A) wherein, R is hydrogen R 1 is hydrogen or hydroxyl; q is an integer from 1 to 6; R 2 is C1-C8 diamine, N-substituted with one or more R 3 ; R 3 is each independently hydrogen or C 1 -C 8 alkyl optionally substituted with one or more oxo, hydroxyl, C 1 -C 8 alkyl, C 1 -C 8 alkenyl, and C 1 -C 8 alkynyl; or R 1 and R 2 are taken together to form C2-C6 heterocycloalkyl; and R 4 is hydrogen or C1-C6 alkyl.
- R is hydrogen
- R 1 is hydrogen or hydroxyl
- q is an integer from 1 to 6
- R 2 is C1-C8 diamine, N-substitute
- Embodiment 10 The composition of embodiment 5 or 9, wherein R is .
- Embodiment 11 The composition of any one of embodiments 5-10, wherein R 1 is hydroxyl.
- Embodiment 12. The composition of any one of embodiments 5-11, wherein R 2 is a C2 diamine, N-substituted with one or more R 3 .
- Embodiment 13 The composition of any one of embodiments 5-11, wherein R 2 is , wherein p is an integer from 1 to 6.
- Embodiment 17 The composition of any one of embodiments 8-16, wherein at least one R 3 is C1-C8 alkyl substituted with at least one of oxo, hydroxyl, and C1-C8 alkenyl.
- composition of any one of embodiments 8-17, wherein the structure of Formula (A) is represented by Formula (A-A): WSGR Docket No.53344-792.601 Formula (A-A) wherein, R 5 is C 1 -C 10 alkyl, C 1 -C 10 alkenyl, or C 1 -C 10 alkynyl.
- Embodiment 19 The composition of any one of embodiments 8-17, wherein the structure of Formula (A) is represented by Formula (A-B): Formula (A-B) wherein, R 5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl.
- Embodiment 20 Embodiment 20.
- composition of any one of embodiments 8-17, wherein the structure of Formula (A) is Formula Formula (A-C) wherein, R 5 is each independently C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl.
- R 5 is each independently C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl.
- the composition of embodiment 17, wherein the structure of Formula (A- C) is: .
- Embodiment 22 The composition of any one of embodiments 8-13, wherein the structure of Formula (A) is represented by Formula (A-D): Formula (A-D) Embodiment 23.
- Embodiment 25 The composition of any one of embodiments 18-20, wherein R 5 is C 1 -C 10 alkenyl.
- Embodiment 26 The composition of embodiment 8 or 9, wherein R is hydrogen.
- Embodiment 27 The composition of embodiment 26, wherein the structure of Formula (A) .
- Embodiment 28 The composition of any one of embodiments 8-10, wherein R 1 and R 2 are taken together to form C 2 heterocycloalkyl.
- Embodiment 29 The composition of any one of embodiments 9-28, wherein m is an integer of 1.
- Embodiment 30 The composition of any one of embodiments 9-28, wherein m is an integer of 1.
- Embodiment 34 The composition of embodiment 33, wherein R 6 is (CH2)pOR 7 .
- Embodiment 35 The composition of embodiment 33, wherein R 6 is (CH2)pOR 7 .
- composition of any one of embodiments 33-40, wherein the structure of Formula (D) is: WSGR Docket No.53344-792.601 .
- Embodiment 42. The composition of any one of embodiments 33-41, wherein the copolymer comprises the structure: .
- Embodiment 43. The composition of any one of the preceding embodiments, wherein the first macromolecule structure comprises a surface.
- Embodiment 44. The composition of any one of the preceding embodiments, wherein the second macromolecule structure comprises a surface.
- the composition of embodiment 43 or 44, wherein the surface comprises a particle.
- Embodiment 46. The composition of embodiment 45, wherein the particle is a nanoparticle.
- composition of embodiment 45 wherein the particle is a microparticle.
- Embodiment 48 The composition of any one of embodiments 45-47, wherein the particle comprises a diameter of from about 100 nm to about 750 nm.
- Embodiment 49 The composition of any one of embodiments 45-48, wherein the particle comprises a diameter of from about 100 nm to about 500 nm.
- Embodiment 50 The composition of any one of embodiments 45-49, wherein the particle comprises a polydispersity index (PDI) of from about 0.01 to about 0.2.
- Embodiment 51 The composition of any one of embodiments 45-50, wherein the particle comprises a PDI of from about 0.1 to about 0.2.
- Embodiment 52 The composition of any one of embodiments 45-50, wherein the particle comprises a PDI of from about 0.1 to about 0.2.
- the composition of any one of embodiments 45-52, wherein the particle comprises is a superparamagnetic iron oxide nanoparticle.
- Embodiment 58. The composition of any one of embodiments 45-57, wherein the polymer is non-covalently coupled to the surface.
- Embodiment 59. The composition of any one of embodiments 45-58, wherein the polymer or copolymer is covalently coupled to the surface via a linker.
- the composition of any one of embodiments 45-59, wherein the first macromolecule structure comprises the structure: wherein, the surface; L is a linker; and A is the copolymer of any one of embodiments 33-42.
- composition of embodiment 64, wherein the stabilizing agent comprises a metal salt.
- Embodiment 66 The composition of embodiment 65, wherein the metal salt comprises aluminum chloride.
- Embodiment 67 The composition of any one of embodiments 9-66, wherein the copolymer is a random copolymer.
- Embodiment 68 The composition of any one of embodiments 9-66, wherein the copolymer is a block copolymer.
- Embodiment 69. The composition of any one of embodiments 8-68, wherein the composition comprises at least 1 wt% of the polymer or copolymer.
- Embodiment 70 The composition of embodiment 64, wherein the stabilizing agent comprises a metal salt.
- Embodiment 66 The composition of embodiment 65, wherein the metal salt comprises aluminum chloride.
- Embodiment 67 The composition of any one of embodiments 9-66, wherein the copolymer is a random copolymer.
- Embodiment 68 The composition of any one
- Embodiment 71. The composition of any one of embodiments 8-70, wherein the polymer or copolymer comprises a molecular weight of from about 0.5 kDa to about 25 kDa.
- Embodiment 72. The composition of any one of embodiments 8-71, wherein the polymer or copolymer comprises a molecular weight of from about 0.5 kDa to about 10 kDa.
- Embodiment 73 Embodiment 73.
- a method of isolating one or more biomolecules from a biological sample comprising: (a) contacting the biological sample comprising one or more biomolecules with a composition of any one of embodiments 1-72 to bind the one or more biomolecules to the at least two macromolecule structures, thereby forming at least two biomolecule corona; and (b) eluting the one or more biomolecules from the at least two macromolecule structures, thereby providing one or more isolated biomolecules, wherein, the at least two macromolecule structures comprise: (i) a first macromolecule structure comprising a neutral to negative surface charge; and WSGR Docket No.53344-792.601 (ii) a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure.
- Embodiment 74 The method of embodiment 73, wherein the method further comprises separating the one or more biomolecules and the at least two macromolecule structures from the biological sample.
- Embodiment 75 The method of embodiment 73 or 74, wherein the method further comprises optionally digesting the one or more biomolecules.
- Embodiment 76 The method of embodiment 73, wherein the method further comprises optionally digesting the one or more biomolecules.
- a method of isolating one or more biomolecules from a biological sample comprising: (a) contacting a population of biomolecules comprising one or more biomolecules with a composition of any one of embodiments 1-72, thereby forming at least two biomolecule corona; (b) separating and optionally digesting the one or more biomolecules and the at least two macromolecule structures from the biological sample; and (c) eluting and optionally digesting the one or more biomolecules from the at least two macromolecule structures, thereby providing one or more isolated biomolecules, wherein, the at least two macromolecule structures comprise: (i) a first macromolecule structure comprising a neutral to negative surface charge; and (ii) a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure.
- Embodiment 77 The method of any one of embodiments 73-76, wherein the first macromolecule structure comprises a surface charge of from about 0 mV to about -15 mV.
- Embodiment 78 The method of any one of embodiments 73-77, wherein the second macromolecule structure comprises a surface charge of from about -35 mV to about -60 mV.
- Embodiment 79 The method of any one of embodiments 73-78, wherein the surface charge is characterized by a zeta potential.
- Embodiment 80 The method of any one of embodiments 73-79, wherein the first macromolecule structure comprises the composition of any one of embodiments 33-72.
- the method of any one of embodiments 73-80, wherein the second macromolecule structure comprises the composition of any one of embodiments 5-32 or 43- 72.
- Embodiment 82. The method of any one of embodiments 73-81, wherein the one or more biomolecules comprises proteins, peptides, or a combination thereof.
- Embodiment 83. The method of any one of embodiments 73-82, wherein the biological sample comprises plasma, serum, or blood.
- the method of any one of embodiments 73-82, wherein the biological sample comprises biofluid.
- Embodiment 85. The method of embodiment 84, wherein the biofluid is a cell-free biofluid.
- kits for isolating one or more biomolecules from a biological sample comprising: at least two macromolecule structures; (i) a first macromolecule structure with a neutral to negative surface charge; and (ii) a second macromolecule structure with a greater negative surface charge than the first macromolecule structure; Embodiment 128.
- the kit further comprises a washing agent configured to wash the one or more biomolecules bound to the at least two macromolecule structures.
- the kit further comprises an elution agent configured to elute the one or more biomolecules from the at least two macromolecule structures.
- Embodiment 130 The kit of embodiment 127, wherein the kit further comprises a denaturing agent.
- a method of preparing a mixture of at least two macromolecule structures, the at least two macromolecule structures comprising recurring units of a first monomer and a second monomer or a first monomer and a third monomer comprising: (a) obtaining a first macromolecule structure comprising a neutral to negative surface charge; (b) obtaining a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure; and (c) forming a mixture comprising the first and second macromolecule structures.
- Embodiment 139 The method of embodiment 138, wherein the first macromolecule structure comprises a surface charge of about 0 mV to about -15 mV.
- Embodiment 140 Embodiment 140.
- the method of embodiment 138 or 139, wherein the second macromolecule structure comprises a surface charge of about -35 mV to about -60 mV.
- Embodiment 141. The method of any one of embodiments 138-140, wherein the surface charge is characterized by a zeta potential.
- Embodiment 142. The method of any one of embodiments 138-141, wherein the first macromolecule structure comprises the composition of any one of embodiments 33-72.
- the method of any one of embodiments 138-142, wherein the second macromolecule structure comprises the composition of any one of embodiments 8-32 or 43- 72.
- a method of preparing a macromolecule structure comprising recurring units of a first component and a second component, the method comprising: (a) providing a mixture of monomers in a solvent comprising a first monomer and a second monomer, wherein the first monomer comprises: wherein q is an integer from 1 to 6; and the second monomer comprises: wherein m is an integer from 1 to 6; (b) contacting a surface and the mixture of monomers, thereby producing a reaction mixture; (c) polymerizing the mixture of monomers to produce a macromolecule immobilized to the surface; (d) contacting the macromolecule immobilized to the surface and an amine, thereby producing an aminated macromolecule; and (e) optionally, contacting the aminated macromolecule with an anhydride optionally substituted with R 2 , wherein R 2 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl.
- Embodiment 145 The method of embodiment 144, wherein the surface comprises a particle.
- Embodiment 146. The method of embodiment 145, wherein the particle is a nanoparticle.
- Embodiment 147. The method of embodiment 145, wherein the particle is a microparticle.
- Embodiment 148. The method of any one of embodiments 145-147, wherein the particle comprises a diameter of from about 100 nm to about 750 nm.
- Embodiment 149 The method of any one of embodiments 145-148, wherein the particle comprises a diameter of from about 100 nm to about 500 nm.
- PDI polydispersity index
- WSGR Docket No.53344-792.601 Embodiment 151.
- the method of any one of embodiments 145-151, wherein the particle comprises iron oxide.
- the method of any one of embodiments 145-152, wherein the particle comprises is a superparamagnetic iron oxide nanoparticle.
- Embodiment 155 The method of any one of embodiments 145-154, wherein the particle comprises an iron oxide core and a silica shell.
- Embodiment 156 The method of any one of embodiments 145-154, wherein the particle comprises iron oxide crystals embedded in a polystyrene core.
- Embodiment 157 The method of any one of embodiments 144-155, wherein (b) comprises contacting in an organic solvent.
- Embodiment 158 The method of any one of embodiments 144-156, wherein (d) comprises contacting in an organic solvent.
- Embodiment 159 The method of any one of embodiments 144-156, wherein (d) comprises contacting in an organic solvent.
- Embodiment 162 wherein the heating comprises heating to a temperature of at least 50°C, 60°C, 70°C, 80°C, or at least 90°C.
- Embodiment 164 The method of any one of embodiments 144-163, wherein the polymerization comprises free radical polymerization, atom transfer radical polymerization (ATRP), emulsion polymerization, or precipitation polymerization.
- Embodiment 165 The method of any one of embodiments 144-164, wherein the macromolecule structure comprises a composition of any one of embodiments 1-42. WSGR Docket No.53344-792.601 Embodiment 166.
- Embodiment 167 Use of a macromolecule structure comprising 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units for binding proteins in a biological sample.
- Embodiment 167 Use of a macromolecule structure comprising the structure of Formula (A-D) and the structure of Formula (A-A) as recurring units for binding proteins in a biological sample.
- Embodiment 168. Use of a macromolecule structure comprising the structure of Formula (A-C) and the structure of Formula (A-B) as recurring units for binding proteins in a biological sample.
- Embodiment 169 Use of the composition of any one of embodiment 1-72 for binding proteins in a biological sample.
- Embodiment 170 Use of the composition of any one of embodiment 1-72 for binding proteins in a biological sample.
- a composition comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units.
- Embodiment 171. A composition comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises ethylene glycol dimethacrylate, monomer 6, and at least one of: monomer 7, monomer 8, monomer 9, and glycidyl methacrylate.
- Embodiment 172 Embodiment 172.
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Abstract
Provided herein are compositions, methods, systems, and kits for isolating one or more biomolecules from a biological solution. In some instances, the compositions, methods, systems, and kits provided herein may comprise one, two or more particles (e.g., comprising macromolecule structures) of differing surface charge. In some embodiments, the particles (e.g., comprising macromolecule structures) comprise a first particle (e.g., comprising a macromolecule structure) with a neutral to negative surface charge, and a second particle (e.g., comprising a macromolecule structure) with a greater negative surface charge than that of the first particle (e.g., comprising a macromolecule structure). In some instances, the combinations of particles provided herein provide for a synergistic relationship, enhancing the number of biomolecules that may be isolated, purified, identified, or the like from a biological solution.
Description
WSGR Docket No.53344-792.601 BIOMOLECULE PREPARATION METHODS, KITS, AND SYSTEMS CROSS-REFERENCE [0001] This application claims benefit of priority to U.S. Provisional Application No. 63/574,179, filed April 3, 2024, which is incorporated herein by reference in its entirety. BACKGROUND [0002] Analysis of biomolecules in complex biological solutions often requires removal of incompatible impurities and undesired biomolecules when using sensitive methods, such as mass spectrometry. Typically, the isolation of biomolecules from complex biological solutions relies on laborious fine tuning of analytical parameters. There is a need for widely applicable and highly efficient methods to remove the undesired components of biological solutions in preparation for further analysis, not relying on usual methodologies including reverse-phase or ion chromatography or suspension trapping. INCORPORATION BY REFERENCE [0003] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. SUMMARY [0004] Provided herein are methods, kits, and systems for preparing and use of particles for proteomics. In some instances, the methods, kits, and systems provided herein rely on the use of a combination of at least two particles (e.g., comprising macromolecule structures) comprising different surface charges for the isolation, purification, and identification of biomolecules (e.g., proteins or peptides). The first macromolecule structure may have a neutral to negative surface charge, such as measured by zeta potential. Meanwhile, the second macromolecule structure may have a highly negative or more negative surface charge compared to that of the first macromolecule structure. The combination of this first and second macromolecule structure in some instances provides a synergistic relationship that allows for increased ability to isolate, purify, and identify biomolecules, such as proteins in comparison to the use of each of the particles (e.g., comprising the macromolecule structures) on their own. Increases in ability to isolate and identify biomolecules present advantages over generally used methods such as various forms of chromatography or suspension trapping, since the methods provided herein are widely applicable and lead to high yields of desired biomolecules, high reproducibility in the identification of biomolecules, and significant number of identifiable biomolecules.
WSGR Docket No.53344-792.601 [0005] Further, in some instances, the methods, kits, and systems provided herein provide for the preparation of biomolecules for further identification or analysis. Typically, analysis of biomolecules by sensitive methods, such as mass spectrometry, require the removal of incompatible components, such as acids, bases, surfactants, chaotropes, buffering agents, and the like. The present methods may provide a versatile pathway to preparing samples for such identification or analysis. [0006] Provided herein, in some embodiments, is a composition comprising two or more particles comprising: (a) a first particle comprising a first macromolecule structure, the first particle comprising a neutral to negative surface charge; and (b) a second particle comprising a second macromolecule structure, the second particle comprising a greater negative surface charge than the first particle. In some embodiments, the first particle has a surface charge of greater than -20 mV. In some embodiments, the first particle has a surface charge of about 0 mV to about -15 mV. In some embodiments, the second particle has a surface charge of less than -20 mV. In some embodiments, the second particle has a surface charge of about -35 mV to about -60 mV. In some embodiments, the surface charge is characterized by a zeta potential. In some embodiments, the ratio of the first particle to the second particle is 10:1 to 1:10. In some embodiments, the ratio of the first particle to the second particle is 5:1 to 1:5. In some embodiments, the ratio of the first particle to the second particle is 1:1 to 1:5. In some embodiments, the ratio of the first particle to the second particle is about 1:4. In some embodiments, the second macromolecule structure comprises a polymer comprising one or more units represented by Formula (A):
Formula (A) wherein, R is hydrogen
R1 is hydrogen or hydroxyl; q is an integer from 1 to 6; R2 is C1-C8 diamine, N-substituted with one or more R3;
WSGR Docket No.53344-792.601 R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; or R1 and R2 are taken together to form C2-C6 heterocycloalkyl; and R4 is hydrogen or C1-C6 alkyl. In some embodiments, the second macromolecule structure comprises a copolymer comprising two or more units represented by Formula (A) and Formula (B):
wherein, R is hydrogen
R1 is hydrogen or hydroxyl; q is an integer from 1 to 6; m is an integer from 1 to 6; R2 is C1-C8 diamine, N-substituted with one or more R3; R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; or R1 and R2 are taken together to form C2-C6 heterocycloalkyl; R4 is each independently hydrogen or C1-C6 alkyl;
is a single bond or a double bond; and * is an attachment point to another unit of Formula (A) or Formula (B) when is a single bond.
[0007] In some embodiments, R is . In some embodiments, R1 is hydroxyl. In some embodiments, R2 is a C2 diamine, N-substituted with one or more R3. In some embodiments, R2
wherein p is an integer from 1 to 6. In some embodiments, the second macromolecule structure comprises a polymer comprising one or more units represented by Formula (C):
WSGR Docket No.53344-792.601
Formula (C) wherein, R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; q is an integer from 1 to 6; and p is an integer from 1 to 6. In some embodiments, p is an integer of 1. In some embodiments, at least one R3 is C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl. In some embodiments, at least one R3 is C1-C8 alkyl substituted with at least one of oxo, hydroxyl, and C1-C8 alkenyl. In some embodiments, the structure of Formula (A) is represented by Formula (A-A):
Formula (A-A) wherein, R5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, the structure of Formula (A) is represented by Formula (A-B):
Formula (A-B) wherein,
WSGR Docket No.53344-792.601 R5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, the structure of Formula (A) is Formula (A-C):
Formula (A-C) wherein, R5 is each independently C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, the structure of Formula (A-C) is:
. In some embodiments, the structure of Formula (A) is represented by Formula (A-D):
Formula (A-D) In some embodiments, q is an integer from 1 to 3. In some embodiments, q is an integer of 1. In some embodiments, R5 is C1-C10 alkenyl. In some embodiments, R is hydrogen. In some embodiments, the structure of Formula (A) is:
. In some embodiments, R1 and R2 are taken together to form C2 heterocycloalkyl. In some embodiments, m is an integer of 1. In some embodiments, R4 is C1-C6 alkyl. In some embodiments, the structure of Formula (B) is:
WSGR Docket No.53344-792.601
. In some embodiments, the copolymer comprises the structure:
. In some embodiments, the first macromolecule structure comprises a copolymer comprising two or more units represented by Formula (D) and Formula (E):
wherein, R4 is each independently hydrogen or C1-C6 alkyl; R6 is hydrogen or (CH2)pOR7; R7 is hydrogen or C1-C6 alkyl; m is an integer from 1 to 6; p is an integer from 1 to 6;
is a single bond or a double bond; and * is an attachment point to another unit of Formula (D) or Formula (E) when is a single bond. In some embodiments, R6 is (CH2)pOR7. In some embodiments, the structure of Formula (E) is represented by Formula (E-A):
WSGR Docket No.53344-792.601
Formula (E-A) In some embodiments, p is an integer of 2. In some embodiments, R7 is H. In some embodiments, R4 is C1-C6 alkyl. In some embodiments, m is an integer of 1. In some embodiments, the structure of Formula (E) is:
. In some embodiments, R6 is hydrogen. In some embodiments, R4 is C1-C6 alkyl. In some embodiments, the structure of Formula (E) is:
. In some embodiments, the structure of Formula (D) is:
. In some embodiments, the copolymer comprises the structure:
. In some embodiments, the first macromolecule structure comprises a copolymer comprising three or more units represented by:
WSGR Docket No.53344-792.601
In some embodiments, the unit represented by
is present in the first macromolecule structure in an amount of less than 5 wt%. In some embodiments, the two or more particles are nanoparticles. In some embodiments, the two or more particles are microparticles. In some embodiments, the two or more particles each individually have a diameter of from about 100 nm to about 750 nm. In some embodiments, the two or more particles each individually have a diameter of from about 100 nm to about 500 nm. In some embodiments, the two or more particles each individually have a polydispersity index (PDI) of from about 0.01 to about 0.2. In some embodiments, the two or more particles each individually have a PDI of from about 0.1 to about 0.2. In some embodiments, the two or more particles comprises iron oxide. In some embodiments, the two or more particles comprises a superparamagnetic iron oxide nanoparticle. In some embodiments, the two or more particles comprises a core-shell structure. In some embodiments, the core of the core-shell structure is paramagnetic. In some embodiments, the two or more particles comprise an iron oxide core and a silica shell. In some embodiments, the particle comprises iron oxide crystals embedded in a polystyrene core. In some embodiments, the polymer or the copolymer is covalently coupled to a surface of the particle. In some embodiments, the polymer is non-covalently coupled to a surface of the particle. In some embodiments, the polymer or copolymer is covalently coupled to a surface of the particle via a linker. In some embodiments, the first particle comprises the structure: wherein,
is a surface of the first particle; L is a linker; and A is a copolymer described herein. In some embodiments, the second particle comprises the structure:
WSGR Docket No.53344-792.601
wherein,
is a surface of the second particle; L is a linker; and B is the polymer or copolymer described herein. In some embodiments, the linker comprises an alkylene, esteralkylene, or aralkylene. In some embodiments, the polymer or copolymer is covalently coupled to the surface via a base polymer. In some embodiments, the composition further comprises a stabilizing agent. In some embodiments, the stabilizing agent comprises a metal salt. In some embodiments, the metal salt comprises aluminum chloride. In some embodiments, the copolymer is a random copolymer. In some embodiments, the copolymer is a block copolymer. In some embodiments, the composition comprises at least 1 wt% of the polymer or copolymer. In some embodiments, the composition comprises from about 1 wt% to about 30 wt% of the polymer or copolymer. In some embodiments, the polymer or copolymer comprises a molecular weight of from about 0.5 kDa to about 25 kDa. In some embodiments, the polymer or copolymer comprises a molecular weight of from about 0.5 kDa to about 10 kDa. [0008] In some embodiments, provided herein is a method of isolating one or more biomolecules from a biological sample, the method comprising: (a) contacting the biological sample comprising one or more biomolecules with a composition provided herein to bind the one or more biomolecules to the at least two particles, thereby forming at least two biomolecule corona; and (b) eluting the one or more biomolecules from the at least two particles, thereby providing one or more isolated biomolecules. [0009] In some embodiments, provided herein is a method of assaying a biological sample, the method comprising: (a) contacting the biological sample with a composition provided herein to form at least two biomolecule corona; (b) assaying the at least two biomolecule corona to detect one or more biomolecules in the biological sample,
WSGR Docket No.53344-792.601 wherein the assaying detects at least 5% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle; or wherein the assaying detects at least 50% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. In some embodiments, assaying detects at least 10% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, assaying detects at least 60% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. In some embodiments, the method further comprises separating the one or more biomolecules and the at least two particles from the biological sample. In some embodiments, the method further comprises optionally digesting, alkylating, and/or lysing the one or more biomolecules to provide one or more digested biomolecules. In some embodiments, the one or more biomolecules comprises proteins, peptides, or a combination thereof. In some embodiments, the biological sample comprises plasma, serum, or blood. In some embodiments, the biological sample comprises biofluid. In some embodiments, the biofluid is a cell-free biofluid. In some embodiments, the method further comprises diluting the one or more biomolecules and at least two particles. In some embodiments, the one or more biomolecules and at least two particles are diluted in a buffer. In some embodiments, the methods further comprise eluting the one or more biomolecules from the two or more particles. In some embodiments, eluting is in the presence of buffer or an aqueous solution. In some embodiments, the contacting is in the presence of a buffer. In some embodiments, the buffer comprise a pH of from about 7 to about 8 (e.g., pH of about 8.5). In some embodiments, the buffer comprises a pH of from about 7.4 to 7.6 (e.g., pH of about 7.5). In some embodiments, the buffer comprises HEPES. In some embodiments, one of the first particle or second particle is contacted with the one or more biomolecules at a concentration of 0.1 mg/mL to 0.2 mg/mL. In some embodiments, one of the first particle or second particle is contacted with the one or more biomolecules at a concentration of 0.5 mg/mL to 0.6 mg/mL. In some embodiments, the first particle and second particle are contacted with the one or more biomolecules at a concentration of 0.6 mg/mL to 0.8 mg/mL. In some embodiments, the method further comprises contacting the one or more biomolecules with the at least two particles in the presence of an organic solvent. In some embodiments, the method comprises purifying the one or more digested biomolecules. In some embodiments, purifying the one or more digested biomolecules comprises contacting the one or more digested biomolecules with a third particle in an organic solvent to form a biomolecule
WSGR Docket No.53344-792.601 corona. In some embodiments, the organic solvent comprises an alcohol, acetonitrile, dichloromethane, dimethylformamide (DMF), dimethylsulfoxide (DMSO), ethyl acetate, hexamethylphosphoramide (HMPA), or tetrahydrofuran. In some embodiments, the organic solvent comprises acetonitrile. In some embodiments, the method comprises eluting the one or more digested biomolecules from the third particle. In some embodiments, eluting comprises contacting the one or more digested biomolecules and third particle with an aqueous solution. In some embodiments, eluting comprises contacting the one or more biomolecules and two or more particles with an aqueous solution. In some embodiments, the aqueous solution comprises an organic solvent. In some embodiments, the aqueous solution comprises an organic solvent in an amount of no more than 50 wt% (e.g., 40 wt%, 30 wt%, 20 wt%, 10 wt%, or no more than 5 wt%). In some embodiments, the aqueous solution comprises an organic solvent in an amount of no more than 50 wt% (e.g., 40 wt%, 30 wt%, 20 wt%, 10 wt%, or no more than 5 wt%). In some embodiments, the method is capable of isolating from about 100 to about 20,000 biomolecules. In some embodiments, the method is capable of isolating at least 1,000 biomolecules. In some embodiments, each of the 1,000 biomolecules comprise a different structure. In some embodiments, an amount of an acid or a base in a composition comprising the population of biomolecules is greater than the amount of the acid or the base in a composition comprising the one or more isolated biomolecules. In some embodiments, an amount of a surfactant(s) in a composition comprising the population of biomolecules is greater than the amount of the surfactant(s) in a composition comprising the one or more isolated biomolecules. In some embodiments, the method further comprises washing the one or more biomolecules and at least two particles with a wash solution. In some embodiments, the wash solution comprises an organic solvent. In some embodiments, the method further comprises identifying the one or more biomolecules. In some embodiments, the method further comprises assaying the one or more digested biomolecules to identify the one or more biomolecules. In some embodiments, the assaying or identifying comprises performing mass spectrometry (MS), liquid chromatography- mass spectrometry (LC-MS), protein sequencing, or a combination thereof. In some embodiments, the method is capable of assaying or identifying from about 1 to about 20,000 biomolecules. In some embodiments, when repeated, the assaying yields a percent quantile normalized coefficient (QNCV) of variation of 30% or less. In some embodiments, when repeated, the assaying yields a percent quantile normalized coefficient (QNCV) of variation of 20% or less. In some embodiments, the method is capable of identifying from about 100 to about 10,000 biomolecules. In some embodiments, the method is capable of identifying at least 100 biomolecules. In some embodiments, the method is capable of identifying at least 2500 biomolecules. In some embodiments, the method is capable of identifying at least 3500 biomolecules. In some
WSGR Docket No.53344-792.601 embodiments, the method is capable of identifying biomolecules over a dynamic range of at least 7, at least 8, at least 9, or at least 10. In some embodiments, the digesting comprises contacting the one or more biomolecules with trypsin, lysin, serine protease, or any combination thereof. In some embodiments, the digesting comprises contacting the one or more biomolecules with a denaturing agent, a reduction agent, an alkylating agent, or any combination thereof. In some embodiments, the denaturing agent comprises sodium dodecyl sulfate, acetic acid, trichloroacetic acid, sulfosalicylic acid, sodium bicarbonate, ethanol, formaldehyde, glutaraldehyde, urea, guanidium chloride, lithium perchlorate, 2-mercaptoethanol, dithiothreitol, tris(2- carboxyethyl)phosphine (TCEP), or any combination thereof. In some embodiments, the reduction agent comprises TCEP, dithiothreitol, beta-mercaptoethanol, glutathione, cysteine, or any combination thereof. In some embodiments, the alkylating agent comprises iodoacetamide, iodoacetic acid, acrylamide, chloroacetamide, or any combination thereof. [0010] In some embodiments, provided herein is a system for isolating one or more biomolecules from a biological sample, the system comprising: (a) a composition provided herein; (b) a suspension solution configured to suspend the at least two particles; (c) a biological sample comprising one or more biomolecules; and (d) an automated system comprising a network of units with differentiated functions configured to isolate one or more biomolecules from the biological sample using the at least two particles. In some embodiments, the network of units comprises: (a) a first unit comprising a multichannel fluid transfer instrument for transferring fluids between units within the system; (b) a second unit comprising a support for storing a plurality of biological samples; and (c) a third unit comprising a support for an array plate possessing partitions that comprise the two or more particles for binding of the one or more biomolecules with the two or more particles. In some embodiments, the network of units further comprises a fourth unit comprising supports for storing a plurality of reagents. In some embodiments, the network of units further comprises a fifth unit comprising supports for storing a reagent to be disposed of. In some embodiments, the network of units further comprises supports for storing consumables used by a multichannel fluid transfer instrument. In some embodiments, the automated system is configured to perform a method provided herein. [0011] In some embodiments, provided herein is a kit for isolating one or more biomolecules from a biological sample, the kit comprising a composition provided herein. In some
WSGR Docket No.53344-792.601 embodiments, provided herein is a kit for preparing one or more biomolecules from a biological sample for assaying by mass spectrometry, the kit comprising a composition provided herein. In some embodiments, comprises a washing agent configured to wash the one or more biomolecules bound to the at least two particles. In some embodiments, the kit comprises an elution agent configured to elute the one or more biomolecules from the at least two particles. In some embodiments, the kit comprises a denaturing agent. In some embodiments, the kit comprises a reducing agent. In some embodiments, the kit further comprises an alkylation agent. In some embodiments, the kit further comprises at least one buffer. In some embodiments, the at least one buffer comprises a digestion buffer, resuspension buffer, denaturation buffer, digestion buffer, or a lysis buffer. In some embodiments, the kit further comprises one or more organic solvents. In some embodiments, the buffer comprises HEPES. In some embodiments, one or more components of the kit are prepackaged into one or more containers. [0012] In some embodiments, provided herein is a method of preparing a mixture of at least two particles, the at least two particles comprising recurring units of a first monomer and a second monomer or a first monomer and a third monomer, the method comprising: (a) obtaining a first particle comprising a neutral to negative surface charge; (b) obtaining a second particle comprising a greater negative surface charge than the first particles; and (c) forming a mixture comprising the first and second particles. In some embodiments, the first particle comprises a surface charge of about 0 mV to about -15 mV. In some embodiments, the second particle comprises a surface charge of about -35 mV to about -60 mV. In some embodiments, the surface charge is characterized by a zeta potential. In some embodiments, the first particle is a first particle described herein. In some embodiments, the second particle is a second particle described herein. [0013] In some embodiments, provided herein is a method of preparing a macromolecule structure comprising recurring units of a first component and a second component, the method comprising: (a) providing a mixture of monomers in a solvent comprising a first monomer and a second monomer, wherein the first monomer comprises:
wherein q is an integer from 1 to 6; and
WSGR Docket No.53344-792.601 the second monomer comprises:
wherein m is an integer from 1 to 6; (b) contacting a surface and the mixture of monomers, thereby producing a reaction mixture; (c) polymerizing the mixture of monomers to produce a macromolecule immobilized to the surface of a particle; (d) contacting the macromolecule immobilized to the surface and an amine, thereby producing an aminated macromolecule; and (e) optionally, contacting the aminated macromolecule with an anhydride optionally substituted with R2, wherein R2 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, the particle is a nanoparticle. In some embodiments, In some embodiments, the particle is a microparticle. In some embodiments, the particle has a diameter of from about 100 nm to about 750 nm. In some embodiments, the particle has a diameter of from about 100 nm to about 500 nm. In some embodiments, the particle has a polydispersity index (PDI) of about 0.01 to about 0.2. In some embodiments, the particle has a PDI of about 0.1 to about 0.2. In some embodiments, the particle comprises iron oxide. In some embodiments, the particle comprises is a superparamagnetic iron oxide nanoparticle. In some embodiments, the particle comprises a core- shell structure. In some embodiments, the particle comprises an iron oxide core and a silica shell. In some embodiments, the particle comprises iron oxide crystals embedded in a polystyrene core. In some embodiments, (b) comprises contacting in an organic solvent. In some embodiments, (d) comprises contacting in an organic solvent. In some embodiments, the organic solvent comprises an alcohol, acetonitrile, dichloromethane, dimethylformamide (DMF), dimethylsulfoxide (DMSO), ethylacetate, hexamethylphosphoramide (HMPA), or tetrahydrofuran. In some embodiments, the organic solvent comprises acetonitrile. In some embodiments, the organic solvent comprises DMF. In some embodiments, the method further comprises heating. In some embodiments, the heating comprises heating to a temperature of at least 50°C, 60°C, 70°C, 80°C, or at least 90°C. In some embodiments, the polymerization comprises free radical polymerization, atom transfer radical polymerization (ATRP), emulsion polymerization, or precipitation polymerization. In some embodiments, the macromolecule structure comprises a composition described herein.
WSGR Docket No.53344-792.601 [0014] In some embodiments, provided herein is a use a macromolecule structure comprising 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units for binding proteins in a biological sample. [0015] In some embodiments, provided herein is a use of a particle comprising a macromolecule structure comprising the structure of Formula (A-D) and the structure of Formula (A-A) as recurring units for binding proteins in a biological sample. [0016] In some embodiments, provided herein is a use of a particle comprising a macromolecule structure comprising the structure of Formula (A-C) and the structure of Formula (A-B) as recurring units for binding proteins in a biological sample. [0017] In some embodiments, provided herein is a use of a composition provided herein for binding proteins in a biological sample. [0018] Provided herein, in some embodiments, is a composition comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units. [0019] Provided herein, in some embodiments, is a composition comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises ethylene glycol dimethacrylate, monomer 6, and at least one of: monomer 7, monomer 8, monomer 9, and glycidyl methacrylate. [0020] Provided herein, in some embodiments, is a composition obtained by a method comprising polymerizing 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles. [0021] Provided herein, in some embodiments, is a composition obtained by a method comprising: (i) polymerizing glycidyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles to form polymer- coated particles; (ii) reacting the polymer-coated magnetic particles with an alkylene diamine to form amine-modified magnetic particles; and (iii) reacting the amine-modified magnetic particles with an optionally substituted succinic acid anhydride. [0022] Provided herein, in some embodiments, is a method comprising: (a) contacting a plasma or serum sample comprising one or more proteins with a composition provided herein, thereby adsorbing at least a portion of the proteins to the magnetic particles; (b) separating the adsorbed proteins and the magnetic particles from the plasma or serum;
WSGR Docket No.53344-792.601 (c) eluting and optionally digesting the adsorbed proteins from the magnetic particles, thereby providing one or more isolated proteins; (d) optionally purifying the isolated proteins using solid phase extraction; and (e) analyzing the isolated proteins using mass spectrometry. [0023] Provided herein, in some embodiments, is a method of making polymer-coated magnetic particles, the method comprising polymerizing 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles. [0024] Provided herein, in some embodiments, is a method of making polymer-coated magnetic particles, the method comprising: (i) polymerizing glycidyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles to form polymer-coated particles; (ii) reacting the polymer-coated magnetic particles with an alkylene diamine to form amine-modified magnetic particles; and (iii) reacting the amine- modified magnetic particles with an optionally substituted succinic acid anhydride. BRIEF DESCRIPTION OF THE DRAWINGS [0025] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings (also “Figure” and “FIG.” herein), of which: [0026] FIG. 1 shows an exemplary preparation scheme for particle (e.g., comprising a macromolecule structure) (A2). [0027] FIG. 2 shows an exemplary preparation scheme for particle (e.g., comprising a macromolecule structure)(A3). [0028] FIG.3 shows protein group (PG) counts for particles (e.g., comprising macromolecule structures) (A1), (A2), and (A1)/(A2) multiplexed in various plasmas. [0029] FIG.4 shows PG counts for particles (e.g., comprising macromolecule structures) (A3), (A4), (A5), and (A6) in 1M Tris (pH 9.5) along with PG counts for multiplexed particles (e.g., comprising macromolecule structures) (A3)&(A4), (A3)&(A5), and (A3)&(A6). [0030] FIG. 5A shows a scheme for loading of a 96-well plate to perform a method provided herein with 40 samples. FIG.5B shows a scheme for loading a 96-well plate to perform a method provided herein with 80 samples. [0031] FIG.6 shows peptide yield and protein group counts evaluated for varying multiplexed compositions of (A1) and (A2) described herein at various concentrations.
WSGR Docket No.53344-792.601 DETAILED DESCRIPTION Certain Definitions [0032] As used herein and in the appended claims, the singular forms "a," "and," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "an agent" includes a plurality of such agents, and reference to "the cell" includes reference to one or more cells (or to a plurality of cells) and equivalents thereof known to those skilled in the art, and so forth. When ranges are used herein for physical properties, such as molecular weight, or chemical properties, such as chemical formulae, all combinations and subcombinations of ranges and specific embodiments therein are intended to be included. The term "about" when referring to a number or a numerical range means that the number or numerical range referred to is an approximation within experimental variability (or within statistical experimental error), and thus the number or numerical range may vary between 1% and 15% of the stated number or numerical range. The term "comprising" (and related terms such as "comprise" or "comprises" or "having" or "including") is not intended to exclude that in other certain embodiments, for example, an embodiment of any composition of matter, composition, method, or process, or the like, described herein, may "consist of" or "consist essentially of" the described features. [0033] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this disclosure belongs. All patents and publications referred to herein are incorporated by reference. [0034] “Amino” refers to the –NH2 radical. [0035] “Cyano” refers to the CN radical. [0036] “Nitro” refers to the NO2 radical. [0037] “Oxo” refers to the =O radical. [0038] “Hydroxyl” refers to the -OH radical. [0039] "Alkyl" refers to an optionally substituted straight-chain, or optionally substituted branched-chain saturated hydrocarbon mono-radical, and preferably having from one to fifteen carbon atoms (i.e., C1-C15 alkyl). In certain embodiments, an alkyl comprises one to thirteen carbon atoms (i.e., C1-C13 alkyl). In certain embodiments, an alkyl comprises one to eight carbon atoms (i.e., C1-C8 alkyl). In other embodiments, an alkyl comprises one to five carbon atoms (i.e., C1-C5 alkyl). In other embodiments, an alkyl comprises one to four carbon atoms (i.e., C1-C4 alkyl). In other embodiments, an alkyl comprises one to three carbon atoms (i.e., C1-C3 alkyl). In other embodiments, an alkyl comprises one to two carbon atoms (i.e., C1-C2 alkyl). Whenever it appears herein, a numerical range such as “C1-C3 alkyl” means that the alkyl group consists of 1 carbon atom, 2 carbon atoms, or 3 carbon atoms. In other embodiments, an alkyl comprises one carbon atom (i.e., C1 alkyl). In other embodiments, an alkyl comprises five to fifteen carbon atoms
WSGR Docket No.53344-792.601 (i.e., C5-C15 alkyl). In other embodiments, an alkyl comprises five to eight carbon atoms (i.e., C5- C8 alkyl). In other embodiments, an alkyl comprises two to five carbon atoms (i.e., C2-C5 alkyl). In other embodiments, an alkyl comprises three to five carbon atoms (i.e., C3-C5 alkyl). In certain embodiments, the alkyl group is selected from methyl, ethyl, 1propyl (n-propyl), 1-methylethyl (isopropyl), 1-butyl (nbutyl), 1-methylpropyl (sec-butyl), 2-methylpropyl (iso-butyl), 1,1dimethylethyl (tertbutyl), 1pentyl (n-pentyl). In other embodiments, examples include, but are not limited to, methyl, ethyl, n-propyl, isopropyl, 2-methyl-1-propyl, 2-methyl-2-propyl, 2- methyl-1-butyl, 3-methyl-1-butyl, 2-methyl-3-butyl, 2,2-dimethyl-1-propyl, 2-methyl-1-pentyl, 3-methyl-1-pentyl, 4-methyl-1-pentyl, 2-methyl-2-pentyl, 3-methyl-2-pentyl, 4-methyl-2-pentyl, 2,2-dimethyl-1-butyl, 3,3-dimethyl-1-butyl, 2-ethyl-1-butyl, n-butyl, isobutyl, sec-butyl, t-butyl, n-pentyl, isopentyl, neopentyl, tert-amyl, and hexyl, and longer alkyl groups, such as heptyl, octyl, and the like. The alkyl is attached to the rest of the molecule by a single bond. Unless stated otherwise specifically in the specification, an alkyl group is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, sulfone, mercapto, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, the alkyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, -OMe, NH2, -NO2, or -C≡CH. In some embodiments, the alkyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, or -OMe. In some embodiments, the alkyl is optionally substituted with halogen such as F. In some embodiments, the alkyl is unsubstituted. Alkyl groups may be a straight chain or comprise one or more branched chains. [0040] As used herein, C1-Cx (or C1-x) includes C1-C2, C1-C3... C1-Cx. By way of example only, a group designated as “C1-C4” indicates that there are one to four carbon atoms in the moiety, i.e. groups containing 1 carbon atom, 2 carbon atoms, 3 carbon atoms or 4 carbon atoms. Thus, by way of example only, “C1-C4 alkyl” indicates that there are one to four carbon atoms in the alkyl group, i.e., the alkyl group is selected from among methyl, ethyl, propyl, iso-propyl, n-butyl, iso- butyl, sec-butyl, and t-butyl. Also, by way of example, C0-C2 alkylene includes a direct bond, - CH2-, and -CH2CH2- linkages. [0041] "Alkoxy" refers to a radical bonded through an oxygen atom of the formula –O-alkyl, where alkyl is an alkyl chain as defined above. Unless stated otherwise specifically in the specification, an alkoxy group can be optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, an alkoxy is optionally substituted with oxo, halogen, -CN, - CF3, OH, -OMe, NH2, or -NO2. In some embodiments, an alkoxy is optionally substituted with oxo, halogen, -CN, -CF3, OH, or -OMe. In some embodiments, the alkoxy is optionally substituted with halogen. In some embodiments, the alkoxy is unsubstituted.
WSGR Docket No.53344-792.601 [0042] "Alkenyl" refers to an optionally substituted straight or branched hydrocarbon chain radical group containing at least one carbon-carbon double bond, and preferably having from two to twelve carbon atoms (i.e., C2-C12 alkenyl). In certain embodiments, an alkenyl comprises two to eight carbon atoms (i.e., C2-C8 alkenyl). In certain embodiments, an alkenyl comprises four to eight carbon atoms (i.e., C4-C6 alkenyl). In other embodiments, an alkenyl comprises six to eight carbon atoms (i.e., C6-C8 alkenyl). In certain embodiments, an alkenyl comprises at least one double bond at the end of a carbon chain. In other embodiments, an alkenyl comprises at least one double bond in the middle of a carbon chain. The group can be in either the cis or trans configuration about the double bond(s) and should be understood to include both isomers. Examples include, but are not limited to, ethenyl (CH=CH2), 1-propenyl (CH2CH=CH2), isopropenyl [C(CH3)=CH2], butenyl, 1,3-butadienyl, and the like. Whenever it appears herein, a numerical range such as “C2-C6 alkenyl” means that the alkenyl group can consist of 2 carbon atoms, 3 carbon atoms, 4 carbon atoms, 5 carbon atoms, or 6 carbon atoms. Unless stated otherwise specifically in the specification, an alkenyl group is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, an alkenyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, -OMe, NH2, or -NO2. In some embodiments, an alkenyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, or -OMe. In some embodiments, the alkenyl is optionally substituted with halogen. The alkenyl is attached to the rest of the molecule by a single bond, for example, ethenyl (i.e., vinyl), prop1enyl (i.e., allyl), but1enyl, pent1enyl, penta1,4dienyl, and the like. Unless stated otherwise specifically in the specification, an alkenyl group is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, an alkenyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, -OMe, NH2, or -NO2. In some embodiments, an alkenyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, or -OMe. In some embodiments, the alkenyl is optionally substituted with halogen. In some embodiments, the alkenyl is unsubstituted. [0043] "Alkynyl" refers to an optionally substituted straight or branched hydrocarbon chain radical group containing at least one carbon-carbon triple bond, and preferably having from two to twelve carbon atoms (i.e., C2-C12 alkynyl). In certain embodiments, an alkynyl comprises two to eight carbon atoms (i.e., C2-C8 alkynyl). In other embodiments, an alkynyl comprises two to six carbon atoms (i.e., C2-C6 alkynyl). In other embodiments, an alkynyl comprises two to four carbon atoms (i.e., C2-C4 alkynyl). Whenever it appears herein, a numerical range such as “C2-C6 alkynyl” means that the alkynyl group can consist of 2 carbon atoms, 3 carbon atoms, 4 carbon atoms, 5 carbon atoms, or 6 carbon atoms. The alkynyl is attached to the rest of the molecule by
WSGR Docket No.53344-792.601 a single bond, for example, ethynyl, propynyl, butynyl, pentynyl, hexynyl, 2-propynyl, 2-butynyl, 1,3-butadiynyl, and the like. Unless stated otherwise specifically in the specification, an alkynyl group is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, an alkynyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, -OMe, NH2, or -NO2. In some embodiments, an alkynyl is optionally substituted with oxo, halogen, -CN, -CF3, OH, or -OMe. In some embodiments, the alkynyl is optionally substituted with halogen. In some embodiments, the alkynyl is unsubstituted. [0044] "Alkylene" or "alkylene chain" refers to an optionally substituted straight or branched divalent hydrocarbon chain linking the rest of the molecule to a radical group containing no unsaturation, and preferably having from one to twelve carbon atoms, for example, methylene, ethylene, propylene, nbutylene, and the like. The alkylene chain is attached to the rest of the molecule through a single bond and to the radical group through a single bond. The points of attachment of the alkylene chain to the rest of the molecule and to the radical group can be through any two carbons within the chain. In certain embodiments, an alkylene comprises one to ten carbon atoms (i.e., C1-C8 alkylene). In certain embodiments, an alkylene comprises one to eight carbon atoms (i.e., C1-C8 alkylene). In other embodiments, an alkylene comprises one to five carbon atoms (i.e., C1-C5 alkylene). In other embodiments, an alkylene comprises one to four carbon atoms (i.e., C1-C4 alkylene). In other embodiments, an alkylene comprises one to three carbon atoms (i.e., C1-C3 alkylene). In other embodiments, an alkylene comprises one to two carbon atoms (i.e., C1-C2 alkylene). In other embodiments, an alkylene comprises one carbon atom (i.e., C1 alkylene). In other embodiments, an alkylene comprises five to eight carbon atoms (i.e., C5-C8 alkylene). In other embodiments, an alkylene comprises two to five carbon atoms (i.e., C2-C5 alkylene). In other embodiments, an alkylene comprises three to five carbon atoms (i.e., C3-C5 alkylene). Unless stated otherwise specifically in the specification, an alkylene group can be optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, an alkylene is optionally substituted with oxo, halogen, -CN, -CF3, OH, -OMe, NH2, or -NO2. In some embodiments, an alkylene is optionally substituted with oxo, halogen, -CN, -CF3, OH, or - OMe. In some embodiments, the alkylene is optionally substituted with halogen. In some embodiments, the alkylene is -CH2-, -CH2CH2-, or -CH2CH2CH2-. In some embodiments, the alkylene is -CH2-. In some embodiments, the alkylene is -CH2CH2-. In some embodiments, the alkylene is -CH2CH2CH2-. In some embodiments, the alkylene is unsubstituted. [0045] "Aryl" refers to a radical derived from a hydrocarbon ring system comprising at least one aromatic ring. In some embodiments, an aryl comprises hydrogens and 5 to 30 carbon atoms.
WSGR Docket No.53344-792.601 The aryl radical can be a monocyclic, bicyclic, tricyclic, or tetracyclic ring system, which can include fused (when fused with a cycloalkyl or heterocycloalkyl ring, the aryl is bonded through an aromatic ring atom) or bridged ring systems. In some embodiments, the aryl is a 6- to 10- membered aryl. In some embodiments, the aryl is a 6-membered aryl. Aryl radicals include, but are not limited to, aryl radicals derived from the hydrocarbon ring systems of anthrylene, naphthalene, phenanthrylene, anthracene, azulene, benzene, chrysene, fluoranthene, fluorene, indane, indene, naphthalene, phenalene, phenanthrene, pleiadene, pyrene, and triphenylene. In some embodiments, the aryl is phenyl. Unless stated otherwise specifically in the specification, an aryl can be optionally substituted, for example, with halogen, amino, alkylamino, aminoalkyl, nitrile, nitro, hydroxyl, alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, -S(O)2NH-C1-C6alkyl, and the like. In some embodiments, an aryl is optionally substituted with halogen, methyl, ethyl, -CN, -CF3, OH, -OMe, NH2, -NO2, -S(O)2NH2, -S(O)2NHCH3, -S(O)2NHCH2CH3, -S(O)2NHCH(CH3)2, -S(O)2N(CH3)2, or -S(O)2NHC(CH3)3. In some embodiments, an aryl is optionally substituted with halogen, methyl, ethyl, -CN, -CF3, OH, or -OMe. In some embodiments, the aryl is optionally substituted with halogen. In some embodiments, the aryl is substituted with alkyl, alkenyl, alkynyl, haloalkyl, or heteroalkyl, wherein each alkyl, alkenyl, alkynyl, haloalkyl, heteroalkyl is independently unsubstituted, or substituted with halogen, methyl, ethyl, -CN, -CF3, OH, -OMe, NH2, or -NO2. In some embodiments, the aryl is unsubstituted. [0046] "Aralkyl" refers to a radical of the formula Rcaryl where Rc is an alkylene chain as defined above, for example, methylene, ethylene, and the like. [0047] "Aralkenyl" refers to a radical of the formula –Rdaryl where Rd is an alkenylene chain as defined above. "Aralkynyl" refers to a radical of the formula Rearyl, where Re is an alkynylene chain as defined above. [0048] “Carbocycle” refers to a saturated, unsaturated, or aromatic rings in which each atom of the ring is carbon. Carbocycle can include 3- to 10-membered monocyclic rings and 6- to 12- membered bicyclic rings (such as spiro, fused, or bridged rings). Each ring of a bicyclic carbocycle can be selected from saturated, unsaturated, and aromatic rings. An aromatic ring, e.g., phenyl, can be fused to a saturated or unsaturated ring, e.g., cyclohexane, cyclopentane, or cyclohexene. Any combination of saturated, unsaturated and aromatic bicyclic rings, as valence permits, are included in the definition of carbocyclic. In an exemplary embodiment, an aromatic ring, e.g., phenyl, can be fused to a saturated or unsaturated ring, e.g., cyclohexane, cyclopentane, or cyclohexene. A bicyclic carbocycle includes any combination of saturated, unsaturated and aromatic bicyclic rings, as valence permits. A bicyclic carbocycle includes any combination of ring sizes such as 4-5 fused ring systems, 5-5 fused ring systems, 5-6 fused ring systems, 6-6 fused
WSGR Docket No.53344-792.601 ring systems, 5-7 fused ring systems, 6-5 fused ring systems, 6-7 fused ring systems, 5-8 fused ring systems, and 6-8 fused ring systems. Exemplary carbocycles include cyclopentyl, cyclohexyl, cyclohexenyl, adamantyl, phenyl, indanyl, and naphthyl. The term “unsaturated carbocycle” refers to carbocycles with at least one degree of unsaturation and excluding aromatic carbocycles. Examples of unsaturated carbocycles include cyclohexadiene, cyclohexene, and cyclopentene. The term “saturated cycloalkyl” as used herein refers to a saturated carbocycle. Exemplary carbocycles include cyclopropyl, cyclopentyl, cyclohexyl, cyclohexenyl, adamantyl, phenyl, indanyl, norbornyl, and naphthyl. Carbocycles can be optionally substituted by one or more substituents such as those substituents described herein. [0049] “Cycloalkyl” refers to a stable, partially or fully saturated, monocyclic or polycyclic carbocyclic ring, which can include fused (when fused with an aryl or a heteroaryl ring, the cycloalkyl is bonded through a non-aromatic ring atom), bridged, or spiro ring systems. Representative cycloalkyls include, but are not limited to, cycloalkyls having from three to fifteen carbon atoms (C3-C15 cycloalkyl), from three to ten carbon atoms (C3-C10 cycloalkyl), from three to eight carbon atoms (C3-C8 cycloalkyl), from three to six carbon atoms (C3-C6 cycloalkyl), from three to five carbon atoms (C3-C5 cycloalkyl), or three to four carbon atoms (C3-C4 cycloalkyl). In some embodiments, the cycloalkyl is a 3- to 6-membered cycloalkyl. In some embodiments, the cycloalkyl is a 5- to 6-membered cycloalkyl. Monocyclic cycloalkyls include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. Polycyclic cycloalkyls or carbocycles include, for example, adamantyl, norbornyl, decalinyl, bicyclo[3.3.0]octane, bicyclo[4.3.0]nonane, cis-decalin, trans-decalin, bicyclo[2.1.1]hexane, bicyclo[2.2.1]heptane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, and bicyclo[3.3.2]decane, and 7,7-dimethyl-bicyclo[2.2.1]heptanyl. Partially saturated cycloalkyls include, for example, cyclopentenyl, cyclohexenyl, cycloheptenyl, and cyclooctenyl. Unless stated otherwise specifically in the specification, a cycloalkyl is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, alkyl, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, a cycloalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, -CF3, -OH, -OMe, -NH2, or -NO2. In some embodiments, a cycloalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, - CF3, -OH, or -OMe. In some embodiments, the cycloalkyl is optionally substituted with halogen. In some embodiments, the cycloalkyl is unsubstituted. [0050] “Cycloalkylalkyl” refers to a radical of the formula –Rccycloalkyl where Rc is an alkylene chain as described above. [0051] “Cycloalkylalkoxy” refers to a radical bonded through an oxygen atom of the formula – O-Rccycloalkyl where Rc is an alkylene chain as described above.
WSGR Docket No.53344-792.601 [0052] “Halo” or “halogen” refers to halogen substituents such as bromo, chloro, fluoro, and iodo substituents. [0053] As used herein, the term "haloalkyl" or “haloalkane” refers to an alkyl radical, as defined above, that is substituted by one or more halogen radicals, for example, trifluoromethyl, dichloromethyl, bromomethyl, 2,2,2-trifluoroethyl, 1-fluoromethyl-2-fluoroethyl, and the like. In some embodiments, the alkyl part of the fluoroalkyl radical is optionally further substituted. Examples of halogen substituted alkanes (“haloalkanes”) include halomethane (e.g., chloromethane, bromomethane, fluoromethane, iodomethane), di-and trihalomethane (e.g., trichloromethane, tribromomethane, trifluoromethane, triiodomethane), 1-haloethane, 2- haloethane, 1,2-dihaloethane, 1-halopropane, 2-halopropane, 3-halopropane, 1,2-dihalopropane, 1,3-dihalopropane, 2,3-dihalopropane, 1,2,3-trihalopropane, and any other suitable combinations of alkanes (or substituted alkanes) and halogens (e.g., Cl, Br, F, I, etc.). When an alkyl group is substituted with more than one halogen radicals, each halogen can be independently selected e.g., 1-chloro-2-fluoroethane. [0054] "Fluoroalkyl" refers to an alkyl radical, as defined above, that is substituted by one or more fluoro radicals, for example, trifluoromethyl, difluoromethyl, fluoromethyl, 2,2,2trifluoroethyl, 1fluoromethyl2fluoroethyl, and the like. [0055] “Hydroxyalkyl” refers to an alkyl radical, as defined above, that is substituted by one or more hydroxyls. In some embodiments, the alkyl is substituted with one hydroxyl. In some embodiments, the alkyl is substituted with one, two, or three hydroxyls. Hydroxyalkyl include, for example, hydroxymethyl, hydroxyethyl, hydroxypropyl, hydroxybutyl, or hydroxypentyl. In some embodiments, the hydroxyalkyl is hydroxymethyl. [0056] “Aminoalkyl” refers to an alkyl radical, as defined above, that is substituted by one or more amines. In some embodiments, the alkyl is substituted with one amine. In some embodiments, the alkyl is substituted with one, two, or three amines. Aminoalkyl include, for example, aminomethyl, aminoethyl, aminopropyl, aminobutyl, or aminopentyl. In some embodiments, the aminoalkyl is aminomethyl. [0057] “Disulfide” refers to two sulfur atoms bonded to each other, where each sulfur comprises an optionally substituted alkyl chain. In some embodiments a disulfide may be R-S-S-R’. In some embodiments, R and R’ may be identical. In some embodiments, R and R’ are different. Each R and R’ may be independently selected from C1-C12 alkyl. In certain embodiments, R or R’ may be substituted with an amine, sulfone, or carboxylic acid. “C1-Cx alkyl substituted with disulfide” as used herein may refer to a disulfide of the structure R-S-S-R’, where R and R’ may be identical or different. Each R and R’ may be independently selected from C1-Cy alkyl, such that the length of R and R’ is the length of the C1-Cx alkyl.
WSGR Docket No.53344-792.601 [0058] The term “heteroalkyl” refers to an alkyl group in which one or more skeletal atoms of the alkyl are selected from an atom other than carbon, e.g., oxygen, nitrogen (e.g., -NH-, -N(alkyl)- ), sulfur, or combinations thereof. A heteroalkyl is attached to the rest of the molecule at a carbon atom of the heteroalkyl. In one aspect, a heteroalkyl is a C1-C6 heteroalkyl wherein the heteroalkyl is comprised of 1 to 6 carbon atoms and one or more atoms other than carbon, e.g., oxygen, nitrogen (e.g. -NH-, -N(alkyl)-), sulfur, or combinations thereof wherein the heteroalkyl is attached to the rest of the molecule at a carbon atom of the heteroalkyl. Examples of such heteroalkyl are, for example, -CH2OCH3, -CH2CH2OCH3, -CH2CH2OCH2CH2OCH3, or - CH(CH3)OCH3. Unless stated otherwise specifically in the specification, a heteroalkyl is optionally substituted for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, alkyl, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, a heteroalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, -CF3, OH, -OMe, NH2, or -NO2. In some embodiments, a heteroalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, -CF3, OH, or -OMe. In some embodiments, the heteroalkyl is optionally substituted with halogen. In some embodiments, the heteroalkyl is unsubstituted. [0059] “Heterocycloalkyl” refers to a stable 3 to 24membered partially or fully saturated ring radical comprising 2 to 23 carbon atoms and at least one ring heteroatoms. In some embodiments, a heterocycloalkyl contains from one to 8 heteroatoms selected from the group consisting of nitrogen, oxygen, phosphorous, and sulfur. Unless stated otherwise specifically in the specification, the heterocycloalkyl radical can be a monocyclic, bicyclic, tricyclic, or tetracyclic ring system, which can include fused (when fused with an aryl or a heteroaryl ring, the heterocycloalkyl is bonded through a non-aromatic ring atom) or bridged ring systems; and the nitrogen, carbon, or sulfur atoms in the heterocycloalkyl radical can be optionally oxidized; the nitrogen atom can be optionally quaternized. [0060] Representative heterocycloalkyls include, but are not limited to, heterocycloalkyls having from two to fifteen carbon atoms (C2-C15 heterocycloalkyl), from two to ten carbon atoms (C2-C10 heterocycloalkyl), from two to eight carbon atoms (C2-C8 heterocycloalkyl), from two to six carbon atoms (C2-C6 heterocycloalkyl), from two to five carbon atoms (C2-C5 heterocycloalkyl), or two to four carbon atoms (C2-C4 heterocycloalkyl). In some embodiments, the heterocycloalkyl is a 3- to 6-membered heterocycloalkyl. In some embodiments, the heterocycloalkyl is a 5- to 6-membered heterocycloalkyl. Examples of such heterocycloalkyl radicals include, but are not limited to, aziridinyl, azetidinyl, dioxolanyl, thienyl[1,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2oxopiperazinyl, 2oxopiperidinyl, 2oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4piperidonyl, pyrrolidinyl, pyrazolidinyl,
WSGR Docket No.53344-792.601 quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1oxothiomorpholinyl, 1,1dioxothiomorpholinyl, 1,3-dihydroisobenzofuran-1- yl, 3-oxo-1,3-dihydroisobenzofuran-1-yl, methyl-2-oxo-1,3-dioxol-4-yl, and 2-oxo-1,3-dioxol-4- yl. The term heterocycloalkyl also includes all ring forms of the carbohydrates, including but not limited to, the monosaccharides, the disaccharides, and the oligosaccharides. It is understood that when referring to the number of carbon atoms in a heterocycloalkyl, the number of carbon atoms in the heterocycloalkyl is not the same as the total number of atoms (including the heteroatoms) that make up the heterocycloalkyl (i.e. skeletal atoms of the heterocycloalkyl ring). Unless stated otherwise specifically in the specification, a heterocycloalkyl is optionally substituted, for example, with oxo, halogen, amino, nitrile, nitro, hydroxyl, alkyl, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, a heterocycloalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, -CF3, OH, -OMe, NH2, or -NO2. In some embodiments, a heterocycloalkyl is optionally substituted with oxo, halogen, methyl, ethyl, -CN, -CF3, OH, or -OMe. In some embodiments, the heterocycloalkyl is optionally substituted with halogen. In some embodiments, the heterocycloalkyl is unsubstituted. [0061] “Heterocycle” or “heterocyclyl” refers to a saturated, unsaturated, or aromatic ring comprising one or more ring heteroatoms. Exemplary heteroatoms include N, O, Si, P, B, and S atoms. Heterocycles include e.g., 3- to 10-membered monocyclic rings and 6- to 12-membered bicyclic rings (such as spiro, fused, or bridged rings). Unless stated otherwise specifically in the specification, the heterocyclyl radical is a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which optionally includes fused, bridged, or spirocyclic ring systems. The heteroatoms in the heterocyclyl radical are optionally oxidized. One or more nitrogen atoms, if present, are optionally quaternized. The heterocyclyl radical can be partially or fully saturated. The heterocyclyl is attached to the rest of the molecule through any atom of the ring(s). Examples of such heterocyclyl radicals include, but are not limited to, dioxolanyl, thienyl[1,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2oxopiperazinyl, 2oxopiperidinyl, 2oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl, tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1oxothiomorpholinyl, and 1,1dioxothiomorpholinyl. Unless stated otherwise specifically in the specification, the term "heterocyclyl" is meant to include heterocyclyl radicals as defined above that are optionally substituted by one or more substituents. For example, a heterocyclyl can be optionally substituted by one or more substituents selected from alkyl, alkenyl, alkynyl, halo, fluoroalkyl, oxo, thioxo, cyano, nitro, optionally substituted aryl, optionally substituted aralkyl, optionally substituted aralkenyl, optionally substituted aralkynyl, optionally
WSGR Docket No.53344-792.601 substituted carbocyclyl, optionally substituted carbocyclylalkyl, optionally substituted heterocyclyl, optionally substituted heterocyclylalkyl, optionally substituted heteroaryl, optionally substituted heteroarylalkyl, -Rb-ORa, -Rb-OC(O)-Ra, -Rb-OC(O)-ORa, -Rb-OC(O)- N(Ra)2, -Rb-N(Ra)2, -Rb-C(O)Ra, -Rb-C(O)ORa, -Rb-C(O)N(Ra)2, -Rb-CN, -Rb-O-Re-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, -Rb-N(Ra)C(O)Ra, -Rb-N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2), where each Ra is independently hydrogen, alkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), fluoroalkyl, cycloalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), cycloalkylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), aralkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heterocyclylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), heteroaryl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), or heteroarylalkyl (optionally substituted with halogen, hydroxy, methoxy, or trifluoromethyl), each Rb is independently a direct bond or a straight or branched alkylene or alkenylene chain, and Re is a straight or branched alkylene or alkenylene chain, and where each of the above substituents is unsubstituted unless otherwise indicated. [0062] “Heteroaryl” or “aromatic heterocycle” refers to a ring system radical comprising carbon atom(s) and one or more ring heteroatoms (e.g., selected from the group consisting of nitrogen, oxygen, phosphorous, silicon, and sulfur), and at least one aromatic ring. In some embodiments, a heteroaryl is a 5 to 14membered ring system radical comprising one to thirteen carbon atoms, one to six heteroatoms selected from the group consisting of nitrogen, oxygen, phosphorous, and sulfur. The heteroaryl radical can be a monocyclic, bicyclic, tricyclic, or tetracyclic ring system, which can include fused (when fused with a cycloalkyl or heterocycloalkyl ring, the heteroaryl is bonded through an aromatic ring atom) or bridged ring systems; and the nitrogen, carbon, or sulfur atoms in the heteroaryl radical can be optionally oxidized; the nitrogen atom can be optionally quaternized. In some embodiments, the heteroaryl is a 5- to 10-membered heteroaryl. In some embodiments, the heteroaryl is a 5- to 6-membered heteroaryl. Examples include, but are not limited to, azepinyl, acridinyl, benzimidazolyl, benzothiazolyl, benzindolyl, benzodioxolyl, benzofuranyl, benzooxazolyl, benzothiazolyl, benzothiadiazolyl, benzo[b][1,4]dioxepinyl, 1,4benzodioxanyl, benzonaphthofuranyl, benzoxazolyl, benzodioxolyl, benzodioxinyl, benzopyranyl, benzopyranonyl, benzofuranyl, benzofuranonyl, benzothienyl (benzothiophenyl), benzotriazolyl, benzo[4,6]imidazo[1,2a]pyridinyl, carbazolyl, cinnolinyl, dibenzofuranyl, dibenzothiophenyl, furanyl, furanonyl, isothiazolyl, imidazolyl, indazolyl, indolyl, indazolyl,
WSGR Docket No.53344-792.601 isoindolyl, indolinyl, isoindolinyl, isoquinolyl, indolizinyl, isoxazolyl, naphthyridinyl, oxadiazolyl, 2oxoazepinyl, oxazolyl, oxiranyl, 1-oxidopyridinyl, 1oxidopyrimidinyl, 1- oxidopyrazinyl, 1-oxidopyridazinyl, 1phenyl1Hpyrrolyl, phenazinyl, phenothiazinyl, phenoxazinyl, phthalazinyl, pteridinyl, purinyl, pyrrolyl, pyrazolyl, pyridinyl, pyrazinyl, pyrimidinyl, pyridazinyl, quinazolinyl, quinoxalinyl, quinolinyl, quinuclidinyl, isoquinolinyl, tetrahydroquinolinyl, thiazolyl, thiadiazolyl, triazolyl, tetrazolyl, triazinyl, and thiophenyl (i.e., thienyl). Unless stated otherwise specifically in the specification, a heteroaryl is optionally substituted, for example, with halogen, amino, nitrile, nitro, hydroxyl, alkyl, alkenyl, alkynyl, haloalkyl, alkoxy, aryl, cycloalkyl, heterocycloalkyl, heteroaryl, and the like. In some embodiments, a heteroaryl is optionally substituted with halogen, methyl, ethyl, -CN, -CF3, OH, -OMe, NH2, or -NO2. In some embodiments, a heteroaryl is optionally substituted with halogen, methyl, ethyl, -CN, -CF3, OH, or -OMe. In some embodiments, the heteroaryl is optionally substituted with halogen. In some embodiments, the heteroaryl is unsubstituted. [0063] The term “substituted” refers to moieties having substituents replacing a hydrogen on one or more carbons or substitutable heteroatoms, e.g., NH, of the structure. It will be understood that “substitution” or “substituted with” includes the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, i.e., a compound which does not spontaneously undergo transformation such as by rearrangement, cyclization, elimination, etc. In certain embodiments, substituted refers to moieties having substituents replacing two hydrogen atoms on the same carbon atom, such as substituting the two hydrogen atoms on a single carbon with an oxo, imino, or thioxo group. As used herein, the term “substituted” is contemplated to include all permissible substituents of organic compounds. In a broad aspect, the permissible substituents include acyclic and cyclic, branched, and unbranched, carbocyclic and heterocyclic, aromatic and non-aromatic substituents of organic compounds. The permissible substituents can be one or more and the same or different for appropriate organic compounds. For purposes of this disclosure, the heteroatoms such as nitrogen can have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms. [0064] In some embodiments, substituents can include any substituents described herein, for example: halogen, hydroxy, oxo (=O), thioxo (=S), cyano (-CN), nitro (-NO2), imino (=N-H), oximo (=N-OH), hydrazine (=N- NH2), -Rb-ORa, -Rb-OC(O)-Ra, -Rb-OC(O)-ORa, -Rb-OC(O)-N(Ra)2, -Rb-N(Ra)2, -Rb-C(O)Ra, -R b-C(O)ORa, -Rb-C(O)N(Ra)2, -Rb-O-Rc-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, -Rb-N(Ra)C(O)Ra, -Rb- N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2), and -Rb-S(O)tN(Ra)2 (where t is 1 or 2); and alkyl, alkenyl, alkynyl, aryl, aralkyl, aralkenyl,
WSGR Docket No.53344-792.601 aralkynyl, cycloalkyl, cycloalkylalkyl, and heterocycle, any of which can be optionally substituted by alkyl, alkenyl, alkynyl, halogen, haloalkyl, haloalkenyl, haloalkynyl, oxo (=O), thioxo (=S), cyano (-CN), nitro (-NO2), imino (=N-H), oximo (=N-OH), hydrazine (=N-NH2), SF5, -Rb-ORa, -Rb-OC(O)-Ra, -Rb-OC(O)-ORa, -Rb-OC(O)-N(Ra)2, -Rb-N(Ra)2, -Rb-C(O)Ra, -Rb- C(O)ORa, -Rb-C(O)N(Ra)2, -Rb-O-Rc-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, -Rb-N(Ra)C(O)Ra, -Rb-N (Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2); wherein each Ra is independently selected from hydrogen, alkyl, cycloalkyl, cycloalkylalkyl, aryl, aralkyl, and heterocycle, wherein each Ra, valence permitting, can be optionally substituted with alkyl, alkenyl, alkynyl, halogen, haloalkyl, haloalkenyl, haloalkynyl, oxo (=O), thioxo (=S), cyano (-CN), nitro (-NO2), imino (=N-H), oximo (=N-OH), hydrazine (=N- NH2), -Rb-ORa, -Rb-OC(O)-Ra, -Rb-OC(O)-ORa, -Rb-OC(O)-N(Ra)2, -Rb-N(Ra)2, -Rb-C(O)Ra, -R b-C(O)ORa, -Rb-C(O)N(Ra)2, -Rb-O-Rc-C(O)N(Ra)2, -Rb-N(Ra)C(O)ORa, -Rb-N(Ra)C(O)Ra, -Rb- N(Ra)S(O)tRa (where t is 1 or 2), -Rb-S(O)tRa (where t is 1 or 2), -Rb-S(O)tORa (where t is 1 or 2) and -Rb-S(O)tN(Ra)2 (where t is 1 or 2); and wherein each Rb is independently selected from a direct bond or a straight or branched alkylene, alkenylene, or alkynylene chain, and each Rc is a straight or branched alkylene, alkenylene or alkynylene chain. [0065] The term “optional” or “optionally” means that the subsequently described event or circumstance may or may not occur, and that the description includes instances where said event or circumstance occurs and instances in which it does not. For example, “optionally substituted alkyl” means either “alkyl” or “substituted alkyl” as defined above. Further, an optionally substituted group can be un-substituted (e.g., -CH2CH3), fully substituted (e.g., -CF2CF3), mono- substituted (e.g., -CH2CH2F) or substituted at a level anywhere in-between fully substituted and mono-substituted (e.g., -CH2CHF2, -CH2CF3, -CF2CH3, -CFHCHF2, etc.). [0066] The term “biomolecule” refers to biological components that may be involved in corona formation, including, but not limited to, for example, proteins, polypeptides, polysaccharides, a sugar, a lipid, a lipoprotein, a metabolite, an oligonucleotide, metabolome, or combination thereof. It is contemplated that the biomolecule coronas of distinct particles may contain some of the same biomolecules, may contain distinct biomolecules with regard to the other sensor elements, and/or may differ in level or quantity, type or conformation of the biomolecule that binds to each sensor element. In one embodiment, the biomolecule is selected from the group of proteins, nucleic acids, lipids, and metabolomes. [0067] Ranges provided herein are understood to be shorthand for all of the values within the range. For example, a range of 1 to 50 is understood to include any number, combination of numbers, or sub-range from the group consisting of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
WSGR Docket No.53344-792.601 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50, as well as all intervening decimal values between the aforementioned integers such as, for example, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, and 1.9. With respect to sub-ranges, “nested sub-ranges” that extend from either end point of the range are specifically contemplated. For example, a nested sub-range of an exemplary range of 1 to 50 can comprise 1 to 10, 1 to 20, 1 to 30, and 1 to 40 in one direction, or 50 to 40, 50 to 30, 50 to 20, and 50 to 10 in the other direction. [0068] The compounds and structures provided herein may be stereoisomeric. In some cases, a compound or structure of the disclosure may form a stereoisomer. In some cases, the stereoisomer may be a diastereomer (e.g., a cis/trans isomer, E/Z isomer, conformer, or rotamer). In some cases, the stereoisomer may be an enantiomer (R,S enantiomers or +/- enantiomers). In some cases, the compound or structure of the disclosure may be enantiopure (e.g., 100% pure). In some cases, the compound or structure may form a racemic mixture of enantiomers (e.g., 50% pure). In some cases, a compound or structure of the disclosure may stabilize as a stereoisomer, where the compound or structure of the disclosure comprises at least about 10%, about 15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%, about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 98.5%, about 99%, about 99.1%, about 99.2%, about 99.3%, about 99.4%, about 99.5%, about 99.6%, about 99.7%, about 99.8%, about 99.9%, or more of a mixture of the compound or structure and the corresponding stereoisomer. [0069] In some embodiments, the macromolecule structures provided herein may be, or may be comprised within or on, a particle, as described herein. In some embodiments, the particles provided herein comprise the macromolecule structures. [0070] Provided herein are particles (e.g., comprising macromolecule structures) (e.g., or combinations of particles (e.g., comprising macromolecule structures)) capable of isolating one or more biomolecules, such as a protein, peptide, or polypeptide from complex biological solutions, methods, and systems of using such particles (e.g., comprising macromolecule structures). In some instances, macromolecules provided herein bind to the one or more biomolecules, allowing for “pull-down” or isolation of the particles (e.g., comprising macromolecule structures) (e.g., via magnetic pull-down or via centrifugation). The particles (e.g., comprising macromolecule structures) herein may differ based on surface charge (e.g., zeta potential), surface functionalities, particle size, or particle composition. Multiple different particles (e.g., comprising macromolecule structures) may be used in tandem (e.g., multiplexing) which may increase the ability of the particles (e.g., comprising macromolecule structures) to isolate biomolecules. In some instances, the combination of particles (e.g., comprising
WSGR Docket No.53344-792.601 macromolecule structures), such as described herein, provide a synergistic relationship that enhances the macromolecule structure’s ability to isolate biomolecules. This increased ability in some instances is compared to the ability of a single macromolecule structure to isolate biomolecules on their own. The methods and macromolecules provided herein aid in avoiding the need for alternative isolation/purification methods such as solid phase chromatography (e.g., reverse-phase/ion exchange) or suspension trapping which may be solvent intensive and may lead to poor recovery, reproducibility issues, or insufficient purification. Additionally, the methods, systems, and compositions provided herein allow for the use of a diverse range of biological sample types, including but not limited to plasma, serum, cells, and tissues, and at lower required sample volumes than comparable methods. In some embodiments, the methods provided herein allow for the preparation of biomolecule samples for analysis by mass spectrometry (MS), such as by selective removal of MS incompatible components from a biological sample. Macromolecule Structures and Particles [0071] In some compositions, methods, kits, and systems provided herein, two particles are used, a first particle with a neutral to negative surface charge, and a second particle, with a highly negative surface charge (e.g., more negative than the first particle). In some compositions, methods, kits, and systems provided herein, two macromolecule structures are used, a first macromolecule structure with a neutral to negative surface charge, and a second macromolecule structure, with a highly negative surface charge (e.g., more negative than the first macromolecule structure). In some instances, the combination of the two differing particles (e.g., comprising macromolecule structures) provides a synergistic relationship, enabling the isolation, purification, quantification, or identification of a larger number of biomolecules than the two particles (e.g., comprising macromolecule structures) on their own. Without being bound by theory, particles (e.g., macromolecules) with similar types of charges (e.g., at least partially negative) may improve the isolation, purification, quantification, or identification of biomolecules because the particles (e.g., macromolecules) repel each other. [0072] Provided herein, in some embodiments, are compositions comprising two or more (e.g., structurally unique) particles (e.g., comprising macromolecule structures). In some embodiments, the compositions comprise a first particle (e.g., comprising a macromolecule structure) and a second particle (e.g., comprising a macromolecule structure). In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a neutral to negative surface charge. In some embodiments, the second particle (e.g., comprising a macromolecule structure) comprises a greater negative (e.g., more negative) surface charge than that of the first particle (e.g., comprising a macromolecule structure).
WSGR Docket No.53344-792.601 [0073] In some embodiments, surface charge herein is measured by zeta potential. In some instances, zeta potential may be measured by electrophoretic light scattering (ELS). In some instances, zeta potential is measured by DLS in 1.5 mM KCl (pH 7.0). In some instances, zeta potential is measured by DLS in 5% PBS (pH 6.8-7.4). In some embodiments, the surface charge (e.g., zeta potential) described herein is measured by dispersing about 20 µg of particles in 5% PBS at a pH of 6.8-7.4. In an exemplary zeta measurement experiment, an instrument such as a Zetasizer Nano ZS (Malvern Instruments, Worcestershire, UK) may be used. Particles for testing in some instances are suspended at 10 mg/mL in water with about 10 min of bath sonication prior to testing. Samples then may be diluted to approximately 0.02 wt%, and DLS performed in water at about 25°C in disposable polystyrene semi-micro cuvettes with about 1 min temperature equilibration time. Results from several runs may be averaged in some instances (e.g., 3 runs of about 1 min), with a 633 nm laser in 173° backscatter mode. DLS results in some instances are then analyzed using the cumulants method and zeta potential measured in 5% pH 7.4 PBS in disposable folded capillary cells (Malvern Instruments, PN DTS1070) at about 25°C with an about 1 min equilibration time. In some instances, three measurements are performed with automatic measurement duration with a minimum of 10 runs and a maximum of 100 runs, and a 1 min hold between measurements. In some instances, the Smoluchowski model is used to determine the zeta potential from the electrophoretic mobility. Used to determine the zeta potential from the electrophoretic mobility. [0074] In some embodiments, a neutral surface charge is characterized by a zeta potential of from about -5 mV to about 5 mV. In some embodiments, a neutral surface charge is characterized by a zeta potential of at most 5 mV (e.g., at most 4 mV, 3 mV, 2 mV, 1 mV, 0.75 mV, 0.5 mV, 0.25 mV, or at most 0.1 mV). In some embodiments, a neutral surface charge is characterized by a zeta potential of at least -5 mV (e.g., at least -4 mV, -3 mV, -2 mV, -1.5 mV, -1 mV, -0.75 mV, -0.5 mV, -0.25 mV, or at least -0.1 mV). In some embodiments, a neutral surface charge is characterized by a zeta potential of about 0 mV. In some embodiments, a neutral surface charge is characterized by a zeta potential of about -1 mV, 0 mV, or 1 mV. [0075] In some embodiments, the first particle (e.g., comprising the first macromolecule structure) provided herein comprises a surface charge (e.g., characterized by a zeta potential) of from about 10 mV to about -15 mV. In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of from about 0 to about -15 mV. In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of from about 0 to about -10 mV. In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of from about -10 to about -20 mV. In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a
WSGR Docket No.53344-792.601 surface charge of at most about 0 mV. In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of at most about -1 mV (e.g., -2 mV, -3 mV, -5 mV, -6 mV, -8 mV, -9 mV, or at most -10 mV). In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a surface charge of at least -15 mV (e.g., -12 mV, -10 mV, -8 mV, -6 mV, -5 mV, -4 mV, -3 mV, -2 mV, or -1 mV). In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a zeta potential of about 0 mV, -1 mV, -2 mV, -3 mV, -4 mV, -5 mV, -6 mV, -7 mV, -8 mV, -9 mV, or -10 mV. In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a zeta potential of about -10 mV, -11 mV, -12 mV, -13 mV, -14 mV, -15 mV, -16 mV, -17 mV, -18 mV, -19 mV, or -20 mV. [0076] In some embodiments, a negative surface charge is characterized by a zeta potential of from about 0 mV to about -80 mV. In some embodiments, a negative surface charge is characterized by a zeta potential of from about 0 mV to about -60 mV. In some embodiments, a negative surface charge is characterized by a zeta potential of from about -5 mV to about -60 mV (e.g., about -10 mV to about -60 mV, about -20 mV to about -60 mV, about -30 mV to about -60 mV, or about -40 mV to about -60 mV). In some embodiments, a negative surface charge is characterized by a zeta potential of at least -80 mV (e.g., at least -70 mV, -60 mV, -50 mV, -40 mV, -30 mV, -20 mV, -10 mV, or at least -5 mV). In some embodiments, a negative surface charge is characterized by a zeta potential of at most 0 mV (e.g., at most -5 mV, -10 mV, -20 mV, -30 mV, -40 mV, -50 mV, or -60 mV). In some embodiments, a negative surface charge is characterized by a zeta potential of about -3 mV, -8 mV, --12 mV, -20 mV, -25 mV, -30 mV, -40 mV, -45 mV, -50 mV, or -55 mV. [0077] In some embodiments, the second particle (e.g., comprising a macromolecule structure) comprises a surface charge (e.g., characterized by a zeta potential) of from about -15 mV to about -60 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) comprises a surface charge of about 0 mV to about -60 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) comprises a surface charge about -35 mV to about -60 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) comprises a surface charge about -40 mV to about -50 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) comprises a surface charge of at least about -60 mV (e.g., -55 mV, -50 mV, -45 mV, -40 mV, -35 mV, -30 mV, or -25 mV). In some embodiments, the second particle (e.g., comprising a macromolecule structure) comprises a surface charge of at most about 0 mV (e.g., -10 mV, -20 mV, -30 mV, -40 mV, -50 mV, or -60 mV). In some embodiments, the second particle (e.g., comprising a macromolecule structure)
WSGR Docket No.53344-792.601 comprises a surface charge of about -36 mV (e.g., -38 mV, -40 mV, -42 mV, -44 mV, -46 mV, - 48 mV, -50 mV, -52 mV, -54 mV, -56 mV, -58 mV, or -60 mV). [0078] In some embodiments, the first particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of about -3 mV (e.g., such as described in Example 1). In some embodiments, the first particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of from about 0 mV to about -15 mV. In some embodiments, the first particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of from about 0 mV to about -10 mV. In some embodiments, the first particle has a surface charge characterized by a zeta potential of from about -10 mV to -20 mV. In some embodiments, the first particle has a surface charge characterized by a zeta potential of -13 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of about -50 mV (e.g., such as described in Example 2). In some embodiments, the second particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of from about - 35 mV to about -60 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of from about – 40 mV to about -60 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of from about -40 mV to -50 mV. In some embodiments, the second particle (e.g., comprising a macromolecule structure) has a surface charge characterized by a zeta potential of about -42 mV. In some embodiments, a surface charge of the second particle (e.g., comprising a macromolecule structure) is characterized by a zeta potential of at least 4-fold more negative than the surface charge of the first particle (e.g., comprising a macromolecule structure). In some embodiments, a surface charge of the second particle (e.g., comprising a macromolecule structure) is characterized by a zeta potential of at least 8-fold more negative than the surface charge of the first particle (e.g., comprising a macromolecule structure). In some embodiments, a surface charge of the second particle (e.g., comprising a macromolecule structure) is characterized by a zeta potential of about 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 11-fold, 12-fold, 13- fold, 14-fold, or 15-fold more negative than the surface charge of the first particle (e.g., comprising a macromolecule structure). [0079] In some embodiments, the compositions herein comprise the multiple different particles (e.g., comprising macromolecule structures) in varying relative amounts. In some embodiments, the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) in varying relative amounts. In some embodiments, the compositions comprise the first particle (e.g., comprising a macromolecule
WSGR Docket No.53344-792.601 structure) and second particle (e.g., comprising a macromolecule structure) at a ratio of about 10:1 to about 1:10. In some embodiments, the compositions comprise the first particle (e.g., comprising a macromolecule structure) and second particle (e.g., comprising a macromolecule structure) at a ratio of about 5:1 to about 1:5. In some embodiments, the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) at a ratio of about 1:1 to about 1:10. In some embodiments, the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) at a ratio of 1:1 to about 1:4 (e.g., 1:2, 1:2.5, 1:3, 1:3.5, or 1:3.75). In some embodiments, the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) at a ratio of about 1:2, 1:1, 1:2, 1:2.5, 1:3, 1:3.5:, 1:3.75, 1:4, 1:4.25, 1:4.5, 1:5, 1:6, 1:7, 1:8, 1:9, or about 1:10. In some embodiments, the compositions comprise the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) at a ratio of about 1:4. In some instances, the ratio is a molar ratio. In some instances, the ratio is a mass ratio. In some instances, the ratio is a surface area ratio. [0080] In some embodiments, the particle (e.g., comprising a macromolecule structure) provided herein comprise a surface and a polymer or co-polymer. In some embodiments, the polymer or co-polymer is covalently attached to the surface. In other embodiments, the polymer or co-polymer is non-covalently attached to the surface. In some embodiments, the co-polymer is a random co-polymer. In some embodiments, the co-polymers herein comprise 2, 3, 4, 5, 6, or more unique monomers. In some embodiments, at least a portion of the monomers within the co- polymers act as cross-linkers. In some instances, the surface comprises a base polymer. In some instances, monomers are covalently crosslinked from the base polymer to form polymers or copolymers extending from the base polymer. [0081] In some embodiments, the particles provided herein comprise macromolecule structures comprising a polymer comprising one or more units represented by Formula (A):
Formula (A)
WSGR Docket No.53344-792.601 [0082] In some embodiments, R is hydrogen or . In some embodiments, R is
hydrogen. In some embodiments, R is . [0083] In some embodiments, when R is hydroxyl, the structure of Formula (A) is represented by:
. [0084] In some embodiments, R1 is hydrogen or hydroxyl. In some embodiments, R1 is hydrogen. In some embodiments, R1 is hydroxyl. [0085] In some embodiments, q is an integer from 1 to 6. In some embodiments, q is 1. In some embodiments, q is 2. In some embodiments, q is 3. In some embodiments, q is 4. In some embodiments, q is 5. In some embodiments, q is 6. [0086] In some embodiments, R2 is optionally substituted C1-C8 diamine. In some embodiments, R2 is C1-C8 diamine, N-substituted with one or more R3. In some embodiments, R2 is C2 diamine, N-substituted with one or more R3. [0087] In some embodiments, R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl. In some embodiments, R3 is hydrogen. In some embodiments, R3 is optionally substituted C1-C8 alkyl. In some embodiments, R3 is C1-C8 alkyl optionally substituted with C1-C8 alkenyl, oxo(s), (in some instances two oxos), and hydroxyl.
[0088] In some embodiments, R2 is , wherein p is an integer from 1 to 6. In some embodiments, p is 1. In some embodiments, p is 2. In some embodiments, p is 3. In some embodiments, p is 4. In some embodiments, p is 5. In some embodiments, p is 6. [0089] In some embodiments, R1 and R2 are taken together to form C2-C6 heterocyloalkyl. In some embodiments, R1 and R2 are taken together, forming the structure:
[0090] In some embodiments, R4 is hydrogen or C1-C6 alkyl. In some embodiments, R4 is hydrogen. In other embodiments, R4 is C1-C6 alkyl. In some embodiments, R4 is C1 alkyl.
WSGR Docket No.53344-792.601 [0091] In some embodiments, the polymer comprises two or more units represented by Formula (A), wherein the two or more units have a different structure. In some embodiments, the two or
more units comprises a first unit represented by Formula (A), wherein R is and R2
. In some embodiments, q is 1 for the first unit. In some embodiments, the two or more units comprises a second unit represented by Formula (A) having the structure of
. In some embodiments, the two or more units comprises a second unit represented by
Formula (A), wherein R1 and R2 are taken together having the structure of . In some embodiments, the two or more units comprises a second unit represented by Formula (A), wherein R is and R2 . In some embodiments, q is 1 for the second unit. In some embodiments, the second unit is a crosslinking unit. In some embodiments, the crosslinking unit is obtained from a monomer having two or more vinyl groups. For example, the crosslinking unit may obtained from divinyl benzene, polyethylene glycol dimethacrylate, or ethylene glycol dimethacrylate. [0092] Provided herein in some embodiments are compositions comprising a macromolecular structure comprising two or more units represented by Formula (A), as described hereinabove, and Formula (B):
WSGR Docket No.53344-792.601 [0093] In some embodiments, R is hydrogen or . In some embodiments, R is
hydrogen. In some embodiments, R is . [0094] In some embodiments, R1 is hydrogen or hydroxyl. In some embodiments, R1 is hydrogen. In some embodiments, R1 is hydroxyl. [0095] In some embodiments, q is an integer from 1 to 6. In some embodiments, q is an integer from 1 to 3. In some embodiments, q is 1. In some embodiments, q is 2. In some embodiments, q is 3. In some embodiments, q is 4. In some embodiments, q is 5. In some embodiments, q is 6. [0096] In some embodiments, m is an integer from 1 to 6. In some embodiments, m is 1. In some embodiments, m is 2. In some embodiments, m is 3. In some embodiments, m is 4. In some embodiments, m is 5. In some embodiments, m is 6. [0097] In some embodiments, R2 is optionally substituted C1-C8 diamine. In some embodiments, R2 is C1-C8 diamine, N-substituted with one or more R3. In some embodiments, R2 is C2 diamine, N-substituted with one or more R3. [0098] In some embodiments, R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C12 alkenyl, and C1-C8 alkynyl. In some embodiments, R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl. In some embodiments, R3 is hydrogen. In some embodiments, R3 is optionally substituted C1-C8 alkyl. In some embodiments, R3 is C1-C8 alkyl optionally substituted with C1-C8 alkenyl, (e.g., 2) oxo, and hydroxyl. In some embodiments, R3 is C1-C8 alkyl optionally substituted with C1-C12 alkenyl, (e.g., 2) oxo, and hydroxyl.
[0099] In some embodiments, R2 is , wherein p is an integer from 1 to 6. In some embodiments, p is 1. In some embodiments, p is 2. In some embodiments, p is 3. In some embodiments, p is 4. In some embodiments, p is 5. In some embodiments, p is 6. [00100] In some embodiments, R1 and R2 are taken together to form C2-C6 heterocyloalkyl. In some embodiments, R1 and R2 are taken together, forming the structure:
[00101] In some embodiments, R4 is hydrogen or C1-C6 alkyl. In some embodiments, R4 is hydrogen. In other embodiments, R4 is C1-C6 alkyl. In some embodiments, R4 is C1 alkyl.
WSGR Docket No.53344-792.601 [00102] In some embodiments, is a single bond or a double bond. In some embodiments, is a single bond. In some embodiments, is a double bond. [00103] In some embodiments * is an attachment point to another unit of Formula (A) or Formula (B), such as when
is a single bond. When * is an attachment point to another unit of Formula (B), the unit of Formula (B) acts as a crosslinking monomer. [00104] In some embodiments, the composition comprises one or more units (e.g., of Formula (A)) represented by Formula (C):
Formula (C) [00105] In some embodiments, R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl. In some embodiments, R3 is hydrogen. In some embodiments, R3 is optionally substituted C1-C8 alkyl. In some embodiments, R3 is C1-C8 alkyl optionally substituted with C1-C8 alkenyl, (e.g., 2) oxo, and hydroxyl. In some embodiments, one
hydrogen. In some embodiments, two
one of R3 is hydrogen. [00106] In some embodiments, the composition comprises one or more units (e.g., of Formula (A)) represented by Formula (A-A):
Formula (A-A) [00107] In some embodiments, R5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, R5 is C1-C10 alkyl. In some embodiments, R5 is C1-C10 alkenyl. In some
WSGR Docket No.53344-792.601 embodiments, R5 is C1-C10 alkynyl. In some embodiments, R5 is C8 alkenyl. In some embodiments, R5 is
. In some embodiments, R5 is
. [00108] In some embodiments, the composition comprises one or more units (e.g., of Formula (A)) represented by Formula (A-B):
Formula (A-B) [00109] In some embodiments, R5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, R5 is C1-C10 alkyl. In some embodiments, R5 is C1-C10 alkenyl. In some embodiments, R5 is C1-C10 alkynyl. In some embodiments, R5 is C8 alkenyl. In some embodiments, R5 is
. In some embodiments, R5 is
. [00110] Without being bound to any particular theory, the units represented by Formula (A-A) and/or Formula (A-B) can exhibit zwitterionic properties which may increase the diversity or number of biomolecules adsorbed to the macromolecular structures. [00111] In some embodiments, the composition comprises one or more units (e.g., of Formula (A)) represented by Formula (A-C):
Formula (A-C) [00112] In some embodiments, R5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, R5 is C1-C10 alkyl. In some embodiments, R5 is C1-C10 alkenyl. In some embodiments, R5 is C1-C10 alkynyl. In some embodiments, R5 is C8 alkenyl. In some embodiments, R5 is
. In some embodiments, R5 is . [00113] In some embodiments, the composition comprises one or more units (e.g., of Formula (A)) represented by the structure:
WSGR Docket No.53344-792.601
[00114] In some embodiments, the composition comprises one or more units (e.g., of Formula (A)) represented by Formula (A-D):
[00115] In some embodiments, in Formula (A), R4 is C1 alkyl, R is , R1 is hydroxyl, R2 is C2 diamine, N-substituted with 1-3 of R3, R3 is each independently hydrogen or C4 alkyl substituted with two oxo, hydroxyl, and C8 alkenyl. In some embodiments, the structure of Formula (B) is:
[00116] In some embodiments, the structure of Formula (B), such as when Formula (B) acts as a crosslinking monomer, is:
[00117] In some embodiments, the particles comprise a macromolecule structure comprising a co-polymer of the structure (A1):
WSGR Docket No.53344-792.601
[00118] In some embodiments, C5H11 as used herein refers to n-C5H11. In some embodiments, C5H11 refers to
. In some embodiments, C5H11 is
. [00119] In some embodiments, the particle comprises a macromolecule structure further comprising methacrylic acid as a monomer unit. The amount of methacrylic acid monomer units may be, in some embodiments, no more than about 10%, no more than about 5%, or no more than about 1% by weight or number of monomer units. The amount of methacrylic acid monomer units may be, in some embodiments, at least 0.1%, at least 0.5%, at least 1% or at least 2% by weight or number of monomer units. Without being bound to any particular theory, methacrylic acid may be incorporated to provide a larger negative surface charge (e.g., negative zeta potential) for the particle (e.g., comprising a macromolecule structure) to obtain improved charge differences between the first particle (e.g., comprising a macromolecule structure) and second particle (e.g., comprising a macromolecule structure) that increase the number or diversity of protein adsorption and/or reduce agglomeration. [00120] In some embodiments, the units of the copolymer are randomly distributed throughout the polymer. [00121] In certain embodiments, the monomers represented by n and m are randomly distributed throughout the polymer. In some embodiments, the second particle comprises a macromolecule structure comprising the co-polymer of structure (A1). [00122] In some embodiments, the second particle comprises a macromolecule structure comprising a co-polymer comprising any number of units represented in Table 1.
WSGR Docket No.53344-792.601 TABLE 1
WSGR Docket No.53344-792.601
[00123] In some embodiments, C5H11 as used herein refers to n-C5H11. In some embodiments, C5H11 refers
[00124] In some embodiments, the copolymer comprises monomer 6 and monomer 3. In some embodiments, the copolymer comprises monomer 6, monomer 3, and monomer 7. In some embodiments, the copolymer comprises monomer 6, monomer 3, and monomer 8. In some embodiments, the copolymer comprises monomer 6, monomer 3, and monomer 9. In some embodiments, the copolymer comprises monomer 6, monomer 3, and monomer 5. In some embodiments, the copolymer comprises monomer 6, monomer 7, and monomer 8. [00125] Provided herein, in some embodiments, is a particle comprising a macromolecule structure comprising a copolymer comprising two or more units represented by Formula (D) and Formula (E):
WSGR Docket No.53344-792.601
[00126] In some embodiments, the particle comprises a macromolecule structure comprising a unit represented by Formula (D). In some embodiments, the particle comprises a macromolecule structure comprising a unit represented by Formula (E). [00127] In some embodiments, R4 is each independently hydrogen or C1-C6 alkyl. In some embodiments, R4 is hydrogen. In some embodiments, R4 is C1-C6 alkyl. In some embodiments, R4 is C1-C3 alkyl. In some embodiments, R4 is C1 alkyl. [00128] In some embodiments, R6 is C1-C6 alkyl optionally substituted with R7. In some embodiments, R6 is hydrogen or (CH2)pOR7. In some embodiments, R6 is hydrogen. [00129] In some embodiments, R7 is hydrogen or C1-C6 alkyl. In some embodiments, R7 is hydrogen. In some embodiments, R7 is C1-C6 alkyl. In some embodiments, R7 is C1-C3 alkyl. In some embodiments, R7 is C1 alkyl. [00130] In some embodiments, m is an integer from 1 to 6. In some embodiments, m is 1. In some embodiments, m is 2. In some embodiments, m is 3. In some embodiments, m is 4. In some embodiments, m is 5. In some embodiments, m is 6. [00131] In some embodiments, p is an integer from 1 to 6. In some embodiments, p is 1. In some embodiments, p is 2. In some embodiments, p is 3. In some embodiments, p is 4. In some embodiments, p is 5. In some embodiments, p is 6. [00132] In some embodiments,
is a single bond or a double bond. In some embodiments, is a single bond. In some embodiments,
is a double bond. [00133] In some embodiments * is an attachment point to another unit of Formula (D) or Formula (E), such as when
is a single bond. When * is an attachment point to another unit of Formula (D), the unit of Formula (B) acts as a crosslinking monomer. [00134] In some embodiments, the macromolecule structure comprises one or more units (e.g., of Formula (E)) represented by the structure of Formula (E-A):
WSGR Docket No.53344-792.601
Formula (E-A) [00135] In some embodiments, In some embodiments, R4 is each independently hydrogen or C1- C6 alkyl. In some embodiments, R4 is hydrogen. In some embodiments, R4 is C1-C6 alkyl. In some embodiments, R4 is C1-C3 alkyl. In some embodiments, R4 is C1 alkyl. [00136] In some embodiments, R7 is hydrogen or C1-C6 alkyl. In some embodiments, R7 is hydrogen. In some embodiments, R7 is C1-C6 alkyl. In some embodiments, R7 is C1-C3 alkyl. In some embodiments, R7 is C1 alkyl. [00137] In some embodiments, p is an integer from 1 to 6. In some embodiments, p is 1. In some embodiments, p is 2. In some embodiments, p is 3. In some embodiments, p is 4. In some embodiments, p is 5. In some embodiments, p is 6. [00138] In some embodiments, the particle comprises a macromolecule structure comprising one or more units (e.g., of Formula (E)) represented by the structure:
. [00139] In some embodiments, the particle comprises a macromolecule structure comprising one or more units (e.g., of Formula (E)) represented by the structure:
. [00140] In some embodiments, the particle comprises a macromolecule structure comprising one or more units (e.g., of Formula (D)) represented by the structure:
WSGR Docket No.53344-792.601 [00141] In some embodiments, is a single bond or a double bond. In some embodiments, is a single bond. In some embodiments, is a double bond. [00142] In some embodiments * is an attachment point to another unit of Formula (D) or Formula (E), such as when
is a single bond. When * is an attachment point to another unit of Formula (D), the unit of Formula (B) acts as a crosslinking monomer. [00143] In some embodiments, the particle comprises a macromolecule structure comprising three or more units (e.g., of Formula (E)) represented by:
[00144] In some embodiments, the structure of Formula (D), such as when Formula (D) acts as a crosslinking monomer, is:
. [00145] In some embodiments, the macromolecule structure comprises a macromolecule structure comprising a co-polymer of the structure (A2):
. [00146] In some embodiments, the particle comprises a macromolecule structure comprising a co-polymer of the structure (A2’):
WSGR Docket No.53344-792.601
[00147] In certain embodiments, the monomers represented by n and m are randomly distributed throughout the polymer. In certain embodiments, the monomers represented by n, m, and p are randomly distributed throughout the polymer. In some embodiments, the first particle comprises a macromolecule structure comprising the co-polymer of structure (A2). In some embodiments, the first particle comprises a macromolecule structure comprising the co-polymer of structure (A2’). [00148] In some embodiments, the first particle comprises a macromolecule structure further comprising methacrylic acid as a monomer unit. The amount of methacrylic acid monomer units may be, in some embodiments, no more than about 10%, no more than about 5%, or no more than about 1% by weight or number of monomer units. The amount of methacrylic acid monomer units may be, in some embodiments, at least 0.1%, at least 0.5%, at least 1% or at least 2% by weight or number of monomer units. Without being bound to any particular theory, methacrylic acid may be incorporated to provide a larger negative surface charge (e.g., negative zeta potential) for the macromolecular structure, which can improve dispersion (and reduce aggregation) of the first macromolecular structure. [00149] In some embodiments, the first particle comprises a macromolecule structure comprising a co-polymer comprising any number of units represented in Table 2.
WSGR Docket No.53344-792.601
[00150] In some embodiments, the copolymer comprises monomer 12 and monomer 13. In some embodiments, the copolymer comprises monomer 12, monomer 13 and methacrylic acid. In some embodiments, the copolymer comprises monomer 12 and monomer 13 and monomer 14. For instance, the copolymer may comprise monomer 14 in an amount of less than 10% (e.g., less than 8%, 6%, or 5%) by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of less than 8% by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of less than 6%. In some embodiments, the copolymer comprises monomer 14 in an amount of less than 5% by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of less than 4% by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of at least 2% by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of at least 3% by weight. In some embodiments, the copolymer comprises monomer 14 in an amount of at least 4% by weight. [00151] In some embodiments, the polymers or copolymers (e.g., comprised on the particles) provided herein may comprise any suitable molecular weight. In some embodiments, the polymers or copolymers comprise a molecular weight of from about 0.1 kDa to about 500 kDa. In some embodiments, the polymers or copolymers comprise a molecular weight of at least 0.1 kDa (e.g.,
WSGR Docket No.53344-792.601 at least 1 kDa, 5 kDa, 10 kDa, 20 kDa, 25 kDa, 50 kDa, 100 kDa, 250 kDa, or at least 500 kDa). In some embodiments, the polymers or copolymers comprise a molecular weight of at most 1000 kDa (e.g., at most 900 kDa, 800 kDa, 750 kDa, 600 kDa, 500 kDa, 250 kDa, 100 kDa, 75 kDa, 50 kDa, 40 kDa, 30 kDa, 25 kDa, 20 kDa, 15 kDa, or at most 10 kDa). In some embodiments, the polymer or copolymer comprises a molecular weight of about 0.1 kDa to about 500 kDa, about 0.5 kDa to about 250 kDa, about 0.5 kDa to about 100 kDa, about 0.5 kDa to about 70 kDa, 0.5 kDa to about 10 kDa, 0.5 kDa to about 15 kDa, or about 1 kDa to about 25 kDa. As used herein, “molecular weight” may refer to number average molecular weight or weight average molecular weight. [00152] In some embodiments, the polymers or copolymers provided herein may comprise any suitable number of recurring units. In some embodiments, the polymer or copolymer comprises from about 1 to about 1,000 recurring units. In some embodiments, the polymer or copolymer comprises at least 1 (e.g., at least 10, 50, 100, 250, 500, 750, or at least 1,000) recurring units. In some embodiments, the polymer or copolymer comprises at most 2,500 (e.g., at most 1,000, 750, 500, 250, 100, 75, 50, 25, or at most 10) recurring units. In some embodiments, the polymer or copolymer comprises from about 1 to about 100 recurring units. In some embodiments, the polymer or copolymer comprises from about 1 to about 250 (e.g., about 1 to about 500, about 1 to about 1,000, about 100 to about 1,000, about 10 to about 500, about 25 to about 750, or about 100 to about 500) recurring units. [00153] In some embodiments, the particles (e.g., comprising macromolecule structures) provided herein comprise a surface. In some embodiments, the first particle (e.g., comprising a macromolecule structure) comprises a surface. In some embodiments, the second particle (e.g., comprising a macromolecule structure) comprises a surface. In some embodiments, the surface of the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) are the same. In some embodiments, the surface of the first particle (e.g., comprising a macromolecule structure) and the second particle (e.g., comprising a macromolecule structure) are different. [00154] In some embodiments, the surfaces herein comprise a particle. In some embodiments, the particles comprise a surface. In some embodiments, the particle is a microparticle. In some embodiments, the particle is a nanoparticle. [00155] In some embodiments, the particle is magnetic, for instance comprising any magnetic material suitable according to one of skill in the art. In some embodiments, the particle is paramagnetic, or comprises a paramagnetic material. In some embodiments, the particle is superparamagnetic or comprises a superparamagnetic material.
WSGR Docket No.53344-792.601 [00156] In some embodiments, the particle comprises a metal material, such as but limited to a metal chalcogenide (e.g., metal oxide), metal halide. In some embodiments, the metal material comprises any one of or any combination of gold, silver, copper, nickel, cobalt, palladium, platinum, iridium, osmium, rhodium, ruthenium, rhenium, vanadium, chromium, manganese, niobium, molybdenum, tungsten, tantalum, iron, and cadmium. In some embodiments, the particle comprises an iron chalcogenide. In some embodiments, the particle comprises iron oxide. In some embodiments, the iron oxide is magnetite. In some embodiments, the iron oxide is maghemite. In some embodiments, the particle comprises a superparamagnetic iron oxide particle (e.g., nanoparticle). [00157] In some embodiments, the particle comprises a core-shell structure. In some embodiments, the core of the core-shell structure comprises a paramagnetic material. In some embodiments, the particle comprises an iron oxide core. In some embodiments, the iron oxide core comprises magnetite. In some embodiments, the iron oxide core comprises maghemite. In some embodiments, the iron oxide core is functionalized with linking (e.g., tethering) moieties and/or polymers or copolymers provided elsewhere herein (e.g., bound covalently or non- covalently). In some embodiments, the particle comprises a silica shell. In some instances, the silica shell is functionalized with linking (e.g., tethering) moieties and/or polymers or copolymers provided elsewhere herein (e.g., bound covalently or non-covalently). In some embodiments, the particle comprises iron oxide crystals. In some embodiments, the particle comprises polystyrene. In some embodiments, the particle comprises iron oxide crystals embedded in a polystyrene core. [00158] In some embodiments, the particles (e.g., comprising macromolecule structures) (e.g., first particle (e.g., comprising a macromolecule structure)) provided herein comprise the structure:
[00159] In some embodiments, the surface (e.g., of the particle) is at least partially coated with silica. In some instances, such as when the surface is at least partially coated with silica, the particles (e.g., comprising macromolecule structures) (e.g., first particle (e.g., comprising a macromolecule structure)) provided herein comprises the structure:
[00160] In some embodiments,
is the surface (e.g., a surface described elsewhere herein). [00161] In some embodiments, L is a linker. [00162] In some embodiments, A is a polymer or copolymer comprising (e.g., randomly distributed) monomers of Formulas (D), (E), (E-A), or represented in Table 2. In some
WSGR Docket No.53344-792.601 embodiments, A is a copolymer comprising randomly distributed monomers of Formulas (D), (E), (E-A), or represented in Table 2. [00163] In some embodiments, the particles (e.g., comprising macromolecule structures) (e.g., second particle (e.g., comprising a macromolecule structure)) provided herein comprise the structure:
[00164] In some embodiments, the surface (e.g., of the particle) is at least partially coated with silica. In some instances, such as when the surface is at least partially coated with silica, the macromolecule structures (e.g., second macromolecule structure) provided herein comprises the structure:
[00165] In some embodiments, is the surface (e.g., a surface described elsewhere herein). [00166] In some embodiments, L is a linker. [00167] In some embodiments, B is a polymer or copolymer comprising (e.g., randomly distributed) monomers or Formulas (A)-(C), (A-A), (A-B), (A-C), (A-D), or represented in Table 1. [00168] In some embodiments, provided herein are compositions comprising a combination of:
[00169] In some embodiments, L, A, B, and are described elsewhere herein. [00170] In some embodiments, the linkers provided herein comprise optionally substituted alkylene (e.g., C1-C20 alkylene), optionally substituted heteroalkylene (e.g., C1-C20 heteroalkylene), or optionally substituted aralkylene (e.g., C1-C20 aralkylene). In some embodiments, the linker comprises optionally substituted C1-C20 alkylene (e.g., C1-C12, C1-C10, or C1-C6). In some embodiments, the linker comprises C1-C20 heteroalkylene. In some embodiments, the linker comprises C1-C20 aralkylene. [00171] In some embodiments, provided herein are compositions comprising a combination of:
WSGR Docket No.53344-792.601
[00172] In some embodiments, provided herein are compositions comprising a combination of:
[00173] In some embodiments, provided herein are compositions comprising a combination of:
[00174] In some embodiments, provided herein are compositions comprising a combination of:
[00175] In some embodiments, L is a linker.
WSGR Docket No.53344-792.601 [00176] In some instances, the terminating alkylene acts as a cross-linker. [00177] In some embodiments, provided herein are compositions comprising a (e.g., first) particle (e.g., comprising a macromolecule structure) comprising one or more units represented by Formulas (A)-(C), (A-A), (A-B), (A-C), (A-D), or represented in Table 1, attached (e.g., covalently) to a surface described elsewhere herein. In some embodiments, provided herein are compositions comprising a (e.g., second) particle (e.g., comprising a macromolecule structure) comprising one or more units represented by Formulas (D), (E), (E-A), or represented in Table 2, attached (e.g., covalently) to a surface described elsewhere herein. In some embodiments, provided herein are compositions comprising a (e.g., first) particle (e.g., comprising a macromolecule structure) comprising one or more units represented by Formulas (A)-(C), (A-A), (A-B), (A-C), (A-D), or represented in Table 1, attached (e.g., covalently) to a surface described elsewhere herein, and a (e.g., second) particle (e.g., comprising a macromolecule structure) comprising one or more units represented by Formulas (D), (E), (E-A), or represented in Table 2, attached (e.g., covalently) to a surface described elsewhere herein. [00178] In some instances, the particles (e.g., comprising macromolecule structures) provided herein, to be used in any of the methods, systems, or kits provided herein are provided in PCT App. No. PCT/US2023/075863, which is incorporated by reference herein in its entirety. [00179] The particle size (e.g., diameter) can be measured by dynamic light scattering (DLS) as an indirect measure of size. The DLS measurement can be an ‘intensity-weighted’ average, which means the size distribution that the mean is calculated from can be weighted by the sixth power of radius. This can be referred to herein as ‘z-average’ or ‘intensity-mean’. Particle size can also be measured by electron microscopy (e.g., SEM, TEM). [00180] In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a diameter (e.g., particle size) of from about 200 nm to about 1000 nm. In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a diameter (e.g., particle size) of from about 300 nm to about 600 nm. In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise a diameter of from about 200 nm to about 800 nm, from about 200 nm to about 600 nm, about 300 nm to about 1000 nm, about 300 nm to about 700 nm, or about 400 nm to about 500 nm. In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a diameter of from about 400 nm to about 500 nm. In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a diameter of from about 410 nm to about 460 nm. In some embodiments, the particles provided herein have a diameter of about 350 nm to about 460 nm. In some embodiments, the particles provided herein have a diameter of about 370 nm to about 445 nm. In some embodiments, the particles (e.g.,
WSGR Docket No.53344-792.601 comprising the macromolecule structures) comprise a diameter of at least 100 nm (e.g., at least 200 nm, 300 nm, 400 nm, 410 nm, 420 nm, 430 nm, 440 nm, 450 nm, 460 nm, 470 nm, 480 nm, 500 nm, 600 nm, 700 nm, 750 nm, 800 nm, 900 nm, or at least 1000 nm). In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise a diameter of at most 1000 nm (e.g., at most 900 nm, at most 800 nm, at most 700, at most 600 nm, 500 nm, 490 nm, 480 nm, 470 nm, 460 nm, 450 nm, 440 nm, 430 nm, 420 nm, 410 nm, or 400 nm). In some embodiments, the particles (e.g., comprising the macromolecule structures) herein comprise a diameter of about 410 nm, 411 nm, 412 nm, 413 nm, 414 nm, 415 nm, 416 nm, 417 nm, 418 nm, 419 nm, 420 nm, 421 nm, 422 nm, 423 nm, 424 nm, 425 nm, 426 nm, 427 nm, 428 nm, 429 nm, 430 nm, 431 nm, 432 nm, 433 nm, 434 nm, 435 nm, 436 nm, 437 nm, 438 nm, 439 nm, 440 nm, 441 nm, 442 nm, 443 nm, 444 nm, 445 nm, 446 nm, 447 nm, 448 nm, 449 nm, 450 nm, 451 nm, 452 nm, 453 nm, 454 nm, 455 nm, 456 nm, 457 nm, 458 nm, 459 nm, 460 nm, 461 nm, 462 nm, 463 nm, 464 nm, 465 nm, 466 nm, 467 nm, 468 nm, 469 nm, or 470 nm. In some embodiments, the particle sizes of the first particle and the second particle are the same. In some embodiments, the particle sizes of the first particle and the second particle are different. In some embodiments, the size of the first particle is about 440 nm (e.g., about 442 nm), such as described in Example 1. In some embodiments, the size of the second particle is about 450 nm (e.g., 446 nm), such as described in Example 2. In some embodiments, the size of the particle depends on the reaction time and wt% of the polymer on the particle. In some embodiments, the diameter of the first particle is about 370 nm to about 445 nm. In some embodiments, the diameter of the second particle is about 370 nm to about 445 nm. [00181] In some embodiments, the particles described herein are freeze dried. In some instances, the particles are freeze dried before being supplied in the kits described herein. The particles comprised in the kits herein may be freeze dried particles which are configured for resuspension by a user. In some embodiments, the resuspended particles, such as after freeze drying or lyophilization have a diameter that is about 20 nm greater than before freeze drying or lyophilization. In some embodiments, the resuspended particles have an average diameter of about 390 nm to about 470 nm. In some embodiments, the resuspended first particles have an average diameter of about 390 nm to about 470 nm. In some embodiments, the resuspended second particles have an average diameter of about 390 nm to about 470 nm. [00182] In some embodiments, the diameter (e.g., as measured by DLS) is the average diameter. [00183] In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise homogenous or heterogenous size distribution. In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a homogenous size distribution. In some instances, polydispersity index (PDI), is used as a measure
WSGR Docket No.53344-792.601 for size distribution. PDI may be measured by techniques such as dynamic light scattering (DLS). A low PDI indicates a more homogenous size distribution and a high PDI indicates a more heterogenous size distribution. In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a PDI of at least 0.01 (e.g., at least 0.025, 0.05, 0.075, 0.1, 0.125, 0.15, 0.175, at least 0.2, or at least 0.5). In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a PDI of at most 0.5 (e.g., at most 0.4, 0.35, 0.3, 0.25, 0.2, 0.175, 0.15, 0.125, or 0.1). In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a PDI of from 0.05 to 0.2. In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise a PDI of from about 0.1 to about 0.2. In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise a PDI of about 0.07, 0.08, 0.09, 0.1, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.25, or 0.25. In some embodiments, the first macromolecule structure comprises a PDI of about 0.12, such as described in Example 1. In some embodiments, the second macromolecule structure comprises a PDI of about 0.14, such as described in Example 2. In some embodiments, the particles have a PDI of less than 0.2. [00184] In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise varying amounts of the polymer or co-polymer, such as any amount suitable according to one of skill in the art. In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise at least 1% w/w of the polymer or co-polymer. In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise at least 2.5% w/w (e.g., 3% w/w, 4% w/w, 5% w/w, 6% w/w, 8% w/w, 10% w/w, 12% w/w, 15% w/w, 20% w/w, or at least 25% w/w) of the polymer or copolymer. In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise at most 35% w/w (e.g., at most 30% w/w, 25% w/w, 20% w/w, 18% w/w, 15% w/w, 12% w/w, 10% w/w, 8% w/w, 7% w/w, 5% w/w, or 2.5% w/w) of the polymer or copolymer. In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise from about 2.5% w/w to about 30% w/w of the polymer or copolymer. In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise from about 2.5% w/w to about 25% w/w (e.g., 5% w/w to about 25% w/w, 5% w/w to about 20% w/w, 5% w/w to about 15% w/w, 10% w/w to about 20% w/w, or about 6% w/w to about 12% w/w). In some embodiments, the macromolecule structure comprises about 1% w/w, 2% w/w, 3% w/w, 4% w/w, 5% w/w, 6% w/w, 7% w/w, 8% w/w, 9% w/w, 10% w/w, 11% w/w, 12% w/w, 13% w/w, 14% w/w, 15% w/w, 16% w/w, 17% w/w, 18% w/w, 19% w/w, or 20% w/w. In some embodiments, such as described in Example 1, the macromolecule structure comprises about 17% w/w of the polymer or copolymer. In some embodiments, such as described
WSGR Docket No.53344-792.601 in Example 2, the macromolecule structure comprises about 13% w/w of the polymer or copolymer. In some embodiments, such as described in Example 2, the macromolecule structure comprises from about 6% w/w to about 13% w/w of the polymer or copolymer. [00185] In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein comprise various morphologies. In some instances, the particles (e.g., comprising the macromolecule structures) may be spherical, colloidal, square shaped, rods, wires, cones, pyramids, or oblong. [00186] In some embodiments, the particles described herein are magnetic particles. [00187] In some embodiments, provided herein is a composition comprising a plurality of particles (e.g., nanoparticles or microparticles provided herein). In some embodiments, the composition comprises an outer polymer surface and a magnetic core. In some embodiments, the outer polymer surface comprises any of the polymers or copolymers provided herein. In some embodiments, the outer polymer surface comprises silica and any of the polymers or copolymers provided herein. In some embodiments, the outer polymer surface comprises ethylene glycol dimethacrylate, monomer 6, and at least one of monomer 7, monomer 8, monomer 9, and glycidyl methacrylate. In some embodiments, the outer polymer surface comprises ethylene glycol dimethacrylate. In some embodiments, the outer polymer surface comprises monomer 6. In some embodiments, the outer polymer surface comprises one or any combination of monomer 7, monomer 8, monomer 9, and glycidyl methacrylate. Methods of Preparation [00188] Provided herein are methods of preparing the any of the particles (e.g., comprising the macromolecule structures) or compositions provided herein. [00189] In some embodiments, provided herein are methods of preparing a mixture of at least two particles (e.g., comprising the macromolecule structures), such as particles (e.g., comprising the macromolecule structures) provided elsewhere herein. In some embodiments, the at least two particles (e.g., comprising the macromolecule structures) comprise recurring units of a first monomer and a second monomer or a first monomer and a third monomer. In some embodiments, the at least two particles (e.g., comprising the macromolecule structures) comprise recurring units of a first monomer and a second monomer or a third monomer and fourth monomer. [00190] In some embodiments, preparation of a first macromolecule structure is described in Example 1 and FIG.1. [00191] In some embodiments, preparation of a second macromolecule structure is described in Example 2 and FIG.2.
WSGR Docket No.53344-792.601 [00192] In some embodiments, the first monomer and the fourth monomer are the same. In some embodiments, the first monomer comprises:
. [00193] In some embodiments, the first monomer (such as when acting as a crosslinking monomer) comprises:
. [00194] In some embodiments, the fourth monomer comprises:
. [00195] In some embodiment, the fourth monomer (such as when acting as a crosslinking monomer) comprises:
. [00196] In some embodiments, the second monomer comprises a unit represented by Formulas (A)-(C), (A-A), (A-B), (A-C), (A-D), or represented in Table 1. [00197] In some embodiments, the third monomer comprises a unit represented Formulas (D), €, (E-A), or represented in Table 2.
WSGR Docket No.53344-792.601 [00198] In some embodiments, the methods comprise obtaining a first macromolecule structure comprising a neutral to negative surface charge, such as by a method described herein. In some embodiments, the first macromolecule structure is a first macromolecule structure as described elsewhere herein. [00199] In some embodiments, the methods comprise obtaining a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure, such as by a method described herein. In some embodiments, the second macromolecule structure is a second macromolecule structure as described elsewhere herein. [00200] In some embodiments, the methods comprising forming a mixture comprising the first and second particles (e.g., comprising the macromolecule structures). In some embodiments, the mixture of the first and second particles (e.g., comprising the macromolecule structures) are prepared in a suspension solution, such as described elsewhere herein. In some embodiments, the mixture of the first and second particles (e.g., comprising the macromolecule structures) are prepared in an aqueous solution. [00201] In some instances, the formation of a mixture comprising the first and second macromolecule structure comprise sonication, such as to disperse the particles (e.g., comprising the macromolecule structures). [00202] In some embodiments, the methods comprise lyophilizing (e.g., freeze drying) the two or more particles (e.g., comprising the macromolecule structures), such as to provide a powder comprising the combination of the two or more particles (e.g., comprising the macromolecule structures). [00203] In some embodiments, provided herein is a method of preparing a macromolecule structure comprises recurring units of at least a first component and a second component. In some embodiments, the method comprises preparing macromolecule structure comprising recurring units of at least a first component and a second component. In some embodiments, the macromolecule structure comprises one or more units represented by Formulas (A)-(C), (A-A), (A-B), (A-C), (A-D), or represented in Table 1, attached (e.g., covalently) to a surface described elsewhere herein. In some embodiments, the macromolecule structure comprises one or more units represented by Formulas (D), (E), (E-A), or represented in Table 2, attached (e.g., covalently) to a surface described elsewhere herein. [00204] In some embodiments, the method comprises providing a mixture of monomers in a solvent. In some embodiments, the mixture of monomers comprises a first monomer and a second monomer. [00205] In some embodiments, the first monomer comprises the structure:
WSGR Docket No.53344-792.601
[00206] In some embodiments, q is an integer from 1 to 6. In some embodiments, q is 1. In some embodiments, q is 2. In some embodiments, q is 3. In some embodiments, q is 4. In some embodiments, q is 5. In some embodiments, q is 6. [00207] In some embodiments, the first monomer is glycidyl methacrylate. In some embodiments, the monomer is selected from hydroxyalkyl methacrylate, aminoalkyl methacrylate, alkynyl methacrylate, glycidylalkyl methacrylate, hydroxyalkyl acrylate, aminoalkyl acrylate, alkynyl acrylate or glycidylalkyl acrylate. [00208] In some embodiments, the second monomer comprises the structure:
[00209] In some embodiments, m is an integer from 1 to 6. In some embodiments, m is 1. In some embodiments, m is 2. In some embodiments, m is 3. In some embodiments, m is 4. In some embodiments, m is 5. In some embodiments, m is 6. [00210] In some embodiments, the second monomer is ethyleneglycol dimethacrylate. In some embodiments, the second monomer comprises a crosslinking monomer. In some embodiments, the crosslinking monomer is a diene. In some embodiments, the cross-linking monomer comprises the structure:
[00211] In some embodiments, R1 is hydrogen or C1-C6 alkyl. In some embodiments, R1 is hydrogen. In some embodiments, R1 is C1-C6 alkyl. In some embodiments, R2 is hydrogen or C1- C6 alkyl. In some embodiments, R2 is hydrogen. In some embodiments, R2 is C1-C6 alkyl. In some embodiments, R3 is hydrogen or C1-C6 alkyl. In some embodiments, R3 is hydrogen. In some embodiments, R3 is C1-C6 alkyl. In some embodiments, R3 is methyl. In some embodiments, R1’ is hydrogen or C1-C6 alkyl. In some embodiments, R1’ is hydrogen. In some embodiments, R1’ is C1-C6 alkyl. In some embodiments, R2’ is hydrogen or C1-C6 alkyl. In some embodiments, R2’ is
WSGR Docket No.53344-792.601 hydrogen. In some embodiments, R2’ is C1-C6 alkyl. In some embodiments, R3’ is hydrogen or C1- C6 alkyl. In some embodiments, R3’ is hydrogen. In some embodiments, R3’ is C1-C6 alkyl. In some embodiments, R3’ is methyl. [00212] In some embodiments, the first and/or second monomers comprise one or more impurities. In some instances, the impurities are polymerized and are comprised within the macromolecule chain. In some embodiments, impurities include impurities within the first monomer and second monomer or non-fully reacted monomers within the polymers or copolymers formed after functionalization. [00213] In some embodiments, the methods comprise contacting a surface and the mixture of monomers (e.g., comprising a first monomer and a second monomer), thereby producing a reaction mixture. In some embodiments, the surface is a surface as provided elsewhere herein. In some embodiments, the surface comprises polymerizable olefins that may polymerize with the mixture of monomers, thus covalently attaching the monomers, and the resulting polymer or copolymer, to the surface. In some embodiments, the surface is reacted with one or more monomers to create a polymer coated surface. In some embodiments, the polymer coated surface may undergo polymerization with the mixture of monomers provided herein. [00214] In some embodiments, contacting is in an organic solvent. In some embodiments, an organic solvent is an organic solvent as described elsewhere herein. In some embodiments, for example, the organic solvent comprises THF, acetonitrile, DMF, DMSO, ethyl acetate, benzene, cyclohexane, or any combination thereof. In some embodiments, the organic solvent comprises acetonitrile. In some embodiments, the organic solvent comprises DMF. [00215] In some embodiments, the method comprises polymerizing the mixture of monomers to produce a macromolecule immobilized to the surface. In some embodiments, polymerizing comprises any one of free radical polymerization, In other embodiments, polymerization comprises “Living”/controlled free-radical polymerization, atom transfer radical polymerization (ATRP), emulsion polymerization, or precipitation polymerization. In some embodiments, polymerizing comprises free radical polymerization. In some embodiments, polymerization comprises ATRP. In some embodiments, polymerization comprises emulsion polymerization. In some embodiments, polymerization comprises precipitation polymerization. In some embodiments, polymerization comprises “Living”/controlled free-radical polymerization. [00216] In some embodiments, polymerization is initiated with a radical initiator. In some instances, the radical initiator comprises azobisisobutyronitrile (AIBN). [00217] In some embodiments, the method comprises contacting the macromolecule immobilized to the surface and an amine, thereby producing an aminated macromolecule. In some
WSGR Docket No.53344-792.601 embodiments, the amine is an alkylamine (e.g., comprising from 1 to 6 carbons (e.g., a C1-C6 alkylamine). In some embodiments, the amine comprises the structure:
[00218] In some embodiments, the amine is an alkylenediamine. In some embodiments, the amine is ethylenediamine. [00219] In some embodiments, R3 and p are described elsewhere herein. In some embodiments, R3 is each independently hydrogen or optionally substituted C1-C8 alkyl. In some embodiments, when an amine is contacted with the macromolecule immobilized to the surface, the resulting macromolecule structure comprises the following structure:
[00220] In some embodiments, q and p are described elsewhere herein. In some embodiments, R3 is each independently hydrogen or optionally substituted C1-C8 alkyl. [00221] In some embodiments, the method comprises contacting the aminated macromolecule with an anhydride. In some embodiments, the anhydride is optionally substituted with R2. In some embodiments, R2 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. In some embodiments, R2 is C1-C10 alkenyl. [00222] In some embodiments, the anhydride comprises a substituted succinic anhydride. In some embodiments, the anhydride comprises octenyl succinic anhydride. In some embodiments, upon contacting with octenyl succinic anhydride, the monomers comprise one or more of the following structures:
WSGR Docket No.53344-792.601
[00223] In some embodiments, any one of the steps in a method provided herein may be completed under inert conditions. In some embodiments, the inert conditions comprise nitrogen gas (N2). [00224] In some embodiments, any one of the steps in a method provided herein may comprise heating. In some embodiments, the method comprises heating to multiple (e.g., 2 or more, or 3 or more) different temperatures during the course of the method. In some embodiments, the method comprises heating to at least 40°C (e.g., 50°C, 60°C, 70°C, 80°C, 90°C, or at least 100°C). In some embodiments, the method comprises heating to at most 120°C (e.g., 110°C, 100°C, 90°C, 80°C, 70°C, 60°C, or 50°C). In some embodiments, the method comprises heating to from about 40°C to about 100°C, 50°C to about 90°C, 50°C to about 80°C, 60°C to about 90°C, 60°C to about 80°C, or 65°C to about 95°C. In some embodiments, the method comprises heating to a temperature of about 40°C, 50°C, 60°C, 65°C, 70°C, 75°C, 80°C, 85°C, 90°C, or 100°C. In some embodiments, the method comprises heating to a temperature of about 60°C. In some embodiments, the method comprises heating to a temperature of about 80°C. [00225] In some embodiments, the methods provided herein comprise quenching (e.g., the reaction). In some embodiments, the quenching is completed using a quenching reagent. In some embodiments, the quenching is completed using, for example, 1,4-benzoquinone. [00226] In some embodiments, the methods provided herein further comprise washing between steps, such as with 1, 2, 3, 4, 5, or more washes with an organic solvent, such as an organic solvent described elsewhere herein. In some embodiments, washing comprises 1, 2, 3, 4, 5 or more washes with any combination of organic solvent and aqueous solvent.
WSGR Docket No.53344-792.601 [00227] In some embodiments, between steps in the methods provided herein, the method comprises sonicating the one or more particles (e.g., comprising the macromolecule structures) in a solvent. [00228] In the methods provided herein, the different monomers may be provided in any suitable ratio. In some embodiments, the first and the second monomer are provided in an amount of about 1:10 to about 10:1 (e.g., 1:5 to 5:1, 1:3 to 3:1, 1:1 to 1:5, or 1:5 to 1:1). In some embodiments, the first and second monomer are provided in a ratio of about 1:1. In some embodiments, the first and second monomer are provided at a ratio of about 1:3, 1:2, 1:1, 2:1, or 3:1. [00229] Methods provided herein may comprise steps of polymerization and/or subsequent reactions on the polymer. The methods provided herein may comprise one or more steps of: polymerizing a glycidyl methacrylate to form a polymer, reacting the polymer with an alkylene diamine to form an aminated polymer, and reacting the aminated polymer with an optionally substituted succinic anhydride. In some embodiments, polymerizing the glycidyl methacrylate comprises polymerizing the glycidyl methacrylate with a divinyl cross-linking monomer. In some embodiments, the alkylene diamine is ethylene glycol. In some embodiments, the optionally substituted succinic anhydride is an alkenylsuccinic anhydride. In some embodiments, the optionally substituted succinic anhydride is an C4-C10 alkenylsuccinic anhydride. In some embodiments, the optionally substituted succinic anhydride is octenylsuccinic anhydride. In some embodiments, provided herein are compositions obtained by a method comprising polymerizing 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles. In some embodiments, provided herein are compositions obtained by a method comprising comprise one or more steps of: polymerizing glycidyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl functionalized magnetic particles to form polymer-coated particles. In some embodiments, the method comprises reacting the polymer-coated magnetic particles with an alkylene diamine to form amine-modified magnetic particles. In some embodiments, the method comprises reacting the amine-modified magnetic particles with an optionally substituted succinic acid anhydride. Methods of Isolating, Purifying, and Assaying Biomolecules [00230] Provided herein are methods of isolating or purifying one or more biomolecules comprised in a biological sample using any of the particles (e.g., comprising the macromolecule structures) described elsewhere herein. [00231] In some embodiments, the particles (e.g., comprising the macromolecule structures) provided herein can be used in the methods disclosed in U.S. Patent Nos.10,866,242, 11,428,688,
WSGR Docket No.53344-792.601 11,906,526, and PCT App. Nos. PCT/US2021/042254 and PCT/US2023/068457, each of which is incorporated by reference herein in its entirety. [00232] In some embodiments, provided herein is a method of isolating (e.g., purifying) one or more biomolecule from a biological sample. [00233] In some embodiments, a biological sample herein comprises plasma, serum, urine, cerebrospinal fluid, synovial fluid, tears, saliva, whole blood, milk, nipple aspirate, ductal lavage, vaginal fluid, nasal fluid, ear fluid, gastric fluid, pancreatic fluid, trabecular fluid, lung lavage, sweat, crevicular fluid, semen, prostatic fluid, sputum, fecal matter, bronchial lavage, fluid from swabbings, bronchial aspirants, fluidized solids, fine needle aspiration samples, tissue homogenates, lymphatic fluid, cell culture samples, or any combination thereof. In some embodiments, a biological sample comprises plasma, serum, or blood. In some embodiments, a biological sample comprises blood. In some embodiments, a biological sample comprises plasma. In some embodiments, a biological sample comprises serum. In some embodiments, the biological sample is a biofluid. In some embodiments, the biological sample is a cell-free biofluid. [00234] In some embodiments, the method comprises contacting a biological sample comprising one or more biomolecules with one, two or more particles (e.g., comprising the macromolecule structures) (e.g., such as particles (e.g., comprising the macromolecule structures) provided elsewhere herein). In some instances, contacting the one or more biomolecules with the one, two or more particles (e.g., comprising the macromolecule structures) results in the formation of at least two biomolecule corona. In some embodiments, one biomolecule corona forms on one of the particles (e.g., comprising the macromolecule structures) (e.g., a first particle (e.g., comprising a macromolecule structure)). In some embodiments, a second biomolecule corona forms on the second macromolecule structure (e.g., the second macromolecule structure). [00235] In some embodiments, the method comprises contacting the biological sample with one or more particles described herein (e.g., such as two distinct particles (e.g., a first particle and a second particle)). In some embodiments, the method comprises contacting the biological sample with one or more particles, wherein the particles are present at any suitable concentration. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at least 0.4 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at least 0.5 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at least 0.55 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at least 0.6 mg/mL. In some embodiments, the first and second particles are contacted with the
WSGR Docket No.53344-792.601 biological sample at a total concentration (e.g., of the first and second particle) of at least 0.65 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at least 0.7 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at most 1 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at most 0.9 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at most 0.85 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of 0.8 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at most 0.75 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of at most 0.7 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of about 0.5 mg/mL to 1 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of 0.6 mg/mL to 0.8 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of about 0.5 mg/mL, about 0.55 mg/mL, about 0.6 mg/mL, about 0.65 mg/mL, about 0.7 mg/mL, about 0.75 mg/mL, about 0.8 mg/mL, about 0.85 mg/mL, about 0.9 mg/mL, or about 0.95 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of about 0.7 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of about 0.45 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of about 0.53 mg/mL. In some embodiments, the first and second particles are contacted with the biological sample at a total concentration (e.g., of the first and second particle) of about 0.6 mg/mL. [00236] In some embodiments, the method comprises contacting the biological sample with a first particle. In some embodiments, the method comprises contacting the biological sample with a first particle at any suitable concentration. In some embodiments, the method comprises contacting the biological with a first particle, wherein the first particles are at a concentration of at least 0.05 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of at least 0.08 mg/mL.
WSGR Docket No.53344-792.601 In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of at least 0.1 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of at least 0.12 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of at most 0.3 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of at most 0.25 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of at most 0.2 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of from 0.05 mg/mL to 0.2 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of from 0.1 mg/mL to 0.2 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of about 0.1 mg/mL, 0.12 mg/mL, 0.13 mg/mL, 0.14 mg/mL, 0.15 mg/mL, 0.16 mg/mL, 0.17 mg/mL, 0.18 mg/mL, 0.19 mg/mL, or 0.2 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of about 0.14 mg/mL. In some embodiments, the method comprises contacting the biological sample with a first particle, wherein the first particles are at a concentration of about 0.09 mg/mL. [00237] In some embodiments, the method comprises contacting the biological sample with a second particle. In some embodiments, the method comprises contacting the biological sample with a second particle at any suitable concentration. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at least 0.4 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at least 0.44 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at least 0.48 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at least 0.5 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at least 0.52 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at least 0.54 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles
WSGR Docket No.53344-792.601 are at a concentration of at least 0.55 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at most 0.7 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at most 0.65 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at most 0.6 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at most 0.58 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of at most 0.56 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of about 0.4 mg/mL to about 0.7 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of about 0.5 mg/mL to about 0.6 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of about 0.5 mg/mL, 0.51 mg/mL, 0.52 mg/mL, 0.53 mg/mL 0.54 mg/mL, 0.55 mg/mL, 0.56 mg/mL, 0.57 mg/mL, 0.58 mg/mL, 0.59 mg/mL, or 0.6 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of about 0.56 mg/mL. In some embodiments, the method comprises contacting the biological sample with the second particle, wherein the second particles are at a concentration of about 0.36 mg/mL. [00238] In some embodiments, the method comprises contacting a biological sample (e.g., plasma or serum) comprising one or more biomolecules (e.g., proteins) with the magnetic particles in any one of the compositions provided herein. [00239] As used herein, a “biomolecule corona” refers to one or more biomolecules adsorbed to a surface of a macromolecule structure described herein. [00240] In some embodiments, multiple (e.g., a plurality) of biomolecules may be adsorbed to particles (e.g., comprising the macromolecule structures) provided herein. In some embodiments, a plurality of unique biomolecules may be adsorbed to a macromolecule structure. In some embodiments, at least 5 (e.g., 10, 20, 30, 40, 60, 80, 100, 200, 400, 600, 800, or at least 1000) (e.g., different) biomolecules are adsorbed to the macromolecule structure. In some embodiments, at most 5000 (e.g., 4000, 3000, 2000, 1000, 800, 600, 400, 200, 100, 60, or at most 20) (e.g., different) biomolecules are adsorbed to a macromolecule structure provided herein. In some embodiments, about 5 to about 5000, about 10 to about 2000, about 100 to about 2000, or about 100 to about 1000 (e.g., different) biomolecules are adsorbed to a macromolecule structure
WSGR Docket No.53344-792.601 provided herein. In some embodiments, at least 100 (e.g., different) biomolecules are adsorbed to a macromolecule structure provided herein. [00241] In some embodiments, the method comprises eluting one or more biomolecules from the at least two particles (e.g., comprising the macromolecule structures). In some embodiments, eluting thereby provides the one or more isolated biomolecules. In some embodiments, the methods comprise eluting the one or more digested biomolecules from the (e.g., third) particle. [00242] In some embodiments, the at least two particles (e.g., comprising the macromolecule structures) comprise a first macromolecule structure comprising a neutral to negative surface charge (e.g., such as a macromolecule structure provided elsewhere herein). [00243] In some embodiments, the at least two particles (e.g., comprising the macromolecule structures) comprise a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure (e.g., such as a macromolecule structure provided elsewhere herein). [00244] In some embodiments, the method comprises separating the adsorbed biomolecules (e.g., proteins) and the magnetic particles from the biological sample (e.g., plasma or serum). The separating may enrich the adsorbed biomolecules. [00245] In some embodiments, the method comprises separating the one or more biomolecules and the at least two particles (e.g., comprising the macromolecule structures) from the biological sample. In some embodiments, separating comprises centrifugation, magnetic separation, or a combination thereof. In some embodiments, separating comprises centrifugation. In some embodiments, separation comprises magnetic separation. In some embodiments, magnetic separation is sufficient to separate the particles (e.g., comprising the macromolecule structures) comprising biomolecule coronas, without the need for further separation by centrifugation. [00246] In some embodiments, the methods provided herein comprise digesting, alkylating, and/or lysing the one or more biomolecules to provide digested biomolecules. In some embodiments, the method comprises digesting the one or more biomolecules. In some embodiments, the method comprises digesting the one or more biomolecules of the one or more biomolecule coronas. In some instances, the digested biomolecule are peptides. [00247] In some embodiments, digestion comprises enzymolysis. In some embodiments, digestion comprises the use of trypsin, lysin, serine protease, chymotrypsin, pepsin, thermolysin, proteinase K, or a combination thereof. In some embodiments, the digestion comprises trypsin. In some embodiments, the digestion comprises lysin. In some embodiments, the digestion comprises serine protease. In some embodiments, the digestion comprises chymotrypsin. In some embodiments, the digestion comprises pepsin. In some embodiments, the digestion comprises thermolysin. In some embodiments, the digestion comprises proteinase K. In some embodiments,
WSGR Docket No.53344-792.601 the digestion comprises use of trypsin/lys-C protease mix. In some embodiments, digestion comprises use of trypsin, endoproteinase Lys-C, or a combination thereof. [00248] Digestion may comprise incubation for 1 hour with the digestion reagents described herein (e.g., trypsin, endoproteinase Lys-C, or a combination thereof). The digestion may be followed my separation as described elsewhere herein. The digestion may be followed by magnetic separation. The method may comprise incubating the particles with the biological sample for at least one hour followed by incubation for 1 hour with the digestion reagents described herein. This may be followed by separation, as described elsewhere herein (e.g., magnetic separation). [00249] In some embodiments, digesting comprises contacting the one or more biomolecules with a denaturing agent. In some embodiments, the denaturing agent comprises sodium dodecyl sulfate, acetic acid, trichloroacetic acid, sulfosalicylic acid, sodium bicarbonate, ethanol, formaldehyde, glutaraldehyde, urea, guanidium chloride, lithium perchlorate, 2-mercaptoethanol, dithiothreitol, tris(2-carboxyethyl)phosphine (TCEP), or any combination thereof. In some embodiments, the denaturing agent comprises sodium dodecyl sulfate. In some embodiments, the denaturing agent comprises acetic acid. In some embodiments, the denaturing agent comprises urea. In some embodiments, the denaturing agent comprises guanidium chloride. In some embodiments, the denaturing agent comprises lithium perchlorate. In some embodiments, the denaturing agent comprises 2-mercaptoethanol. In some embodiments, the denaturing agent comprises dithiothreitol. In some embodiments, the denaturing agent comprises TCEP. [00250] In some embodiments, digesting comprises contacting the one or more biomolecules with a reduction agent. In some embodiments, the reduction agent comprises TCEP. In some embodiments, the reduction agent comprises dithiothreitol. In some embodiments, the reduction agent comprises beta-mercaptoethanol. In some embodiments, the reduction agent comprises glutathione. In some embodiments, the reduction agent comprises cysteine. [00251] In some embodiments, digesting comprises contacting the one or more biomolecules with an alkylating agent. In some embodiments, the alkylating agent comprises iodoacetamide, iodoacetic acid, acrylamide, chloroacetamide, or any combination thereof. In some embodiments, the alkylating agent comprises iodoacetamide. In some embodiments, the alkylating agent comprises iodoacetic acid. In some embodiments, the alkylating agent comprises acrylamide. In some embodiments, the alkylating agent comprises chloroacetamide. [00252] In some embodiments, the digesting comprises lysing the one or more biomolecules with a lysis agent. Lysis agents may comprise CHAPS, deoxycholate, Triton™ X-100, NP40, Tween 20, or a combination thereof.
WSGR Docket No.53344-792.601 [00253] In some embodiments, the method comprises separating and optionally digesting the one or more biomolecules and the at least two particles (e.g., comprising the macromolecule structures) from the biological sample. [00254] In some embodiments, the step of eluting comprises digesting the one or more biomolecules. [00255] In some embodiments, the method comprises eluting and optionally digesting, such as via digestion provided elsewhere herein, the adsorbed biomolecules (e.g., proteins) from the magnetic particles, thereby providing one or more isolated biomolecules (e.g., proteins). [00256] In some embodiments, the digested, lysed, and/or alkylated biomolecules are purified. In some embodiments, the methods comprise purifying the one or more digested biomolecules. In some embodiments, purifying the digested biomolecules prepares the biomolecules for mass spectrometry analysis by removing impurities that may interfere with analysis or render the sample unsuitable for analysis by mass spectrometry. [00257] In some embodiments, purifying the one or more digested biomolecules comprises contacting the one or more digested biomolecules with a particle (e.g., a third particle). The particle (e.g., a third particle) may be a particle described herein. The particle (e.g., a third particle) may be a PEGylated particle. The particle (e.g., a third particle) may be a particle described in PCT/US2024/040565, which is incorporated by reference herein in its entirety. In some embodiments, the particle (e.g., a third particle) may have the structure:
WSGR Docket No.53344-792.601
. [00258] In some embodiments, the particle (e.g., third particle) has the structure
. [00259] In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at any suitable concentration such as to purify the digested biomolecules. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of at least 25 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of at least 30 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of at least 35 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of at least 40 mg/mL. In some
WSGR Docket No.53344-792.601 embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of at most 60 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of at most 55 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of at most 50 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of at most 45 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of about 30 mg/mL to about 50 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of about 40 mg/mL to about 50 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of about 40 mg/mL to about 45 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of about 40 mg/mL, about 41 mg/mL, about 42 mg/mL, about 43 mg/mL, about 44 mg/mL, about 45 mg/mL, about 46 mg/mL. about 47 mg/mL, about 48 mg/mL, about 49 mg/mL, or about 50 mg/mL. In some embodiments, the particle (e.g., third particle) is contacted with the digested biomolecules at a concentration of about 42 mg/mL. [00260] In some embodiments, the methods comprise contacting one or more biomolecules with the particles (e.g., comprising the macromolecule structures) in the presence of an organic solvent, such as an organic solvent described elsewhere herein. In some embodiments, the methods comprise contacting one or more biomolecules with the particles (e.g., comprising the macromolecule structures) in the absence of an organic solvent. In some embodiments, the methods comprise contacting one or more biomolecules with the particles (e.g., comprising the macromolecule structures) in the presence of less than 10% by volume of organic solvent. In some embodiments, the methods comprise contacting one or more biomolecules with the particles (e.g., comprising the macromolecule structures) in the presence of less than 5% by volume of organic solvent. In some embodiments, the methods comprise contacting one or more biomolecules with the particles (e.g., comprising the macromolecule structures) in the presence of less than 5% by volume of organic solvent. [00261] In some embodiments, the methods comprise contacting the digested biomolecules with the particle (e.g., a third particle) in the presence of an organic solvent. In some embodiments, the methods comprise contacting the digested biomolecules with the particle (e.g., a third particle) in the absence of an organic solvent. In some embodiments, the methods comprise contacting the digested biomolecules with the particle (e.g., a third particle) in the presence of less than 10% by volume of organic solvent. In some embodiments, the methods comprise contacting the digested biomolecules with the particle (e.g., a third particle) in the presence of less than 5% by volume of
WSGR Docket No.53344-792.601 organic solvent. In some embodiments, the methods comprise contacting the digested biomolecules with the particle (e.g., a third particle) in the presence of less than 5% by volume of organic solvent. [00262] In some embodiments, contacting as provided herein comprises contacting in the presence of a buffer, such as a buffer described elsewhere herein. [00263] In some embodiments, the methods provided herein comprise diluting the one or more biomolecules and the particles (e.g., comprising the macromolecule structures). In some embodiments, the one or more biomolecules and the particles (e.g., comprising the macromolecule structures) are diluted in a buffer, such as a buffer provided elsewhere herein. In some instances, the one or more biomolecules and the particles (e.g., comprising the macromolecule structures) are diluted in an aqueous solution. [00264] In some embodiments, a buffer as provided herein comprises a pH of from about 7 to about 10. In some embodiments, a buffer as provided herein comprises a pH of from about 7 to about 8. In some embodiments, a buffer as provided herein comprises a pH of at least about 8. In some embodiments, a buffer as provided herein comprises a pH of from about 8 to about 10. In some embodiments, a buffer as provided herein comprises a pH of from about 8 to about 9. In some embodiments, the buffer comprises a pH of about 8.5. In some embodiments, a buffer as provided herein comprises a pH of about 7. In some embodiments, a buffer as provided herein comprises a pH of about 7.1. In some embodiments, a buffer as provided herein comprises a pH of about 7.2. In some embodiments, a buffer as provided herein comprises a pH of about 7.3. In some embodiments, a buffer as provided herein comprises a pH of about 7.4. In some embodiments, a buffer as provided herein comprises a pH of about 7.5. In some embodiments, a buffer as provided herein comprises a pH of about 7.6. In some embodiments, a buffer as provided herein comprises a pH of about 7.7. In some embodiments, a buffer as provided herein comprises a pH of about 7.8. In some embodiments, a buffer as provided herein comprises a pH of about 7.9. In some embodiments, a buffer as provided herein comprises a pH of about 8. In some embodiments, the pH of the In some embodiments, a buffer as provided herein comprises a pH of about 6.9. In some embodiments, a buffer as provided herein comprises a pH of about 6.8. In some embodiments, a buffer as provided herein comprises a pH of about 6.7. In some embodiments, a buffer as provided herein comprises a pH of about 6.6. In some embodiments, a buffer as provided herein comprises a pH of about 6.5. In some embodiments, a buffer may be any suitable buffer according to one of skill in the art. In some embodiments, the buffer comprises phosphate buffer, Tris, HEPES, MES, MOPS, TES, CAPS, Bicine, or Bis-Tris. In some embodiments, the buffering agent is CAPS. In some embodiments, the buffering agent is HEPES. In some embodiments, the buffering agent does not comprise a primary amine. Without being bound to any particular theory,
WSGR Docket No.53344-792.601 it is believed the buffering agents with primary amines may interfere with protein (including peptides) quantification methods, which can be used to quantify samples before performing mass spectrometry. [00265] In some embodiments, non-limiting examples of organic solvents provided herein include ethanol, methanol, isopropanol, butanol, dimethylsulfoxide (DMSO), dimethylformamide (DMF), hexane, pentane, benzene, acetonitrile, acetone, acetonitrile, carbon tetrachloride, chloroform, N,N-dimethylacetamide, cyclohexane, diethylene glycol, diethyl ether, ethyl acetate, and tetrahydrofuran (THF). In some embodiments, the organic solvent is tetrahydrofuran. In some embodiments, the organic solvent is dimethylformamide. In some embodiments, the organic solvent is N,N-dimethylacetamide. In some embodiments, the organic solvents provided herein comprise a combination of two or more organic solvents. In some embodiments, the organic solvent comprises an alcohol, acetonitrile, dichloromethane, dimethylformamide (DMF), dimethylsulfoxide (DMSO), ethyl acetate, hexamethylphosphoramide (HMPA), or tetrahydrofuran. In some embodiments, the organic solvent comprises DMF. In some embodiments, the organic solvent comprises acetonitrile. [00266] In some embodiments, eluting comprises the use of an elution buffer, such as a buffer described elsewhere herein. In some embodiments, the elution buffer comprises an aqueous solution. [00267] In some embodiments, eluting comprises use of any organic solvent according to one of skill in the art. In some embodiments, an aqueous solution comprises an organic solvent in an amount of no more than 50 wt% (e.g., 40 wt%, 30 wt%, 20 wt%, 10 wt%, or no more than 5 wt%). In some embodiments, the aqueous solution comprises an organic solvent in an amount of at least 1 wt% (e.g., 2 wt%, 3 wt%, 4 wt%, or at least 5 wt%). In some embodiments, the aqueous solution comprises between 0.1 wt% and 5 wt% of organic solvent. In some embodiments, the aqueous solution comprises between 0.5 wt% and 4 wt% of organic solvent. In some embodiments, the aqueous solution comprises between 1 wt% and 4 wt% of organic solvent. In some embodiments, the aqueous solution comprises about 3 wt% of organic solvent, such as an organic solvent described elsewhere herein. [00268] In some embodiments, the methods provided herein are capable of isolating (e.g., purifying) at least 50 biomolecules. In some embodiments, the methods provided herein are capable of isolating at least 100 (e.g., 250, 500, 750, 1,000, 1,500, 2,000, 2,500, or at least 3000 biomolecules). In some embodiments, the methods provided herein are capable of isolating at least about 1,000 biomolecules. In some embodiments, the methods provided herein are capable of isolating at most 20,000 biomolecules (e.g., at most 15,000, 12,500, 10,000, 8,000, 7,000, 6,000, 5,000, 4,000, 3,000, or at most 2,500) biomolecules. In some embodiments, the methods provided
WSGR Docket No.53344-792.601 herein are capable of isolating from about 100 to about 20,000 biomolecules (e.g., about 100 to about 10,000 biomolecules, about 500 to about 7,500 biomolecules, about 500 to about 5,000 biomolecules, or about 1,000 to about 5,000 biomolecules). In some embodiments, the methods provided herein are capable of isolating a plurality of unique biomolecules simultaneously. [00269] In some embodiments, such as exemplified in Example 3, the combination of a first macromolecule structure and a second macromolecule structure, wherein the first macromolecule structure has as neutral to negative surface charge and the second macromolecule structure has a highly negative surface charge (e.g., more negative than the first macromolecule structure), provides a synergistic relationship allowing for identification, isolation, purification, or quantification of a larger number of biomolecules. In some embodiments, the combination of the two particles (e.g., comprising the macromolecule structures) increases the number of biomolecules identified by at least 3% (e.g., 4%, 5%, 6%, 7%, 8%, 9%, or at least 10%). In some embodiments, the combination of the two particles (e.g., comprising the macromolecule structures) increases the number of biomolecules identified by at least 25% (e.g., 20%, 18%, 16%, 14%, 12%, or at least 10%). In some embodiments, the combination of the two particles (e.g., comprising the macromolecule structures) increases the number of biomolecules identified by from about 3% to about 25%, about 4% to about 20%, about 5% to about 18%, about 6% to about 15%, or about 8% to about 15%. In some embodiments, the combination of the two or more particles (e.g., comprising the macromolecule structures) increases the number of biomolecules identified by about 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19%, or about 20%. [00270] In some embodiments, the methods provided herein further comprise washing the one or more biomolecules and the particles (e.g., comprising the macromolecule structures) with a wash solution. In some embodiments, the wash solution aids in removal of any of the impurities described elsewhere herein. In some embodiments, the wash solution comprises an organic solvent, such as an organic solvent described elsewhere herein. In some embodiments, the wash solution comprises an aqueous solution. In some embodiments, the wash solution comprises a buffer. In some embodiments, the washing may be performed after adsorbing the one or more biomolecules to the particles (e.g., comprising the macromolecule structures), and before eluting the one or more biomolecules. [00271] In some embodiments, the methods provided herein comprise purifying the isolated biomolecules (e.g., proteins), such as by solid phase extraction. In some embodiments, the solid phase extraction comprises use of a third particle, such as a third particle described elsewhere herein.
WSGR Docket No.53344-792.601 [00272] In some embodiments, the methods comprise isolating (e.g., purifying) the one or more biomolecules from one or more impurities, including not limited to surfactants, acids, bases, buffering agents, chaotropes, or a combination thereof. In some embodiments, the methods comprise isolating (e.g. purifying) the one or more digested biomolecules from one or more impurities, including not limited to surfactants, acids, bases, buffering agents, chaotropes, or a combination thereof. In some embodiments, the isolating comprises solid phase extraction. For example, the eluted biomolecules may be adsorbed to a C18 material, washed to remove impurities, and then eluted. In some embodiments, the isolating comprises precipitating the eluted biomolecules onto a solid phase using an organic solvent (e.g., acetonitrile), washing the adsorbed biomolecules to remove impurities, and then eluting the adsorbed biomolecules. As an example, the isolating may be performed using the methods described in PCT/US2024/054605, which is hereby incorporated by reference in its entirety. In some embodiments, the solid phase comprises particles. In some embodiments, the solid phase comprises magnetic particles. In some embodiments, the isolating comprises contacting with the third particle described elsewhere herein. In some embodiments, the solid phase comprises a polyalkylene glycol (PAG) methacrylate, polyalkylene glycol (PAG) acrylate, polyalkylene glycol (PAG) methacrylamide, polyalkylene glycol (PAG) acrylamide, polyalkylene glycol (PAG) vinyl ether, and combinations thereof. In some embodiments, the solid phase comprises polyethylene glycol (PEG) methacrylate. [00273] In some embodiments, the methods provided herein comprise removing a surfactant from the biological sample. In some embodiments, the methods provided herein comprise removing at least 90% (e.g., at least 95%, at least 97.5%, at least 98%, at least 99%, at least 99.5%) of a surfactant. In some embodiments, the methods provided herein comprise removing about 90% to about 99.9%, about 90% to about 99%, about 90% to about 98%, about 92% to about 97.5%, or about 93% to about 99% of a surfactant. In some embodiments, the amount of surfactants in the composition comprising the population of biomolecules is greater than the amount of surfactants in a composition comprising the one or more isolated biomolecules. In some embodiments, the amount of surfactants in a composition comprising the population of biomolecules is greater than the amount of surfactants in a composition comprising the one or more isolated biomolecules by at least 10 wt% (e.g., 20 wt%, 30 wt%, 50 wt%, 80 wt%, 90 wt%, 100 wt%). In some embodiments, the amount of surfactants in a composition comprising the population of biomolecules is greater than the amount of surfactants in a composition comprising the one or more isolated biomolecules by at least 70 wt%. In some embodiments, the amount of surfactants in a composition comprising the population of biomolecules (e.g., proteins or peptides) is greater than the amount of surfactants in a composition comprising the one or more isolated
WSGR Docket No.53344-792.601 biomolecules by at most 100 wt% (e.g., 99 wt%, 95 wt%, 90 wt%, 80 wt%, 70 wt%, 60 wt%). In some embodiments, the amount of surfactants in a composition comprising the population of biomolecules is greater than the amount of surfactants in a composition comprising the one or more isolated biomolecules by about 10 wt% to about 100 wt%, 10 wt% to about 90 wt%, 20 wt% to about 100 wt%, 30 wt% to about 100 wt%, 50 wt% to about 100 wt%, 50 wt% to about 80 wt%, or about 80 wt% to about 100 wt%. Non-limiting examples of surfactants that may be greater include sodium lauryl sulfate, Triton X-100, TWEEN, NP-40, CHAPS, Octyl glucoside, and decyl maltoside. In some embodiments, the surfactant is sodium lauryl sulfate. In some embodiments, the surfactant is CHAPS. In some embodiments, the surfactant is a synthetic molecule. [00274] In some embodiments, the methods provided herein comprise removing a buffering agent from the biological sample. In some embodiments, the methods provided herein comprise removing at least 90% (e.g., at least 95%, at least 97.5%, at least 98%, at least 99%, at least 99.5%) of a buffering agent. In some embodiments, the methods provided herein comprise removing about 90% to about 99.9%, about 90% to about 99%, about 90% to about 98%, about 92% to about 97.5%, or about 93% to about 99% of a buffering agent. In some embodiments, the amount of buffering agent in the composition comprising the population of biomolecules is greater than the amount of buffering agent in a composition comprising the one or more isolated biomolecules. In some embodiments, the amount of buffering agent in a composition comprising the population of biomolecules is greater than the amount of buffering agent in a composition comprising the one or more isolated biomolecules by at least 10 wt% (e.g., 20 wt%, 30 wt%, 50 wt%, 80 wt%, 90 wt%, 100 wt%). In some embodiments, the amount of buffering agent in a composition comprising the population of biomolecules is greater than the amount of buffering agent in a composition comprising the one or more isolated biomolecules by at least 70 wt%. In some embodiments, the amount of buffering agent in a composition comprising the population of biomolecules (e.g., proteins or peptides) is greater than the amount of buffering agent in a composition comprising the one or more isolated biomolecules by at most 100 wt% (e.g., 99 wt%, 95 wt%, 90 wt%, 80 wt%, 70 wt%, 60 wt%). In some embodiments, the amount of buffering agent in a composition comprising the population of biomolecules is greater than the amount of buffering agent in a composition comprising the one or more isolated biomolecules by about 10 wt% to about 100 wt%, 10 wt% to about 90 wt%, 20 wt% to about 100 wt%, 30 wt% to about 100 wt%, 50 wt% to about 100 wt%, 50 wt% to about 80 wt%, or about 80 wt% to about 100 wt%. Non-limiting examples of buffering agents that may be greater include phosphate buffer, Tris, HEPES, MES, MOPS, TES, CAPS, Bicine, and Bis-Tris. In some embodiments, the buffering agent is CAPS. In some embodiments, the buffering agent is HEPES.
WSGR Docket No.53344-792.601 [00275] In some embodiments, the methods provided herein comprise removing a chaotrope from the biological sample. In some embodiments, the methods provided herein comprise removing at least 90% (e.g., at least 95%, at least 97.5%, at least 98%, at least 99%, at least 99.5%) of a chaotrope. In some embodiments, the methods provided herein comprise removing about 90% to about 99.9%, about 90% to about 99%, about 90% to about 98%, about 92% to about 97.5%, or about 93% to about 99% of a chaotrope. In some embodiments, the amount of chaotropes in the composition comprising the population of biomolecules is greater than the amount of chaotropes in a composition comprising the one or more isolated biomolecules. In some embodiments, the amount of chaotropes in a composition comprising the population of biomolecules is greater than the amount of chaotropes in a composition comprising the one or more isolated biomolecules by at least 10 wt% (e.g., at least 20 wt%, 30 wt%, 50 wt%, 80 wt%, at least 90 wt%, or 100 wt%). In some embodiments, the amount of chaotropes in a composition comprising the population of biomolecules is greater than the amount of chaotropes in a composition comprising the one or more isolated biomolecules by at least 70 wt%. In some embodiments, the amount of chaotropes in a composition comprising the population of biomolecules (e.g., proteins or peptides) is greater than the amount of chaotropes in a composition comprising the one or more isolated biomolecules by at most 100 wt% (e.g., 99 wt%, 95 wt%, 90 wt%, 80 wt%, 70 wt%, 60 wt%). In some embodiments, the amount of chaotropes in a composition comprising the population of biomolecules is greater than the amount of chaotropes in a composition comprising the one or more isolated biomolecules by about 10 wt% to about 100 wt%, 10 wt% to about 90 wt%, 20 wt% to about 100 wt%, 30 wt% to about 100 wt%, 50 wt% to about 100 wt%, 50 wt% to about 80 wt%, or about 80 wt% to about 100 wt%. Non-limiting examples of chaotropes that may be greater include urea, guanidine hydrochloride, sodium thiocyanate, and perchlorate salts. In some embodiments, the chaotrope is urea. [00276] In some embodiments, the methods provided herein comprise removing an acid from the biological sample. In some embodiments, the methods provided herein comprise removing at least 90% (e.g., at least 95%, at least 97.5%, at least 98%, at least 99%, at least 99.5%) of an acid. In some embodiments, the methods provided herein comprise removing about 90% to about 99.9%, about 90% to about 99%, about 90% to about 98%, about 92% to about 97.5%, or about 93% to about 99% of an acid. In some embodiments, the amount of acid in the composition comprising the population of biomolecules is greater than the amount of acid in a composition comprising the one or more isolated biomolecules. In some embodiments, the amount of acid in a composition comprising the population of biomolecules is greater than the amount of acid in a composition comprising the one or more isolated biomolecules by at least 10 wt% (e.g., 20 wt%, 30 wt%, 50 wt%, 80 wt%, 90 wt%, 100 wt%). In some embodiments, the amount of acid in a composition
WSGR Docket No.53344-792.601 comprising the population of biomolecules is greater than the amount of acid in a composition comprising the one or more isolated biomolecules by at least 70 wt%. In some embodiments, the amount of acid in a composition comprising the population of biomolecules (e.g., proteins or peptides) is greater than the amount of acid in a composition comprising the one or more isolated biomolecules by at most 100 wt% (e.g., 99 wt%, 95 wt%, 90 wt%, 80 wt%, 70 wt%, 60 wt%). In some embodiments, the amount of acid in a composition comprising the population of biomolecules is greater than the amount of acid in a composition comprising the one or more isolated biomolecules by about 10 wt% to about 100 wt%, 10 wt% to about 90 wt%, 20 wt% to about 100 wt%, 30 wt% to about 100 wt%, 50 wt% to about 100 wt%, 50 wt% to about 80 wt%, or about 80 wt% to about 100 wt%. [00277] In some embodiments, the methods provided herein comprise removing a base from the biological sample. In some embodiments, the methods provided herein comprise removing at least 90% (e.g., at least 95%, at least 97.5%, at least 98%, at least 99%, at least 99.5%) of a base. In some embodiments, the methods provided herein comprise removing about 90% to about 99.9%, about 90% to about 99%, about 90% to about 98%, about 92% to about 97.5%, or about 93% to about 99% of a base. In some embodiments, the amount of base in the composition comprising the population of biomolecules is greater than the amount of base in a composition comprising the one or more isolated biomolecules. In some embodiments, the amount of base in a composition comprising the population of biomolecules is greater than the amount of base in a composition comprising the one or more isolated biomolecules by at least 10 wt% (e.g., at least 20 wt%, 30 wt%, 50 wt%, 80 wt%, 90 wt%, or at least 100 wt%). In some embodiments, the amount of base in a composition comprising the population of biomolecules is greater than the amount of base in a composition comprising the one or more isolated biomolecules by at least 70 wt%. In some embodiments, the amount of base in a composition comprising the population of biomolecules (e.g., proteins or peptides) is greater than the amount of base in a composition comprising the one or more isolated biomolecules by at most 100 wt% (e.g., 99 wt%, 95 wt%, 90 wt%, 80 wt%, 70 wt%, or at most 60 wt%). In some embodiments, the amount of base in a composition comprising the population of biomolecules is greater than the amount of base in a composition comprising the one or more isolated biomolecules by about 10 wt% to about 100 wt%, 10 wt% to about 90 wt%, 20 wt% to about 100 wt%, 30 wt% to about 100 wt%, 50 wt% to about 100 wt%, 50 wt% to about 80 wt%, or about 80 wt% to about 100 wt%. [00278] In some embodiments, the methods provided herein comprise providing one or more isolated biomolecules that are at least 75% (e.g., at least 80%, 85%, 90%, 93%, 95%, 97%, 98%, 99%, 99.5%, or at least 99.9%) pure. In some embodiments, the methods provided herein comprise providing one or more isolated biomolecules that are at most 99.9% (e.g., at most 99%, 98%, 97%,
WSGR Docket No.53344-792.601 96%, 95%, 94%, or at most 92%) pure. In some embodiments, the methods provided herein comprise providing one or more isolated biomolecules that are about 75% to about 99.9% pure, about 80% to about 99.9% pure, about 85% to about 99.9% pure, about 90% to about 99.9% pure, about 90% to about 99% pure, or about 90% to about 97% pure. [00279] In some embodiments, the methods herein comprise assaying (e.g., identifying, measuring, and/or quantifying) the one or more isolated biomolecules. In some embodiments, provided herein are methods of assaying a biological sample using the compositions provided herein. In some embodiments, the methods comprise assaying one or more digested biomolecules to identify the one or more biomolecules from a biological sample. In some embodiments, the methods comprise assaying the purified isolated proteins (e.g., such as purified by solid phase extraction). In some embodiments, the methods comprise analyzing the isolated proteins using mass spectrometry. In some embodiments, such as when the method comprises digestion, the isolated proteins are or comprise peptides. [00280] In some embodiments, the method comprises contacting the biological sample with a composition provided herein to form at least two biomolecule corona. In some embodiments, the method comprises assaying the at least two biomolecule corona to detect one or more biomolecules in the biological sample. [00281] In some embodiments, the assaying detects at least 2% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, the assaying detects at least 5% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, the assaying detects at least 7% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, the assaying detects at least 10% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, the assaying detects at least 12% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, the assaying detects at least 15% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. In some embodiments, the assaying detects at least 20% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle.
WSGR Docket No.53344-792.601 [00282] In some embodiments, the assaying detects at least 30% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. In some embodiments, the assaying detects at least 40% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. In some embodiments, the assaying detects at least 50% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. In some embodiments, the assaying detects at least 60% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. In some embodiments, the assaying detects at least 70% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. [00283] In some embodiments, the method does not comprise pre-selection of the detected biomolecules before assaying. [00284] In some embodiments, the methods herein comprise detecting or identifying the one or more (e.g., isolated biomolecules). In some embodiments, the (e.g., isolated biomolecules) biomolecules can be identified, measured, and quantified using a number of different analytical techniques. For example, the (e.g., isolated biomolecules) biomolecules may be analyzed using SDS-PAGE or any gel-based separation technique. The (e.g., isolated biomolecules) biomolecules can also be identified, measured, and quantified using an immunoassay, such as ELISA. In other embodiments, the (e.g., isolated biomolecules) biomolecules can be identified, measured, and quantified using mass spectrometry, high performance liquid chromatography, LC-MS, LC- MS/MS, Edman degradation, immunoaffinity techniques, and methods disclosed in EP3548652, WO2019083856, WO2019133892, each of which is incorporated herein by reference in its entirety. [00285] In some embodiments, the methods provided herein are capable of identifying at least 50 biomolecules. In some embodiments, the methods provided herein are capable of identifying at least 100 (e.g., 250, 500, 750, 1,000, 1,500, 2,000, 2,500, or at least 3000 biomolecules). In some embodiments, the methods provided herein are capable of identifying at least about 1,000 biomolecules. In some embodiments, the methods provided herein are capable of identifying at most 20,000 biomolecules (e.g., at most 15,000, 12,500, 10,000, 8,000, 7,000, 6,000, 5,000, 4,000, 3,000, or at most 2,500) biomolecules. In some embodiments, the methods provided herein are capable of identifying from about 100 to about 20,000 biomolecules (e.g., about 100 to about 10,000 biomolecules, about 500 to about 7,500 biomolecules, about 500 to about 5,000 biomolecules, or about 1,000 to about 5,000 biomolecules).
WSGR Docket No.53344-792.601 [00286] In some embodiments, the methods provided herein are capable of identifying (e.g., isolated) biomolecules over a dynamic range of at least 2 (e.g., at least 3, 4, 5, 6, 7, 8, 9, or at least 10). In some embodiments, the methods herein are capable of identifying (e.g., isolated) biomolecules over a dynamic range of at least 7, at least 8, at least 9, or at least 10. [00287] In some embodiments, the methods herein further comprise repeating the methods described herein, wherein, when repeated, the incubating, isolating, and assaying yields a percent quantile normalized coefficient (QNCV) of variation of 30% or less, as determined by comparing a peptide mass spectrometry feature from at least three full-assay replicates for each surface in the one or more surfaces. In some embodiments, when repeated, the incubating, isolating, and assaying yields a percent quantile normalized coefficient (QNCV) of variation of 25% or less, as determined by comparing a peptide mass spectrometry feature from at least three full-assay replicates for each surface in the one or more surfaces. In some embodiments, when repeated, the incubating, isolating, and assaying yields a percent quantile normalized coefficient (QNCV) of variation of 20% or less, as determined by comparing a peptide mass spectrometry feature from at least three full-assay replicates for each surface in the one or more surfaces. In some embodiments, the assaying is capable of identifying proteins over a dynamic range of at least 6, at least 7, at least 8, at least 9, or at least 10. In some embodiments, the assaying is capable of identifying proteins over a dynamic range of no more than 12, no more than 11, no more than 10, no more than 9, no more than 8, or no more than 7. [00288] Also provided herein is a method for assaying a plurality of biomolecules (e.g., proteins), the method comprising: (a) contacting a biological sample comprising one or more biomolecules with the particles described herein (e.g., first and second particle), thereby adsorbing at least a portion of the biomolecules to the magnetic particles forming a biomolecule corona; (b) separating the adsorbed proteins and the particles from the biological sample (e.g., by a separation technique described elsewhere herein); (c) digesting (e.g., such as by methods described herein) the adsorbed biomolecules thereby providing one or more digested biomolecules (e.g., peptides); (d) purifying the digested biomolecules (e.g., peptides) such as with a third particle described herein, and (e) analyzing the purified digested biomolecules to assay the plurality of biomolecules. [00289] The methods provided herein may comprise methods for preparing a (e.g., biological) sample for analysis, such as by any analytical technique provided elsewhere herein. For instance, the methods provided herein may comprise methods for preparing a biological sample for analysis by mass spectrometry. [00290] Also provided herein are uses of any of the particles (e.g., comprising the macromolecule structures) described elsewhere herein for binding proteins in a biological sample.
WSGR Docket No.53344-792.601 [00291] In some embodiments, provided herein is the use of macromolecule structure comprising 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units for binding proteins in a biological sample. [00292] In some embodiments, the uses and methods provided herein comprise using the structures of Formula (A-D) and Formula (A-A) as recurring units for binding proteins in a biological sample. [00293] In some embodiments, the uses and methods provided herein comprise using the structures of Formula (A-C) and Formula (A-B) as recurring units for binding proteins in a biological sample. [00294] In some embodiments, the uses and methods provided herein comprise the use of any of the compositions provided herein for binding proteins in a biological sample. [00295] In some embodiments, the time to form the protein coronas and wash the resulting particles comprising the protein coronas (e.g., such when assaying 40 or 80 samples) using a method herein is about 95 minutes (e.g., no more than 100 minutes). In some embodiments, the time to denature and digest the biomolecules of the protein coronas using the methods herein is about 105 minutes (e.g., no more than 110 minutes). In some embodiments, the time to purify the digested biomolecules using the methods herein, such as with the (e.g., third) particle is about 55 minutes (e.g., no more than 1 hour). [00296] In some embodiments, further provided herein are methods of quantifying peptides purified by the methods provided herein. In some embodiments, also provided herein are methods of reconstituting peptides purified by the methods provided herein. The reconstituted peptides may be reconstituted in a solution with a concentration and volume suitable for analysis by mass spectrometry. Systems for Isolating and Identifying Biomolecules [00297] Provided herein are systems for isolating one or more biomolecules from a biological sample. In some embodiments, the systems may purify one or more biomolecules from a biological sample. In some embodiments, the systems may assay (e.g., identify, measure, or quantify) one or more biomolecules. [00298] In some embodiments, the system comprises a plurality of particles (e.g., comprising the macromolecule structures). In some embodiments, the system comprises at least two particles (e.g., comprising the macromolecule structures). In some embodiments, the at least two particles (e.g., comprising the macromolecule structures) comprise a first macromolecule structure with a neutral to negative surface charge. In some embodiments, the at least two particles (e.g., comprising the macromolecule structures) comprise a first macromolecule structure (e.g., such as
WSGR Docket No.53344-792.601 a macromolecule structure provided elsewhere herein). In some embodiments, the at least two particles (e.g., comprising the macromolecule structures) comprise a second macromolecule structure (e.g., such as a macromolecule structure provided elsewhere herein). [00299] In some embodiments, the system comprise any composition provided elsewhere herein. [00300] In some embodiments, the system is configured to perform any one of the methods provided elsewhere herein. [00301] In some embodiments, the system comprises a suspension solution. In some instances, the suspension solution is configured to suspend the at least two particles (e.g., comprising the macromolecule structures). In some embodiments, the suspension solution comprises a buffer. In some embodiments, the suspension solution comprises Tris, EDTA, CHAPS, or HEPES buffer. In some embodiments, the suspension solution comprises HEPES buffer. In some embodiments, the suspension solution comprises a buffer at a concentration of about 10 mM, 25 mM, 30 mM, 50 mM, 75 mM, 100 mM, 125 mM, 200 mM, 250 mM, or about 300 mM. In some embodiments, the suspension solution comprises the buffer at an amount of about 300 mM. As an example, a suspension solution may comprise 300 mM HEPES buffer. In another example, the suspension solution may be 10mM Tris HCl pH 7.4, 1 mM EDTA. [00302] In some embodiments, the system comprises a biological sample, such as a biological sample provided elsewhere herein. In some embodiments, the biological sample comprises a plurality of biomolecules. [00303] In some embodiments, the system comprises an automated system comprising a network of units with differentiated functions configured to isolate one or more biomolecules from the biological sample using the at least two particles (e.g., comprising the macromolecule structures). [00304] In some embodiments, the present disclosure provides an automated system comprising a network of units as described in U.S. Patent No. 11,630,112, which is incorporated herein by reference in its entirety. In some embodiments, the network of units may comprise differentiated functions in distinguishing states of a complex biological sample using two or more particles (e.g., comprising the macromolecule structures) having surfaces with different physicochemical properties. [00305] In some embodiments, the system comprises a first unit comprising a multichannel fluid transfer instrument for transferring fluids between units within the system. In some embodiments, the first unit comprises a degree of mobility that enables access to all other units within the system. In some embodiments, the first unit comprises a capacity to perform pipetting functions. [00306] In some embodiments, the system comprises a second unit comprising a support for storing a plurality of biological samples. In some embodiments, the second unit can facilitate a transfer of the sample for mass spectrometry to a mass spectrometry unit. In some embodiments,
WSGR Docket No.53344-792.601 the second unit can facilitate a transfer of the sample for analysis, such as by any analytical technique described herein. [00307] In some embodiments, the system comprises a third unit comprising a support for an array plate possessing partitions that comprise the one or more macromolecule structure for binding of the one or more biomolecules with the two or more particles (e.g., comprising the macromolecule structures). [00308] In some embodiments, the support of the second and/or third unit comprises support for a single plate, a 6 well plate, a 12 well plate, a 96 well plate, or a rack of microtubes. In some embodiments, the second and/or unit comprises a thermal unit capable of modulating the temperature of said support and a sample. In some embodiments, the second and/or third unit comprises a rotational unit capable of physically agitating and/or mixing a sample. [00309] In some embodiments, the network of units comprises a fourth unit comprising supports for storing a plurality of reagents. In some embodiments, the fourth unit comprises a set of reagents for: generating the sensor array plate; washing an unbound sample; and/or preparing a sample for mass spectrometry. In some embodiments, contacting the biological sample with a specified partition of the sensor array comprises pipetting a specified volume of the biological sample into the specific partition of the sensor array. [00310] In some embodiments, contacting the biological sample with a specified partition of the sensor array comprises pipetting a volume of at least 10 µL (e.g., at least 20 µL, 50 µL, 100 µL, 250 µL, 500 µL, or at least 1000 µL) of the biological sample into the specific partition of the sensor array. In some embodiments, contacting the biological sample with a specified partition of the sensor array comprises pipetting a volume of no more than 1000 µL (e.g., no more than 500 µL, 250 µL, 150 µL, 100 µL, 75 µL, 50 µL, or no more than 30 µL). In some embodiments, the biological sample may be diluted with water or buffer. In some embodiments, the biological sample may be diluted at least 2-fold (e.g., at least 3-fold, 4-fold, or at least 5-fold). In some embodiments, the biological sample may be diluted no more than 20-fold (e.g., no more than 10- fold, 8-fold, or no more than 5-fold). In some embodiments, biological sample is diluted with water or buffer from about 2-fold to about 5-fold. [00311] In some embodiments, the network of units comprises a fifth unit comprising supports for storing a reagent to be disposed of. [00312] In some embodiments, the network of units comprises a sixth unit comprising supports for storing consumables used by a multichannel fluid transfer instrument. [00313] In some embodiments, the two or more particles (e.g., comprising the macromolecule structures) having surfaces with different physicochemical properties for binding a population of analytes (e.g., biomolecules) within the biological sample are immobilized to a macromolecule
WSGR Docket No.53344-792.601 structure within a partition of the sensory array. In some embodiments, the two or more particles (e.g., comprising the macromolecule structures) comprise different physicochemical properties for binding a population of analytes (e.g., biomolecules) within the biological sample. In some embodiments, the system comprises a step wherein the sensor array plate is transferred to an additional seventh unit that comprises a magnetized support and a thermal unit capable of modulating the temperature of said support and a sample and incubated for an additional amount of time. [00314] In some embodiments, incubating the biological sample with at least two particles (e.g., comprising the macromolecule structures) contained within the partition of the sensor array plate comprises an incubation time of at least about 10 seconds (e.g., at least about 15 seconds, 20 seconds, 25 seconds, 30 seconds, 40 seconds, 50 seconds, 60 seconds, 90 seconds, 2 minutes, 4 minutes, 5 minutes, 6 minutes, 8 minutes, 10 minutes, 15 minutes 20 minutes, 30 minutes, 45 minutes, 60 minutes, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 8 hours, 10 hours, 12 hours, 14 hours, 16 hours, 18 hours, 20 hours, or at least about 24 hours). In some embodiments, incubating the biological sample with the plurality of particles (e.g., comprising the macromolecule structures) contained within the partition of the sensor array plate comprises an incubation time of no more than 24 hours (e.g., no more than 12 hours, 6 hours, 3 hours, 2 hours, 90 minutes, 75 minutes, 45 minutes, or no more than 30 minutes). In some embodiments, incubating the biological sample with the plurality of particles (e.g., comprising the macromolecule structures) contained within the partition of the sensor array plate comprises an incubation time of 30 minutes to 3 hours. In some embodiments, incubating the biological sample with the plurality of particles comprises an incubation time of no more than 100 minutes. [00315] In some embodiments, incubating the biological sample with the at least two particles (e.g., comprising the macromolecule structures) contained within the partition of the substrate comprises an incubation temperature of at least 4°C (e.g., at least 5°C, 10°C, 15°C, 20°C, 25°C, 30°C, 35°C, or at least 40°C). In some embodiments, the incubation temperature is at most 50°C (e.g., at most 45°C, 40°C, 38°C, 35°C, 30°C, 25°C, or 20°C). In some embodiments, the incubation temperature is from about 4°C to about 40°C. In some embodiments, the incubation temperature is from about 30°C to about 40°C. In some embodiments, the incubation temperature is about 30°C, 31°C, 32°C, 33°C, 34°C, 35°C, 36°C, 37°C, 38°C, 39°C, or 40°C. [00316] In some embodiments, provided herein is an automated apparatus to identify biomolecules in a biological sample. In some embodiments, the systems provided herein are automated systems. In some embodiments, the automated apparatus comprises a sample preparation unit; a substrate comprising a plurality of channels; a plurality of pipettes; a plurality of solutions; a plurality of particles (e.g., comprising the macromolecule structures) as provided
WSGR Docket No.53344-792.601 elsewhere herein. In some embodiments, the automated apparatus comprises a sample preparation unit. In some embodiments, the automated apparatus comprises a substrate comprising a plurality of channels. In some embodiments, the automated apparatus comprises a plurality of pipettes. In some embodiments, the automated apparatus comprises a plurality of solutions. In some embodiments, the automated apparatus comprises a plurality of particles (e.g., comprising the macromolecule structures), such as described elsewhere herein. [00317] In some embodiments, the automated apparatus is configured to form a biomolecule corona and digest the biomolecule corona (or two or more biomolecule coronas). In some embodiments, the automated apparatus is configured for digestion (e.g., by enzymolysis), such as using any digestion agent provided herein (e.g., trypsin) of the biomolecule corona. In some embodiments, the automated apparatus is configured for BCA, gel, or trypsin digestion of the biomolecule corona. [00318] In some embodiments, the automated apparatus is enclosed. In some embodiments, the automated apparatus is sterilized before use. In some embodiments, the automated apparatus is configured to a mass spectrometer. In some embodiments, the automated apparatus is temperature controlled. [00319] In some embodiments, provided herein is an automated apparatus for generating a subset of biomolecules from a biological sample. In some embodiments, the automated apparatus comprises a substrate comprising a plurality of partitions, a first unit comprising the biological sample, and a loading unit that is movable across the substrate and is capable of transferring a volume (e.g., a volume of buffer) between different units of the apparatus. In some embodiments, the substrate is a multi-well plate. [00320] In some instances, the plurality of partitions comprises a plurality of sensor elements. In some embodiments, the plurality of sensor elements may comprise particles (e.g., comprising the macromolecule structures) as provided elsewhere herein. For example, the sensor elements may include a first macromolecule structure (e.g., such as a first macromolecule structure provided elsewhere herein) and a second macromolecule structure (e.g., such as a second macromolecule structure provided elsewhere herein). [00321] A partition from among the plurality of partitions may comprise 1 to 100 types of sensor elements (e.g., distinct particles (e.g., comprising the macromolecule structures)). A partition from among the plurality of partitions may comprise 2 to 50 types of sensor elements. A partition from among the plurality of partitions may comprise 2 to 20 types of sensor elements. A partition from among the plurality of partitions may comprise 2 to 5 types of sensor elements. A partition from among the plurality of partitions may comprise 3 to 8 types of sensor elements. A partition from among the plurality of partitions may comprise 4 to 10 types of sensor elements. A partition from
WSGR Docket No.53344-792.601 among the plurality of partitions may comprise 5 to 12 types of sensor elements. A partition from among the plurality of partitions may comprise 6 to 15 types of sensor elements. A partition from among the plurality of partitions may comprise 8 to 20 types of sensor elements. A partition from among the plurality of partitions may comprise 2 types of sensor elements. A partition from among the plurality of partitions may comprise at least 2 types of sensor elements. A partition from among the plurality of partitions may comprise 3 types of sensor elements. [00322] Two or more partitions from among the plurality of partitions may comprise different quantities of sensor elements. Two or more partitions from among the plurality of partitions may comprise different types of sensor elements. In some embodiments, a partition amongst the plurality of partitions comprises a combination of types and/or quantities of sensor element(s) that differ from other partitions in the plurality. In some instances, a subset of partitions in a plurality of partitions may each contain a combination of distinct sensor elements that is distinct from other partitions in the plurality. [00323] In some embodiments, sensor elements are stored in dry form inside of or within the partitions. In some embodiments, dry sensor elements may be reconstituted or rehydrated prior to use. In some instances, sensor elements may be stored within solutions. In some embodiments, a substrate partition may comprise a solution comprising a high concentration of particles (e.g., comprising the macromolecule structures). [00324] Partitions from among the plurality of partitions comprise different concentrations or amounts (e.g., by mass/molar amount per unit volume of sample) of sensor elements. A partition from among the plurality of partitions may comprise from 1 pM to 100 nM of sensor elements. A partition from among the plurality of partitions comprise may from 1 pM to 500 pM of sensor elements. A partition from among the plurality of partitions may comprise from 10 pM to 1 nM of sensor elements. A partition from among the plurality of partitions may comprise from 100 pM to 10 nM of sensor elements. A partition from among the plurality of partitions may comprise from 500 pM to 100 nM of sensor elements. A partition from among the plurality of partitions may comprise from 50 µg/ml to 300 µg/ml of sensor elements. A partition from among the plurality of partitions may comprise from 100 µg/ml to 500 µg/ml of sensor elements. A partition from among the plurality of partitions may comprise from 250 µg/ml to 750 µg/ml of sensor elements. A partition from among the plurality of partitions may comprise from 400 µg/ml to 1 mg/ml of sensor elements. A partition from among the plurality of partitions may comprise from 600 µg/ml to 1.5 mg/ml of sensor elements. A partition from among the plurality of partitions may comprise from 800 µg/ml to 2 mg/ml of sensor elements. A partition from among the plurality of partitions may comprise from 1 mg/ml to 3 mg/ml of sensor elements. A partition from among the
WSGR Docket No.53344-792.601 plurality of partitions may comprise from 2 mg/ml to 5 mg/ml of sensor elements. A partition from among the plurality of partitions may comprise more than 5 mg/ml of sensor elements. [00325] In some embodiments, the loading unit may be configured to move between and transfer volumes (e.g., a volume of a solution or a powder) between any units, compartments, or partitions within the apparatus. The loading unit may be configured to move precise volumes (e.g., within 0.1%, 0.01%, 0.001% of the specified volume). The loading unit may be configured to collect a volume from the substrate or a compartment or partition within the substrate and dispense the volume back into the substrate or compartment or partition within the substrate, or to dispense the volume or a portion of the volume into a different unit, compartment, or partition. In some instances, the loading unit is configured to move multiple volumes simultaneously, such as 2 to 400 separate volumes. The loading unit may comprise a plurality of pipette tips. [00326] In some embodiments, the loading unit may be configured to move a volume of a liquid. In some embodiments, the volume may be at least 0.1 µL (e.g., at least 0.4 µL, 0.6 µL 0.8 µL, 1 µL, 5 µL, 10 µL, 25 µL, 100 µL, or at least 250 µL). In some embodiments, the volume may be at most 5 mL (e.g., at most 2 mL, 1 mL, 750 µL, 500 µL, 250 µL, 200 µL, 100 µL, or at most 50 µL). In some embodiments, the volume may be about 0.1 μl, 0.2 μl, 0.3 μl, 0.4 μl, 0.5 μl, 0.6 μl, 0.7 μl, 0.8 μl, 0.9 μl, 1 μl, 2 μl, 3 μl, 4 μl, 5 μl, 6 μl, 7 μl, 8 μl, 9 μl, 10 μl, 12 μl, 15 μl, 20 μl, 25 μl, 30 μl, 40 μl, 50 μl, 60 μl, 70 μl, 80 μl, 90 μl, 100 μl, 120 μl, 150 μl, 180 μl, 200 μl, 250 μl, 300 μl, 400 μl, 500 μl, 600 μl, 800 μl, 1 ml, or more than 1 ml. In some embodiments, the liquid may be a biological sample or solution. [00327] In some embodiments, the solution comprises a wash solution, such as a wash solution provided elsewhere herein. In some embodiments, the solution comprises a resuspension solution (e.g., such as a suspension solution provided elsewhere herein). In some embodiments, the solution comprises a denaturing solution. In some embodiments, the solution comprises a buffer (e.g., such as a buffer or buffering agent described elsewhere herein). In some embodiments, the solution comprises a reagent (e.g., a reducing reagent). In some embodiments, the solution comprises a wash solution, a resuspension solution, a denaturing solution, a buffer, a reagent (e.g., a reducing reagent), or any combination thereof. In some embodiments, the solution comprises a biological sample. [00328] In part owing to these functionalities, the loading unit can be capable of partitioning a sample. In some embodiments, this comprises dividing a sample into a number of partitions. A sample can be divided into at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 20, 25, 30, 40, 50, 60, 70, 80, 90, 100, 120, 150, 180, 200, 250, 300, 350, 400, 500, or more partitions. A sample can be divided into 96, 192, or 384 partitions. The automated apparatus can comprise multiple substrates comprising partitions. The automated apparatus may comprise 1, 2, 3, 4, 5, or more substrates
WSGR Docket No.53344-792.601 comprising partitions. In some cases, the loading unit loads different volumes of the biological sample into different partitions. In some cases, the loading unit loads identical volumes into two or more partitions. The volume of biological sample loaded into a partition may be about 0.1 μl, 0.2 μl, 0.3 μl, 0.4 μl, 0.5 μl, 0.6 μl, 0.7 μl, 0.8 μl, 0.9 μl, 1 μl, 2 μl, 3 μl, 4 μl, 5 μl, 6 μl, 7 μl, 8 μl, 9 μl, 10 μl, 12 μl, 15 μl, 20 μl, 25 μl, 30 μl, 40 μl, 50 μl, 60 μl, 70 μl, 80 μl, 90 μl, 100 μl, 120 μl, 150 μl, 180 μl, 200 μl, 250 μl, 300 μl, 400 μl, 500 μl, 600 μl, 800 μl, 1 ml, or more than 1 ml. The volume of biological sample loaded into a partition may be about 10 μl to 400 μl. The volume of biological sample loaded into a partition may be about 5 μl to 150 μl. The volume of biological sample loaded into a partition may be about 35 μl to 80 μl. In some cases, the loading unit may partition two or more biological samples. For example, a sample storage unit may comprise two biological samples that the system partitions into one well plate. In some embodiments, the loading unit can facilitate a transfer of the sample for mass spectrometry to a mass spectrometry unit. [00329] The system may be configured to perform a dilution on a sample or a sample partition. A sample or sample partition may be diluted with buffer, water (e.g., purified water), a non- aqueous solvent, or any combination thereof. The diluent may be stored in the automated apparatus prior to dispensation into a substrate partition. The automated apparatus may store a plurality of diluents differing in pH, salinity, osmolarity, viscosity, dielectric constant, or any combination thereof. The diluents may be used to adjust the chemical properties of a sample or sample partition. The automated apparatus may dilute a sample or sample partition by 2-fold, 3- fold, 4-fold, 5-fold, 6-fold, 8-fold, 10-fold, 15-fold, 20-fold, 30-fold, 40-fold, 50-fold, 75-fold, 100-fold, 150-fold, 200-fold, 300-fold, 400-fold, 500-fold or greater. In some embodiments, the automated apparatus may dilute a sample or sample partition by about 2-fold to about 5-fold. The automated apparatus may perform different dilutions on two samples or sample partitions. The system may perform different dilutions on each partition from among a plurality of partitions. For example, the system may perform different dilutions on each of the 96 sample partitions in a 96 well plate. In some cases, the different dilutions comprise different degrees of dilution (e.g., 2- fold vs. 4-fold). In some cases, the different dilutions comprise dilution with different solutions (e.g., different buffers). In some cases, two sample partitions may be made to differ in one or more chemical properties, such as pH, salinity, or viscosity. [00330] In some cases, the system may modify the chemical composition of a sample or sample partition. The system may modify or adjust the pH, salinity, osmolarity, dielectric constant, viscosity, buffer types, salt types, sugar types, detergent types, or any combination thereof for a sample or sample partition. Such modification or adjustments may comprise mixing a reagent
WSGR Docket No.53344-792.601 from the fourth unit with a sample or sample partition. The system may differently modify the chemical composition of two samples or sample partitions. [00331] In some embodiments, the systems or automated apparatuses provided herein comprise an incubation element. The incubation element may contact, support, or hold another component of the automated apparatus (e.g., the substrate or a unit). The incubation unit may contact, support, or hold multiple components of the automated apparatus. The incubation element may contact the substrate to facilitate heat transfer between the incubation element and the substrate. The incubation unit may be configured to control the temperature of the one or more components of the automated apparatus, such as by heating or cooling. The incubation element may be capable of cooling a component of the apparatus to from 20 °C to 1 °C. The incubation element may be capable of heating a component of the apparatus to from 25 °C to 100 °C. The incubation element may be capable of setting the temperature a component of the apparatus to from 4 °C to 37 °C. The incubation element may be configured to heat or cool different portions of a component of the automated apparatus to different temperatures. For example, the incubation element may hold a first partition in the substrate at 30 °C and a second partition in the substrate at 35 °C. The incubation element may control the temperature of a sample or partition. The incubation element may comprise a temperature sensor (e.g., a thermocouple) for detecting the temperature within a partition or container. The incubation element may calibrate its heating or cooling to the readout from the temperature sensor. [00332] The incubation element may be configured to physically agitate a component of the automated apparatus. The agitation may be in the form of shaking or spinning, vibrating, rocking, sonicating, or any combination thereof. The incubation element may be capable of providing multiple agitation intensities and/or frequencies. For example, the incubation element may comprise multiple settings for shaking at different frequencies and amplitudes. The incubation element may also be capable of stirring and or mixing a volume (e.g., a portion of the biological sample). [00333] The automated apparatus may comprise a unit comprising a resuspension solution. The loading unit may be capable of transferring a volume of the resuspension solution to a partition from among the plurality of partitions of the substrate. In some cases, this results in the dilution of a sample present within the partition and can further result in the desorption of a plurality of biomolecules from a biomolecule corona disposed on a sensor element within the partition. The quantity of biomolecules desorbed from a biomolecule corona can depend on the volume of the resuspension solution added to the partition, the temperature of the partition, the composition of the resuspension solution (e.g., the salinity, osmolarity, viscosity, dielectric constant, or pH), the volume of the biological sample within the partition, and the sensor element type and the
WSGR Docket No.53344-792.601 composition of biomolecules in the biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of less than 5% of the biomolecules from a biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of 10% to 20% of the biomolecules from a biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of 20% to 30% of the biomolecules from a biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of 30% to 40% of the biomolecules from a biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of 40% to 50% of the biomolecules from a biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of 50% to 60% of the biomolecules from a biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of 60% to 70% of the biomolecules from a biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of 70% to 80% of the biomolecules from a biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of 80% to 90% of the biomolecules from a biomolecule corona. The transfer of a volume of the resuspension solution into a partition may result in the desorption of more than 90% of the biomolecules from a biomolecule corona. [00334] In some cases, multiple rounds of desorption are performed. In each round, the supernatant comprising the desorbed biomolecules may be collected, analyzed, or discarded. The types and abundances of biomolecules in the supernatant may differ between desorption rounds. The automated apparatus may perform one or more desorption and discard cycles (i.e., washes), followed by one or more desorption cycles comprising sample collection and/or analysis. [00335] The resuspension solution may be tailored to optimize enrichment of particular biomarkers. The resuspension solution may comprise a buffer, such as Tris-EDTA (TE), CHAPS, PBS, citrate, HEPES, MES, CHES, or another bio buffer. The resuspension solution may comprise Tris EDTA (TE) 150mM KCl 0.05% CHAPS buffer. The resuspension solution may comprise 10 mM TrisHCl pH 7.4, 1 mM EDTA. The resuspension solution may comprise 300 mM HEPES. The resuspension solution may also contain or be highly purified water (e.g., distilled or deionized water). Biomolecule desorption may be augmented by heating or agitation by an incubation element. The supernatant may be transferred to a new partition following desorption. A resuspension solution may be used to dilute a sample. [00336] The automated apparatus may comprise a unit comprising a denaturing solution (e.g., a denaturing agent). The denaturing solution may comprise a protease. The denaturing solution may comprise a chemical capable of performing peptide cleavage (e.g., cyanogen bromide, formic
WSGR Docket No.53344-792.601 acid, or hydroxylamine, 2-nitro-5-thiocyanatobenzoic acid). The denaturing solution may comprise a chemical denaturant such as guanidine, urea, sodium deoxycholate, acetonitrile, trichloroacetic acid, acetic acid, sulfosalicylic acid, sodium bicarbonate, ethanol, perchlorate, dodecyl sulfate, or any combination thereof. The denaturing solution may comprise a reductant, such as 2-mercaptoethanol, dithiothreitol, or tris(2-carboxyethyl)phosphine. The protease may be trypsin. The denaturing solution may be added to a partition following desorption. The denaturing solution may be added to a partition comprising biomolecule coronas. [00337] The automated apparatus may comprise a magnet or array of magnets. The automated apparatus may be capable of moving the substrate onto and off of the magnet or array of magnets. The array of magnets may be structured so that a plurality of magnets from the array of magnets can rest directly underneath a plurality of partitions from the substrate. The magnet may be capable of immobilizing magnetic sensor elements (e.g., magnetic particles (e.g., comprising the macromolecule structures) provided herein) within a partition on the substrate. For example, the magnet may prevent magnetic particles (e.g., comprising the macromolecule structures) from being removed from a partition during a wash step. The magnet may also create a pellet from a collection of magnetic particles (e.g., comprising the macromolecule structures). The magnet may create a macromolecule structure pellet in less than 10 minutes. The magnet may create a particle pellet in less than 5 minutes. The macromolecule structure pellet may comprise a particle with a biomolecule corona. [00338] The automated apparatus may comprise a purification unit. The purification unit may comprise a plurality of partitions comprising an adsorbent or resin. The purification unit may comprise a solid-phase extraction array or plate. The solid-phase extraction array or plate may comprise a polar stationary phase material. The solid-phase extraction array or plate may comprise a non-polar stationary phase material. The solid-phase extraction array or plate may comprise a C18 stationary phase material (e.g., octadecyl group silica gel). In some embodiments, the automated apparatus comprises a unit with a conditioning solution for the purification unit (e.g., a conditioning solution for a solid-phase extraction material). The automated apparatus may comprise a unit with an elution solution for removing biomolecules from the purification unit. The purification unit may comprise a solution comprising the third particles described herein. [00339] In some embodiments, a supernatant is removed from the sensor array plate. In some instances, the automated apparatus may perform a series of wash steps. A wash step may remove biomolecules that are not bound to the sensor elements within the partition. A wash step may desorb a subset of biomolecules bound to sensor elements within a partition. For example, a wash step may result in the desorption and removal of a subset of soft corona analytes, while leaving the majority of hard corona analytes bound to the sensor element.
WSGR Docket No.53344-792.601 [00340] In some embodiments, the present disclosure provides an automated apparatus to identify proteins in a biological sample, the automated apparatus comprising: a sample preparation unit; a substrate comprising a plurality of channels; a plurality of pipettes; a plurality of solutions, a plurality of particles (e.g., comprising the macromolecule structures), such as particles (e.g., comprising the macromolecule structures) provided elsewhere herein, and wherein the automated apparatus is configured to form a biomolecule corona and digest the biomolecule corona. In some embodiments, the automated apparatus comprises a sample preparation unit. In some embodiments, the automated apparatus comprises a substrate comprising a plurality of channels. In some embodiments, the automated apparatus comprises a plurality of pipettes. In some embodiments, the automated apparatus comprises a plurality of solutions. In some embodiments, the automated apparatus comprises a plurality of particles (e.g., comprising the macromolecule structures). In some embodiments, the automated apparatus is configured to form a biomolecule corona and digest the biomolecule corona. [00341] In some embodiments, the automated apparatus or system is enclosed. Kits [00342] Provided herein, in some embodiments, are kits for isolating one or more biomolecules from a biological sample. In some embodiments, the kit is for purifying one or more biomolecules from a biological sample. In other embodiments, the kits provided herein are for preparation of a biological sample for analysis, such as by analytical technique provided herein (e.g., mass spectrometry). The kit may comprise the components described in Table 7. [00343] In some embodiments, the kits are pre-packaged in discrete aliquots. In some embodiments, the kits comprise a plurality (e.g., at least two) of different particles (e.g., comprising the macromolecule structures) pre-packaged, wherein each macromolecule structure of the plurality is packaged separately. In other embodiments, the plurality (e.g., at least two) of particles (e.g., comprising the macromolecule structures) can be packaged together to comprise a combination of particles (e.g., comprising the macromolecule structures) in a single package. In some instances, the particles (e.g., comprising the macromolecule structures) of the kits provided herein may be freeze dried and stored in sealed containers. [00344] In some embodiments, the kits comprise particles (e.g., comprising the macromolecule structures), such as particles (e.g., comprising the macromolecule structures) provided elsewhere herein. In some embodiments, the kits comprise at least two particles (e.g., comprising the macromolecule structures). In some embodiments, the particles (e.g., comprising the macromolecule structures) comprise a first macromolecule structure. In some embodiments, the first macromolecule structure comprises a neutral to negative surface charge. In some
WSGR Docket No.53344-792.601 embodiments, the particles (e.g., comprising the macromolecule structures) comprise a second macromolecule structure. In some embodiments, the second macromolecule structure comprises a negative surface charge. In some instances, the second macromolecule structure comprises a greater negative surface charge than that of the first macromolecule structure. [00345] In some embodiments, the kits provided herein comprise a buffer. Non-limiting examples of buffers that may be greater include Tris, phosphate buffer, HEPES, MES, MOPS, TES, TE, CAPS, Bicine, and Bis-Tris. In some embodiments, the buffer is CAPS. In some embodiments, the buffer is HEPES. In some embodiments, the buffer comprises 200-750, 100- 750, 250-750, 300-7250, 400-750, 400-1000, 500-1000, or 500-750 mM HEPES. In some embodiments, the buffer is 300 mM HEPES. In some embodiments, buffers include but are not limited to a digestion buffer, resuspension buffer, dilution buffer, denaturation buffer, or a lysis buffer. [00346] In some embodiments, the kits provided herein comprise a washing agent (e.g., a washing solution). In some embodiments, a washing agent comprise a wash solution as described elsewhere herein. [00347] In some embodiments, the kits provided herein comprise an elution agent. In some embodiments, the elution agent is an elution buffer as described elsewhere herein. [00348] In some embodiments, the kits comprise a digestion solution or digestion agent, such as a digestion solution or digestion agent provided elsewhere herein. In some embodiments, the digestion solution comprises Trypsin. In some embodiments, the digestion solution comprises Trypsin/LysC protease. [00349] In some embodiments, the kits comprise a denaturing solution or denaturing agent. In some embodiments, the denaturing agent comprises at least one of: sodium dodecyl sulfate, acetic acid, trichloroacetic acid, sulfosalicylic acid, sodium bicarbonate, ethanol, formaldehyde, glutaraldehyde, urea, guanidium chloride, lithium perchlorate, 2-mercaptoethanol, dithiothreitol, tris(2-carboxyethyl)phosphine (TCEP), or any combination thereof. [00350] In some embodiments, the kit comprises a reducing agent. In some embodiments, the reducing agent comprises TCEP, dithiothreitol, beta-mercaptoethanol, glutathione, cysteine, or any combination thereof. [00351] In some embodiments, the kit comprises an alkylating agent. In some embodiments, the alkylating agent comprises iodoacetamide, iodoacetic acid, acrylamide, chloroacetamide, or any combination thereof. [00352] In some embodiments, the kit comprises a solid support for solid phase extraction. In some embodiments, the kit comprises a polar stationary phase material. In some embodiments, the kit comprises a non-polar stationary phase material. In some embodiments, the kit comprises
WSGR Docket No.53344-792.601 a C18 stationary phase material (e.g., octadecyl group silica gel). In some embodiments, the kit comprises conditioning solution for the solid phase extraction material. In some embodiments, the solid support comprises magnetic particles. In some embodiments, the kit comprises an organic solvent (e.g., acetonitrile) to precipitate biomolecules onto the magnetic particles. [00353] In some embodiments, the kit comprises cleanup particles. [00354] In some embodiments, the kit comprises a wash solution. [00355] In some embodiments, the kit comprises a multi-well plate. In some embodiments, the multi-well plate is a 4 well plate. In some embodiments, the multi-well plate is a In some embodiments, the multi-well plate is a 12 well plate. In some embodiments, the multi-well plate is a 24 well plate. In some embodiments, the multi-well plate is a 48 well plate. In some embodiments, the multi-well plate is a 96 well plate. In some embodiments, the multi-well plate is a 384 well plate. In some embodiments, the multi-well plate is a 1536 well plate. [00356] In some embodiments, the kit comprises a diluent. In some embodiments, the diluent is an organic solvent. In some embodiments, the diluent is water. In some embodiments, the diluent is a buffer. In some embodiments, the diluent is an organic solvent, water, a buffer, or any combination thereof. [00357] In some embodiments, the kit comprises a reconstitution solution. The reconstitution solution may be suitable to reconstitute lyophilized particles described herein. [00358] In some embodiments, the kit further comprises an organic solvent, such as an organic solvent described elsewhere herein. [00359] In some embodiments, the kit further comprises a cysteine blocking reagent. In some embodiments, the cysteine blocking reagent comprises methyl methanethiosulfonate, iodoacetamide, N-ethylmaleimide, methylsulfonyl benzothiazole, or any combination thereof. [00360] Kits may also, in some embodiments, comprise one or more of outer packaging, lot numbers, and instructions for use of the kit with the methods provided herein. [00361] While preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure. It is intended that the following claims define the scope of the disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby.
WSGR Docket No.53344-792.601 EXAMPLES [00362] The following examples are provided to further illustrate some embodiments of the present disclosure but are not intended to limit the scope of the disclosure; it will be understood by their exemplary nature that other procedures, methodologies, or techniques known to those skilled in the art may alternatively be used. Example 1: Preparation of a First Particle [00363] A particle comprising randomly distributed ethyleneglycol dimethacrylate and hydroxyethylmethacrylate were prepared according to FIG. 1. Olefin functionalized superparamagnetic iron oxide@silica nanoparticles (12 g) were provided and optionally dispersed in acetonitrile. Separately, (hydroxyethyl)methacrylate (HEMA) (12 g, 92.2 mmol) and ethyleneglycol dimethacrylate (EGDMA) (18 g, 90.8 mmol) were dissolved in acetonitrile to form a mixture which was added to the superparamagnetic iron oxide nanoparticles in acetonitrile. Separately, AIBN (1.4 g, 8.8 mmol) was dissolved in acetonitrile to form an initiator mixture. The solution of HEMA, EGDMA, and superparamagnetic iron oxide nanoparticles was purged with N2 for 15 minutes and heat to 80°C under N2. Under N2, after heating, the initiator mixture was added (total acetonitrile volume of 2.4 L). After addition of the initiator mixture, the reaction vessel was purged with N2 for at least 15 minutes. The reaction mixture was allowed to heat at 80°C for 2.5 hrs. After reaction, the particles (e.g., comprising the macromolecule structures) were pulled down using a magnet, washed once with THF and at least 3 times with water to provide the final macromolecule structure. According to TGA, the macromolecule structure comprised about 16.7% of the polymer material. The particle sizes were 442.7 nm as measured by DLS with a PDI of 0.123. The zeta potential was -2.8 mV. Example 2: Preparation of a Second Particle [00364] A particle comprising randomly distributed ethyleneglycol methacrylate and
were prepared according to FIG. 2. Olefin functionalized superparamagnetic iron oxide@silica nanoparticles (15 g) were provided and dispersed in acetonitrile for 15 minutes by sonication. The reaction vessel was purged with N2 and heat up to 80°C under N2. The resulting heated mixture was purged with N2 for 15 minutes. AIBN was added after dissolving AIBN in acetonitrile and the resulting mixture was allowed to purge with N2 for at least 15 minutes. In addition to the addition of AIBN, EGDMA (23g, 116 mmol) and glycidylmethacrylate (GMA) (18 g, 127 mmol) were dissolved in acetonitrile and added under N2 (total DMF volume: 3.015 L). The solution was allowed to react for 1.5, 2, 2.5, 3, 3.5, or 4 hours
WSGR Docket No.53344-792.601 before being quenched with 1,4-benzoquinone. This macromolecule structure was washed once with THF, twice with DMF, and dispersed in DMF for subsequent reactions. The resulting macromolecule structure (10 g) in DMF was sonicate for 15 minutes followed by heating to 80°C under N2. Ethylenediamine (62.4 g, 1040 mmol) was added to the reaction mixture and allowed to react overnight (16 hours). The resulting amine functionalized macromolecule structure was washed with DMF twice and dispersed in DMF for subsequent reactions (total DMF volume 2.009 L). The amine functionalized macromolecule structure (10 g) was dispersed in DMF with sonication for 15 minutes. The reaction mixture was heated to 60°C under N2 to which triethylamine (14.4 g, 142 mmol) and (trans-2-octenyl) succinic anhydride (21.6 g, 103 mmol) were added and allowed to stir at 60°C overnight (16 hrs). The resulting macromolecule structure was washed with ethanol once and at least three times with water. were added and allowed to stir at 60°C overnight (16 hrs). The resulting macromolecule structure was washed with ethanol once and at least three times with water. [00365] The particle size, zeta potential, and % polymer (as determined by TGA) were dependent on the length of time before quenching with benzoquinone in the first reaction (Table 3 and Table 4). TABLE 3
TABLE 4
Example 3: Performance of Multiplexed Particles [00366] The particles (e.g., comprising the macromolecule structures) provided herein were assessed for their performance in isolating protein groups both individually and while multiplexed. In one example, to assess the performance of particles (e.g., comprising the macromolecule
WSGR Docket No.53344-792.601 structures) (A2) and (A1), provided herein, the particles (e.g., comprising the macromolecule structures) were exposed to three different plasma samples, both on their own, and as a combination of (A2) and (A1). In the combination, the ratio of (A2):(A1) was about 4:1. The total concentration of particles (e.g., comprising the macromolecule structures) in each of the experiments was about 0.31 mg/mL with a particle:plasma volume ratio of about 100 µL:100 µL. The results are depicted in FIG. 3, which shows that the multiplexed particles (A2) and (A1) perform better when combined as opposed to each type of particle on its own. Without being bound to any theory, this may indicate to synergistic relationship between the negatively charged and neutral to negatively charged particles (e.g., comprising the macromolecule structures). [00367] Particles (A1) and (A2) were evaluated at varying concentrations in equal volumes of particles and plasma (100 µL:100µL) as shown in FIG. 6. Concentrations of total particles evaluated were 0.45 mg/mL, 0.45 mg/mL, and 0.6 mg/mL. Peptide mass (µg) and protein group counts were evaluated for samples with a multiplexed composition of (A1) and (A2) in a ratio of 4:1, 1:4, and (A2) alone. The ratios are weight ratios, for example, in the 4:1 (A1):(A2) multiplexed samples, 0.36 mg/mL of (A1) and 0.09 mg/mL of (A2) may be combined to arrive at the composition used. The results in FIG.6 may indicate that multiplexing of (A1) and (A2) can result in higher peptide mass yields at all concentrations of nanoparticle used. FIG. 6 also may indicate that increasing amounts of (A2) relative to (A1) e.g., 1:4 (A1):(A2) may result in increased protein group identification. [00368] In another example, particles (e.g., comprising the macromolecule structures) (A3), (A4), (A5), and (A6), depicted below, were similarly assessed for a synergistic relationship when multiplexed. In this instance, (A3), (A4), and (A5) had highly negative surface charges, whereas (A6) had an almost neutral surface charge.
WSGR Docket No.53344-792.601
[00369] In this instance, the protein group count improvement from multiplexing was assessed, complexing (A3) with other negative particles (e.g., comprising the macromolecule structures) or almost neutral particles (e.g., comprising the macromolecule structures) (A6). The improvement by multiplexing, was 8% for combining (A3) and (A4), 8% for combining (A3) and (A5) and 13% for combining (A3) and (A6) when compared to the use of either of the particles (e.g., comprising the macromolecule structures) alone. The comparative increase in effectiveness upon multiplexing may further indicate a synergistic relationship between highly negative and negative to neutral macromolecule surfaces. Example 4: Biomolecule Assaying Reproducibility [00370] In one example, to assess the performance of particles (e.g., comprising the macromolecule structures) (A2) and (A1), four (4) independent automated biomolecule assays were executed to generate 4 plates of peptides. Each plate contained pooled plasma samples with either 40 or 80 technical replicates across the plate. In each well of the plates the macromolecule structures were exposed to the plasma samples for 1 h and then the unbound proteins washed away. The bound plasma proteins were digested off the particles using trypsin/lys-C proteases and incubation for 1 h. The resulting peptides were separated from the macromolecular structures. Peptides were analyzed on an Thermo Scientific Vanquish Neo UHPLC coupled to a Thermo Scientific Orbitrap Exploris 480 Mass spectrometer with a 25 minute DIA acquisition gradient, and processed using two library free data processing recipes that either included (Recipe 370) or excluded (Recipe 216) having Match Between Runs turned on in the processing pipeline.
WSGR Docket No.53344-792.601 TABLE 5
Example 5: Biomolecule Assay Protocol [00371] Methods of assaying biomolecules may be completed using the following protocol. The assay protocol and methods herein may provide high-throughput, unbiased, deep, rapid proteomics analysis of biological samples, such as plasma, serum, and tissue or cell lysates (or other biological samples provided herein). The protocol may comprise an assay step, a peptide quantification step, and a peptide reconstitution step, which may be run separately. Materials [00372] The assay methods may be used to assay 40 or 80 biomolecules (peptide) samples on a single 96 well plate. The estimated time for each step of an exemplary method provided herein, is shown in Table 6, such as for an 80 or 40 sample analysis. Table 6
WSGR Docket No.53344-792.601 [00373] The assay may require use of an assay kit, such as a kit provided herein (i.e., assay kit). In cases where peptide quantification and peptide reconstitution are desired, an additional kit may be required (i.e., a PQR kit). [00374] The assay kit for analysis of 40 or 80 samples may contain the following reagents in Table 6. The kit may also include a labware box including a binding reservoir, black lid, 2 cleanup plates, clear lid, collection plate, nanoparticle plate, preparation plate, 2 reagents reservoirs, and a sample transfer plate. The labware box may not be refrigerated whereas the reagents kit (i.e., Table 7) may be refrigerated. The method may also make use of a peptide calibration kit. TABLE 7
[00375] The methods of biomolecule (peptide) preparation, quantification, and reconstitution may require the following additional equipment: (1) a centrifuge with plate adapter that can achieve a relative centrifugal force of 500 x g and accommodate a standard 96 well microplate; (2) a fluorometric microplate reader that can measure peptide concentration via fluorescence (Ex. 390, Em.475 nm) in a 96-well plate format; (3) a refrigerated microcentrifuge that can achieve a relative centrifugal force of 5000 x g, maintain a temperature of 4°C, and accommodate sample tubes; and (4) a vacuum concentrator capable of maintaining refrigerated temperature at vacuum and accommodate a standard 96 well microplate. Additional required materials may include 1-10 mL pipette with tips or 10 mL serological pipettes, 20-200 μL pipette with tips or 2-20 µL pipette, 20-200 µL multichannel pipette with tips, 100-1000 µL pipette with tips, 300 µL nested conductive tips (NCTs), 70% isopropyl alcohol or 70% ethanol, aluminum sealing foil 5 x 3 in, Axygen AxyMats 96 round well sealing mat for PCR microplates, deionized water, disposable
WSGR Docket No.53344-792.601 latex gloves, Eppendorf twin.tec PCR Plates 96 LoBind, semi-skirted, 250 µL, PCR clean, colorless, Kimwipes or similar lint-free tissues, Pierce quantitative fluorometric peptide assay, and a consistent supply of reagent-grade water (i.e., 18.2 MΩ supply or equivalent). [00376] During the assay, additional wells (e.g., in the 96 well plate) are dedicated to the following controls: (1) process control: a pooled plasmas sample that is processed through the entirety of the workflow, including corona formation, trypsin digestion, and peptide cleanup; (2) digestion control: a pooled plasma sample that is processed through workflow steps after the corona formation, including trypsin digestion and peptide cleanup, used for diagnostic and troubleshooting efforts; (3) user control: an available well for the end user to supply their own on plate control sample of interest; and (4) cleanup control: a digested peptide sample generated from pooled plasma sample that is only processed through the peptide cleanup steps of the assay, also used for diagnostic and troubleshooting efforts. Methods [00377] To carry out the method of assaying biomolecules, the centrifuge is first set to 4°C. If the biological (e.g., plasma) samples are frozen, they are removed from the freezer and thawed in an ice-water bath. The plasma samples should not be allowed to warm to room temperature and should be kept on ice or at 4°C until they are loaded into the sample prep plate and into the instrument. The labware is removed from the above-mentioned labware box and the Trypsin/LysC tube is placed on ice. The refrigerated reagents kit is removed from refrigeration (e.g., 4°C) and the enzyme reconstitution solution is placed on ice, the vials of Trypsin/LysC protease MS grade are placed on ice, and the remaining reagents are stored at room temperature. On ice, the Trypsin/LysC tube is prepared by adding 500 µL of enzyme reconstitution solution of one vial of Trypsin/LysC Protease MS Grade for a final concentration of 0.2 µg/µL. This solution is pipetted 2-3 times to mix. These steps are repeated for the remaining Trypsin/LysC vials. 500 µL from each of the Trypsin/LysC vials are transferred into the Trypsin/LysC tube and then the Trypsin/LysC tube is transferred to the chiller cooled to 4°C. The reagents from the reagent kit are loaded into Carriers A-D. [00378] The samples are loaded into the 96 well plate, an example of the loading of the 96 well plates for carrying out the assay or methods described herein is shown in FIG.5A for a 40-sample assay or FIG. 5B for an 80-sample assay. For each biological (e.g., plasma) sample, 120 µL of sample is transferred into the respective well of the 96 well plate (i.e., wells 1-80 for an 80-sample assay or wells 41-80 for a 40-sample assay). 120 µL of the control sample is added to well A11. The sample transfer plate is sealed followed by centrifugation at 500 x g for 15 seconds and the sample transfer plate is loaded into Carrier A. The assay method is then run. This portion of the
WSGR Docket No.53344-792.601 method may also refer to the corona formation and wash step, denaturation and digestion step, and peptide cleanup step. Peptide Quantification [00379] Peptide quantification may be completed. Required materials for the peptide quantification may include the PQR kit, described above, as well as an acid-resistant CentriVap centrifugal vacuum concentrator, a fluorescence intensity microplate reader, 50 µL nested conductive tips (NCTs), 300 µL NCTs, aluminum sealing foil 5 x 3 in, a Pierce quantitative fluorometric peptide assay, and pipettes with tips varying from 1-10 mL to 10-1000 µL. The PQR kit may include a black lid, quantification plate, quantification reservoir, reconstitution reservoir, recovery solution, and standards prep plate. The collection plate, standards prep plate, quantification reservoir, single 300 µL tip rack, 300 mL reservoir filled with 150 mL of 70% isopropyl alcohol, quantification plate, black plate lid, and single rack of 50 µL conductive tips are placed in the instrument. In the quantification reservoir, in separate wells are placed 2.4 mL of peptide assay reagent, 3 mL of recovery solution, and 5 mL of peptide assay buffer in two separate wells. In the standards prep plate in one well is placed 150 µL of digest standard. After loading of the samples and reagents, the peptide quantification method is run. Peptide Reconstitution [00380] Peptide reconstitution may be completed, which can reconstitute the dried peptides to the concentration and volume needed for mass spectrometry. The peptide reconstitution method may require use of the PQR kit described above as well as 300 µL NCTs, aluminum sealing foil 5 x 3 in, Axygen AxyMats 96 round well sealing mat for PCR microplates, peptide reconstitution buffer, and pipettes with tips varying from 1-10 mL to 10-1000 µL. To complete the peptide reconstitution, an appropriate sized bottle large enough to hold a sufficient volume to make a single batch for the anticipated study size is obtained, assuming 4 mL per plate. For example, an 800 sample study uses 10 plates/kit, requiring 40 mL of peptide calibration reconstitution buffer. The peptide reconstitution buffer is prepared by removing the PepCalMix tubes from -20°C storage and thawing at room temperature, adding 1 mL of peptide calibration recon buffer to each PepCalMix tube, vortexing the PepCalMix tubes for 10-15 seconds, centrifuging the PepCalMix tube for 1 min at 16,000 x g, and combinig the entire contents of each PepCalMix tube with peptide calibration reconstitution buffer at a ratio of 1 tube per 10 mL of buffer in the large storage bottle, and shaking to mix. The buffer is provided into the peptide calibration reconstitution tubes at 4 mL per tube and the prepared aliquots are frozen at -80°C. Before carrying out the reconstitution method, the aliquots are thawed to room temperature in a room temperature water bath. Optionally, the samples may be sonicated for about 10 seconds and/or vortexed briefly. If a control is used in the assay, it may be removed from -20°C storage, 24 µL of peptide reconstitution buffer
WSGR Docket No.53344-792.601 is added to the control tube and allowed to stand for 1 minute, and mixed by gently pipetting, after which the control is placed on ice to be used within 24 hours. The samples at which point are loaded into the instrument to carry out the reconstitution method. EMBODIMENTS [00381] Provided herein are exemplary embodiments: Embodiment 1. A composition comprising two or more macromolecule structures comprising: (a) a first macromolecule structure comprising a neutral to negative surface charge; and (b) a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure. Embodiment 2. The composition of embodiment 1, wherein the first macromolecule structure comprises a surface charge of about 0 mV to about -15 mV. Embodiment 3. The composition of any one of the preceding embodiments, wherein the second macromolecule structure comprises a surface charge of about -35 mV to about -60 mV. Embodiment 4. The composition of any one of the preceding embodiments, wherein the surface charge is characterized by a zeta potential. Embodiment 5. The composition of any one of the preceding embodiments, wherein the ratio of the first macromolecule structure to the second macromolecule structure is 10:1 to 1:10. Embodiment 6. The composition of any one of the preceding embodiments, wherein the ratio of the first macromolecule structure to the second macromolecule structure is 5:1 to 1:5. Embodiment 7. The composition of any one of the preceding embodiments, wherein the ratio of the first macromolecule structure to the second macromolecule structure is 1:1 to 1:5. Embodiment 8. The composition of any one of embodiments 1-7, wherein the second macromolecule structure comprises a polymer comprising one or more units represented by Formula (A):
WSGR Docket No.53344-792.601 Formula (A) wherein, R is hydrogen
R1 is hydrogen or hydroxyl; q is an integer from 1 to 6; R2 is C1-C8 diamine, N-substituted with one or more R3; R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; or R1 and R2 are taken together to form C2-C6 heterocycloalkyl; and R4 is hydrogen or C1-C6 alkyl. Embodiment 9. The composition of any one of embodiments 1-7, wherein the second macromolecule structure comprises a copolymer comprising two or more units represented by Formula (A) and Formula (B):
wherein, R is hydrogen
R1 is hydrogen or hydroxyl; q is an integer from 1 to 6; m is an integer from 1 to 6; R2 is C1-C8 diamine, N-substituted with one or more R3; R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; or R1 and R2 are taken together to form C2-C6 heterocycloalkyl; R4 is each independently hydrogen or C1-C6 alkyl;
is a single bond or a double bond; and
WSGR Docket No.53344-792.601 * is an attachment point to another unit of Formula (A) or Formula (B) when is a single bond. Embodiment 10. The composition of embodiment 5 or 9, wherein R is
. Embodiment 11. The composition of any one of embodiments 5-10, wherein R1 is hydroxyl. Embodiment 12. The composition of any one of embodiments 5-11, wherein R2 is a C2 diamine, N-substituted with one or more R3. Embodiment 13. The composition of any one of embodiments 5-11, wherein R2 is
, wherein p is an integer from 1 to 6. Embodiment 14. The composition of any one of embodiments 8-13, wherein the second macromolecule structure comprises a polymer comprising one or more units represented by Formula (C):
Formula (C) wherein, R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; q is an integer from 1 to 6; and p is an integer from 1 to 6. Embodiment 15. The composition of any one of embodiments 13-14, wherein p is an integer of 1. Embodiment 16. The composition of any one of embodiments 8-15, wherein at least one R3 is C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl. Embodiment 17. The composition of any one of embodiments 8-16, wherein at least one R3 is C1-C8 alkyl substituted with at least one of oxo, hydroxyl, and C1-C8 alkenyl. Embodiment 18. The composition of any one of embodiments 8-17, wherein the structure of Formula (A) is represented by Formula (A-A):
WSGR Docket No.53344-792.601
Formula (A-A) wherein, R5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. Embodiment 19. The composition of any one of embodiments 8-17, wherein the structure of Formula (A) is represented by Formula (A-B):
Formula (A-B) wherein, R5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. Embodiment 20. The composition of any one of embodiments 8-17, wherein the structure of Formula (A) is Formula
Formula (A-C) wherein, R5 is each independently C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl.
WSGR Docket No.53344-792.601 Embodiment 21. The composition of embodiment 17, wherein the structure of Formula (A- C) is:
. Embodiment 22. The composition of any one of embodiments 8-13, wherein the structure of Formula (A) is represented by Formula (A-D):
Formula (A-D) Embodiment 23. The composition of any one of embodiments 8-21, wherein q is an integer from 1 to 3. Embodiment 24. The composition of any one of embodiments 8-23, wherein q is an integer of 1. Embodiment 25. The composition of any one of embodiments 18-20, wherein R5 is C1-C10 alkenyl. Embodiment 26. The composition of embodiment 8 or 9, wherein R is hydrogen. Embodiment 27. The composition of embodiment 26, wherein the structure of Formula (A)
. Embodiment 28. The composition of any one of embodiments 8-10, wherein R1 and R2 are taken together to form C2 heterocycloalkyl. Embodiment 29. The composition of any one of embodiments 9-28, wherein m is an integer of 1. Embodiment 30. The composition of any one of embodiments 9-29, wherein R4 is C1-C6 alkyl.
WSGR Docket No.53344-792.601 Embodiment 31. The composition of any one of embodiments 9-30, wherein the structure of Formula (B) is:
. Embodiment 32. The composition of any one of embodiments 9-31, wherein the copolymer comprises the structure:
. Embodiment 33. The composition of any one of embodiments 1-7, wherein the first macromolecule structure comprises a copolymer comprising two or more units represented by Formula (D) and Formula (E):
wherein, R4 is each independently hydrogen or C1-C6 alkyl; R6 is hydrogen or (CH2)pOR7; R7 is hydrogen or C1-C6 alkyl; m is an integer from 1 to 6; p is an integer from 1 to 6;
WSGR Docket No.53344-792.601 is a single bond or a double bond; and * is an attachment point to another unit of Formula (D) or Formula (E) when
single bond. Embodiment 34. The composition of embodiment 33, wherein R6 is (CH2)pOR7. Embodiment 35. The composition of embodiment 33 or 34, wherein the structure of Formula (E) is represented by Formula (E-A):
Formula (E-A) Embodiment 36. The composition of any one of embodiments 33-35, wherein p is an integer of 2. Embodiment 37. The composition of any one of embodiments 33-36, wherein R7 is H. Embodiment 38. The composition of any one of embodiments 33-37, wherein R4 is C1-C6 alkyl. Embodiment 39. The composition of any one of embodiments 33-38, wherein m is an integer of 1. Embodiment 40. The composition of any one of embodiments 33-39, wherein the structure of Formula (E) is:
. Embodiment 41. The composition of any one of embodiments 33-40, wherein the structure of Formula (D) is:
WSGR Docket No.53344-792.601
. Embodiment 42. The composition of any one of embodiments 33-41, wherein the copolymer comprises the structure:
. Embodiment 43. The composition of any one of the preceding embodiments, wherein the first macromolecule structure comprises a surface. Embodiment 44. The composition of any one of the preceding embodiments, wherein the second macromolecule structure comprises a surface. Embodiment 45. The composition of embodiment 43 or 44, wherein the surface comprises a particle. Embodiment 46. The composition of embodiment 45, wherein the particle is a nanoparticle. Embodiment 47. The composition of embodiment 45, wherein the particle is a microparticle. Embodiment 48. The composition of any one of embodiments 45-47, wherein the particle comprises a diameter of from about 100 nm to about 750 nm. Embodiment 49. The composition of any one of embodiments 45-48, wherein the particle comprises a diameter of from about 100 nm to about 500 nm. Embodiment 50. The composition of any one of embodiments 45-49, wherein the particle comprises a polydispersity index (PDI) of from about 0.01 to about 0.2. Embodiment 51. The composition of any one of embodiments 45-50, wherein the particle comprises a PDI of from about 0.1 to about 0.2. Embodiment 52. The composition of any one of embodiments 45-51, wherein the particle comprises iron oxide.
WSGR Docket No.53344-792.601 Embodiment 53. The composition of any one of embodiments 45-52, wherein the particle comprises is a superparamagnetic iron oxide nanoparticle. Embodiment 54. The composition of any one of embodiments 45-53, wherein the particle comprises a core-shell structure. Embodiment 55. The composition of any one of embodiments 45-54, wherein the particle comprises an iron oxide core and a silica shell. Embodiment 56. The composition of any one of embodiments 45-54, wherein the particle comprises iron oxide crystals embedded in a polystyrene core. Embodiment 57. The composition of any one of embodiments 45-56, wherein the polymer or the copolymer is covalently coupled to the surface. Embodiment 58. The composition of any one of embodiments 45-57, wherein the polymer is non-covalently coupled to the surface. Embodiment 59. The composition of any one of embodiments 45-58, wherein the polymer or copolymer is covalently coupled to the surface via a linker. Embodiment 60. The composition of any one of embodiments 45-59, wherein the first macromolecule structure comprises the structure:
wherein,
the surface; L is a linker; and A is the copolymer of any one of embodiments 33-42. Embodiment 61. The composition of any one of embodiments 45-60, wherein the second macromolecule structure comprises the structure:
wherein,
the surface;
WSGR Docket No.53344-792.601 L is a linker; and B is the polymer or copolymer of any one of embodiments 5-32. Embodiment 62. The composition of any one of embodiments 59-61, wherein the linker comprises an alkylene, esteralkylene, or aralkylene. Embodiment 63. The composition of any one of embodiments 45-58, wherein the polymer or copolymer is covalently coupled to the surface via a base polymer. Embodiment 64. The composition of any one of embodiments 1-62, wherein the composition further comprises a stabilizing agent. Embodiment 65. The composition of embodiment 64, wherein the stabilizing agent comprises a metal salt. Embodiment 66. The composition of embodiment 65, wherein the metal salt comprises aluminum chloride. Embodiment 67. The composition of any one of embodiments 9-66, wherein the copolymer is a random copolymer. Embodiment 68. The composition of any one of embodiments 9-66, wherein the copolymer is a block copolymer. Embodiment 69. The composition of any one of embodiments 8-68, wherein the composition comprises at least 1 wt% of the polymer or copolymer. Embodiment 70. The composition of any one of embodiments 8-69, wherein the composition comprises from about 1 wt% to about 30 wt% of the polymer or copolymer. Embodiment 71. The composition of any one of embodiments 8-70, wherein the polymer or copolymer comprises a molecular weight of from about 0.5 kDa to about 25 kDa. Embodiment 72. The composition of any one of embodiments 8-71, wherein the polymer or copolymer comprises a molecular weight of from about 0.5 kDa to about 10 kDa. Embodiment 73. A method of isolating one or more biomolecules from a biological sample, the method comprising: (a) contacting the biological sample comprising one or more biomolecules with a composition of any one of embodiments 1-72 to bind the one or more biomolecules to the at least two macromolecule structures, thereby forming at least two biomolecule corona; and (b) eluting the one or more biomolecules from the at least two macromolecule structures, thereby providing one or more isolated biomolecules, wherein, the at least two macromolecule structures comprise: (i) a first macromolecule structure comprising a neutral to negative surface charge; and
WSGR Docket No.53344-792.601 (ii) a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure. Embodiment 74. The method of embodiment 73, wherein the method further comprises separating the one or more biomolecules and the at least two macromolecule structures from the biological sample. Embodiment 75. The method of embodiment 73 or 74, wherein the method further comprises optionally digesting the one or more biomolecules. Embodiment 76. A method of isolating one or more biomolecules from a biological sample, the method comprising: (a) contacting a population of biomolecules comprising one or more biomolecules with a composition of any one of embodiments 1-72, thereby forming at least two biomolecule corona; (b) separating and optionally digesting the one or more biomolecules and the at least two macromolecule structures from the biological sample; and (c) eluting and optionally digesting the one or more biomolecules from the at least two macromolecule structures, thereby providing one or more isolated biomolecules, wherein, the at least two macromolecule structures comprise: (i) a first macromolecule structure comprising a neutral to negative surface charge; and (ii) a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure. Embodiment 77. The method of any one of embodiments 73-76, wherein the first macromolecule structure comprises a surface charge of from about 0 mV to about -15 mV. Embodiment 78. The method of any one of embodiments 73-77, wherein the second macromolecule structure comprises a surface charge of from about -35 mV to about -60 mV. Embodiment 79. The method of any one of embodiments 73-78, wherein the surface charge is characterized by a zeta potential. Embodiment 80. The method of any one of embodiments 73-79, wherein the first macromolecule structure comprises the composition of any one of embodiments 33-72. Embodiment 81. The method of any one of embodiments 73-80, wherein the second macromolecule structure comprises the composition of any one of embodiments 5-32 or 43- 72. Embodiment 82. The method of any one of embodiments 73-81, wherein the one or more biomolecules comprises proteins, peptides, or a combination thereof.
WSGR Docket No.53344-792.601 Embodiment 83. The method of any one of embodiments 73-82, wherein the biological sample comprises plasma, serum, or blood. Embodiment 84. The method of any one of embodiments 73-82, wherein the biological sample comprises biofluid. Embodiment 85. The method of embodiment 84, wherein the biofluid is a cell-free biofluid. Embodiment 86. The method of any one of embodiments 73-85, wherein the method further comprises diluting the one or more biomolecules and at least two macromolecule structures. Embodiment 87. The method of embodiment 86, wherein the one or more biomolecules and at least two macromolecule structures are diluted in a buffer. Embodiment 88. The method of any one of embodiments 73-87, wherein eluting is in the presence of buffer or an aqueous solution. Embodiment 89. The method of any one of embodiments 73-88, wherein the contacting is in the presence of a buffer. Embodiment 90. The method of any one of embodiments 87-89, wherein the buffer comprise a pH of from about 8 to about 9 (e.g., pH of about 8.5). Embodiment 91. The method of any one of embodiment 87-90, wherein the buffer comprises HEPES. Embodiment 92. The method of any one of embodiments 73-91, wherein the method further comprises contacting the one or more biomolecules with the at least two macromolecule structures in the presence of an organic solvent. Embodiment 93. The method of embodiment 92, wherein the organic solvent comprises an alcohol, acetonitrile, dichloromethane, dimethylformamide (DMF), dimethylsulfoxide (DMSO), ethyl acetate, hexamethylphosphoramide (HMPA), or tetrahydrofuran. Embodiment 94. The method of embodiment 92 or 93, wherein the organic solvent comprises acetonitrile. Embodiment 95. The method of any one of embodiments 73-94, wherein eluting comprises contacting the one or more biomolecules and two or more macromolecule structure with an aqueous solution. Embodiment 96. The method of embodiment 95, wherein the aqueous solution comprises an organic solvent. Embodiment 97. The method of embodiment 96, wherein the aqueous solution comprises an organic solvent in an amount of no more than 50 wt% (e.g., 40 wt%, 30 wt%, 20 wt%, 10 wt%, or no more than 5 wt%).
WSGR Docket No.53344-792.601 Embodiment 98. The method of any one of embodiments 73-97, wherein the method is capable of isolating from about 100 to about 20,000 biomolecules. Embodiment 99. The method of any one of embodiments 73-98, wherein the method is capable of isolating at least 1,000 biomolecules. Embodiment 100. The method of embodiment 99, wherein each of the 1,000 biomolecules comprise a different structure. Embodiment 101. The method of any one of embodiments 73-100, wherein an amount of an acid or a base in a composition comprising the population of biomolecules is greater than the amount of the acid or the base in a composition comprising the one or more isolated biomolecules. Embodiment 102. The method of any one of embodiments 73-101, wherein an amount of a surfactant(s) in a composition comprising the population of biomolecules is greater than the amount of the surfactant(s) in a composition comprising the one or more isolated biomolecules. Embodiment 103. The method of any one of embodiments 73-102, wherein the method further comprises washing the one or more biomolecules and at least two macromolecule structures with a wash solution. Embodiment 104. The method of embodiment 103, wherein the wash solution comprises an organic solvent. Embodiment 105. The method of any one of embodiments 73-104, wherein the method further comprises identifying the one or more biomolecules. Embodiment 106. The method of embodiment 105, wherein the identifying comprises performing mass spectrometry (MS), liquid chromatography-mass spectrometry (LC-MS), protein sequencing, or a combination thereof. Embodiment 107. The method of embodiment 105 or 106, wherein the method is capable of identifying from about 1 to about 20,000 biomolecules. Embodiment 108. The method of any one of embodiments 105-107, wherein the method is capable of identifying from about 100 to about 10,000 biomolecules. Embodiment 109. The method of any one of embodiments 105 or 106, wherein the method is capable of identifying at least 100 biomolecules. Embodiment 110. The method of any one of embodiments 105-109, wherein the method is capable of identifying biomolecules over a dynamic range of at least 7, at least 8, at least 9, or at least 10.
WSGR Docket No.53344-792.601 Embodiment 111. The method of any one of embodiments 75-110, wherein the digesting comprises contacting the one or more biomolecules with trypsin, lysin, serine protease, or any combination thereof. Embodiment 112. The method of any one of embodiments 75-111, wherein the digesting comprises contacting the one or more biomolecules with a denaturing agent, a reduction agent, an alkylating agent, or any combination thereof. Embodiment 113. The method of embodiment 112, wherein the denaturing agent comprises sodium dodecyl sulfate, acetic acid, trichloroacetic acid, sulfosalicylic acid, sodium bicarbonate, ethanol, formaldehyde, glutaraldehyde, urea, guanidium chloride, lithium perchlorate, 2-mercaptoethanol, dithiothreitol, tris(2-carboxyethyl)phosphine (TCEP), or any combination thereof. Embodiment 114. The method of embodiment 112, wherein the reduction agent comprises TCEP, dithiothreitol, beta-mercaptoethanol, glutathione, cysteine, or any combination thereof. Embodiment 115. The method of embodiment 112, wherein the alkylating agent comprises iodoacetamide, iodoacetic acid, acrylamide, chloroacetamide, or any combination thereof. Embodiment 116. A system for isolating one or more biomolecules from a biological sample, the system comprising: (a) at least two macromolecule structures comprising: (i) a first macromolecule structure with a neutral to negative surface charge; and (ii) a second macromolecule structure with a greater negative surface charge than the first macromolecule structure, wherein the at least two macromolecule structures are configured to bind one or more biomolecules; (b) a suspension solution configured to suspend the at least two macromolecule structures; (c) a biological sample comprising one or more biomolecules; and (d) an automated system comprising a network of units with differentiated functions configured to isolate one or more biomolecules from the biological sample using the at least two macromolecule structures. Embodiment 117. The system of embodiment 116, wherein the network of units comprises: (a) a first unit comprising a multichannel fluid transfer instrument for transferring fluids between units within the system; (b) a second unit comprising a support for storing a plurality of biological samples; and (c) a third unit comprising a support for an array plate possessing partitions that comprise the one or more macromolecule structure for binding of the one or more biomolecules with the two or more macromolecule structures.
WSGR Docket No.53344-792.601 Embodiment 118. The system of embodiment 116 or 117, wherein the network of units further comprises a fourth unit comprising supports for storing a plurality of reagents. Embodiment 119. The system of any one of embodiments 116-118, wherein the network of units further comprises a fifth unit comprising supports for storing a reagent to be disposed of. Embodiment 120. The system of any one of embodiments 116-119, wherein the network of units further comprises supports for storing consumables used by a multichannel fluid transfer instrument. Embodiment 121. The system of any one of embodiments 116-120, wherein the first macromolecule structure comprises a surface charge of about 0 mV to about -15 mV. Embodiment 122. The system of any one of embodiments 116-121, wherein the second macromolecule structure comprises a surface charge of about -35 mV to about -60 mV. Embodiment 123. The system of any one of embodiments 116-122, wherein the surface charge is characterized by a zeta potential. Embodiment 124. The system of any one of embodiments 116-123, wherein the first macromolecule structure comprises the composition of any one of embodiments 33-72. Embodiment 125. The system of any one of embodiments 116-124, wherein the second macromolecule structure comprises the composition of any one of embodiments 8-32 or 43- 72. Embodiment 126. The system of any one of embodiments 116-125, wherein the automated system is configured to perform the method of any one of embodiments 73-115. Embodiment 127. A kit for isolating one or more biomolecules from a biological sample, the kit comprising: at least two macromolecule structures; (i) a first macromolecule structure with a neutral to negative surface charge; and (ii) a second macromolecule structure with a greater negative surface charge than the first macromolecule structure; Embodiment 128. The kit of embodiment 127, wherein the kit further comprises a washing agent configured to wash the one or more biomolecules bound to the at least two macromolecule structures. Embodiment 129. The kit of embodiment 127, wherein the kit further comprises an elution agent configured to elute the one or more biomolecules from the at least two macromolecule structures. Embodiment 130. The kit of embodiment 127, wherein the kit further comprises a denaturing agent.
WSGR Docket No.53344-792.601 Embodiment 131. The kit of embodiment 127, wherein the kit further comprises a reducing agent. Embodiment 132. The kit of any one of embodiments 127-131, wherein the kit further comprises an alkylation agent. Embodiment 133. The kit of any one of embodiments 127-132, wherein the kit further comprises at least one buffer. Embodiment 134. The kit of embodiment 133, wherein the at least one buffer comprises a digestion buffer, resuspension buffer, denaturation buffer, digestion buffer, or a lysis buffer. Embodiment 135. The kit of any one of embodiments 127-134, wherein the kit further comprises one or more organic solvents. Embodiment 136. The kit of any one of embodiments 134-135, wherein the buffer comprises HEPES. Embodiment 137. The kit of any one of embodiments 127-136, wherein one or more components of the kit are prepackaged into one or more containers. Embodiment 138. A method of preparing a mixture of at least two macromolecule structures, the at least two macromolecule structures comprising recurring units of a first monomer and a second monomer or a first monomer and a third monomer, the method comprising: (a) obtaining a first macromolecule structure comprising a neutral to negative surface charge; (b) obtaining a second macromolecule structure comprising a greater negative surface charge than the first macromolecule structure; and (c) forming a mixture comprising the first and second macromolecule structures. Embodiment 139. The method of embodiment 138, wherein the first macromolecule structure comprises a surface charge of about 0 mV to about -15 mV. Embodiment 140. The method of embodiment 138 or 139, wherein the second macromolecule structure comprises a surface charge of about -35 mV to about -60 mV. Embodiment 141. The method of any one of embodiments 138-140, wherein the surface charge is characterized by a zeta potential. Embodiment 142. The method of any one of embodiments 138-141, wherein the first macromolecule structure comprises the composition of any one of embodiments 33-72. Embodiment 143. The method of any one of embodiments 138-142, wherein the second macromolecule structure comprises the composition of any one of embodiments 8-32 or 43- 72.
WSGR Docket No.53344-792.601 Embodiment 144. A method of preparing a macromolecule structure comprising recurring units of a first component and a second component, the method comprising: (a) providing a mixture of monomers in a solvent comprising a first monomer and a second monomer, wherein the first monomer comprises:
wherein q is an integer from 1 to 6; and the second monomer comprises:
wherein m is an integer from 1 to 6; (b) contacting a surface and the mixture of monomers, thereby producing a reaction mixture; (c) polymerizing the mixture of monomers to produce a macromolecule immobilized to the surface; (d) contacting the macromolecule immobilized to the surface and an amine, thereby producing an aminated macromolecule; and (e) optionally, contacting the aminated macromolecule with an anhydride optionally substituted with R2, wherein R2 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. Embodiment 145. The method of embodiment 144, wherein the surface comprises a particle. Embodiment 146. The method of embodiment 145, wherein the particle is a nanoparticle. Embodiment 147. The method of embodiment 145, wherein the particle is a microparticle. Embodiment 148. The method of any one of embodiments 145-147, wherein the particle comprises a diameter of from about 100 nm to about 750 nm. Embodiment 149. The method of any one of embodiments 145-148, wherein the particle comprises a diameter of from about 100 nm to about 500 nm. Embodiment 150. The method of any one of embodiments 145-149, wherein the particle comprises a polydispersity index (PDI) of about 0.01 to about 0.2.
WSGR Docket No.53344-792.601 Embodiment 151. The method of any one of embodiments 145-150, wherein the particle comprises a PDI of about 0.1 to about 0.2. Embodiment 152. The method of any one of embodiments 145-151, wherein the particle comprises iron oxide. Embodiment 153. The method of any one of embodiments 145-152, wherein the particle comprises is a superparamagnetic iron oxide nanoparticle. Embodiment 154. The method of any one of embodiments 145-153, wherein the particle comprises a core-shell structure. Embodiment 155. The method of any one of embodiments 145-154, wherein the particle comprises an iron oxide core and a silica shell. Embodiment 156. The method of any one of embodiments 145-154, wherein the particle comprises iron oxide crystals embedded in a polystyrene core. Embodiment 157. The method of any one of embodiments 144-155, wherein (b) comprises contacting in an organic solvent. Embodiment 158. The method of any one of embodiments 144-156, wherein (d) comprises contacting in an organic solvent. Embodiment 159. The method of embodiment 157 or 158, wherein the organic solvent comprises an alcohol, acetonitrile, dichloromethane, dimethylformamide (DMF), dimethylsulfoxide (DMSO), ethylacetate, hexamethylphosphoramide (HMPA), or tetrahydrofuran. Embodiment 160. The method of embodiment 159, wherein the organic solvent comprises acetonitrile. Embodiment 161. The method of embodiment 159, wherein the organic solvent comprises DMF. Embodiment 162. The method of any one of embodiments 144-161, wherein the method further comprises heating. Embodiment 163. The method of embodiment 162, wherein the heating comprises heating to a temperature of at least 50°C, 60°C, 70°C, 80°C, or at least 90°C. Embodiment 164. The method of any one of embodiments 144-163, wherein the polymerization comprises free radical polymerization, atom transfer radical polymerization (ATRP), emulsion polymerization, or precipitation polymerization. Embodiment 165. The method of any one of embodiments 144-164, wherein the macromolecule structure comprises a composition of any one of embodiments 1-42.
WSGR Docket No.53344-792.601 Embodiment 166. Use of a macromolecule structure comprising 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units for binding proteins in a biological sample. Embodiment 167. Use of a macromolecule structure comprising the structure of Formula (A-D) and the structure of Formula (A-A) as recurring units for binding proteins in a biological sample. Embodiment 168. Use of a macromolecule structure comprising the structure of Formula (A-C) and the structure of Formula (A-B) as recurring units for binding proteins in a biological sample. Embodiment 169. Use of the composition of any one of embodiment 1-72 for binding proteins in a biological sample. Embodiment 170. A composition comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units. Embodiment 171. A composition comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises ethylene glycol dimethacrylate, monomer 6, and at least one of: monomer 7, monomer 8, monomer 9, and glycidyl methacrylate. Embodiment 172. A composition obtained by a method comprising polymerizing 2- hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles. Embodiment 173. A composition obtained by a method comprising: (i) polymerizing glycidyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles to form polymer-coated particles; (ii) reacting the polymer-coated magnetic particles with an alkylene diamine to form amine-modified magnetic particles; and (iii) reacting the amine-modified magnetic particles with an optionally substituted succinic acid anhydride. Embodiment 174. A method comprising: (a) contacting a plasma or serum sample comprising one or more proteins with the magnetic particles in the composition of any one of embodiments 170-173, thereby adsorbing at least a portion of the proteins to the magnetic particles; (b) separating the adsorbed proteins and the magnetic particles from the plasma or serum;
WSGR Docket No.53344-792.601 (c) eluting and optionally digesting the adsorbed proteins from the magnetic particles, thereby providing one or more isolated proteins; (d) optionally purifying the isolated proteins using solid phase extraction; and (e) analyzing the isolated proteins using mass spectrometry. Embodiment 175. A method of making polymer-coated magnetic particles, the method comprising polymerizing 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles. Embodiment 176. A method of making polymer-coated magnetic particles, the method comprising: (i) polymerizing glycidyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles to form polymer- coated particles; (ii) reacting the polymer-coated magnetic particles with an alkylene diamine to form amine-modified magnetic particles; and (iii) reacting the amine-modified magnetic particles with an optionally substituted succinic acid anhydride. [00382] While preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the present disclosure may be employed in practicing the present disclosure. It is intended that the following claims define the scope of the present disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby. The section headings used herein are for organizational purposes only and are not to be construed as limiting the subject matter described.
Claims
WSGR Docket No.53344-792.601 CLAIMS We claim: 1. A composition comprising two or more particles comprising: (a) a first particle comprising a first macromolecule structure, the first particle comprising a neutral to negative surface charge; and (b) a second particle comprising a second macromolecule structure, the second particle comprising a greater negative surface charge than the first particle. 2. The composition of claim 1, wherein the first particle has a surface charge of greater than -20 mV. 3. The composition of claim 1 or 2, wherein the first particle has a surface charge of about 0 mV to about -15 mV. 4. The composition of any one of the preceding claims, wherein the second particle has a surface charge of less than -20 mV. 5. The composition of any one of the preceding claims, wherein the second particle has a surface charge of about -35 mV to about -60 mV. 6. The composition of any one of the preceding claims, wherein the surface charge is characterized by a zeta potential. 7. The composition of any one of the preceding claims, wherein the ratio of the first particle to the second particle is 10:1 to 1:10. 8. The composition of any one of the preceding claims, wherein the ratio of the first particle to the second particle is 5:1 to 1:5. 9. The composition of any one of the preceding claims, wherein the ratio of the first particle to the second particle is 1:1 to 1:5. 10. The composition of any one of the preceding claims, wherein the ratio of the first particle to the second particle is about 1:4. 11. The composition of any one of the preceding claims, wherein the second macromolecule structure comprises a polymer comprising one or more units represented by Formula (A):
WSGR Docket No.53344-792.601
Formula (A) wherein, R is hydrogen
R1 is hydrogen or hydroxyl; q is an integer from 1 to 6; R2 is C1-C8 diamine, N-substituted with one or more R3; R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; or R1 and R2 are taken together to form C2-C6 heterocycloalkyl; and R4 is hydrogen or C1-C6 alkyl. 12. The composition of any one of claims 1-10, wherein the second macromolecule structure comprises a copolymer comprising two or more units represented by Formula (A) and Formula (B):
wherein, R is hydrogen
R1 is hydrogen or hydroxyl; q is an integer from 1 to 6; m is an integer from 1 to 6; R2 is C1-C8 diamine, N-substituted with one or more R3; R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; or
WSGR Docket No.53344-792.601 R1 and R2 are taken together to form C2-C6 heterocycloalkyl; R4 is each independently hydrogen or C1-C6 alkyl;
is a single bond or a double bond; and * is an attachment point to another unit of Formula (A) or Formula (B) when is a single bond.
13. The composition of claim 11 or 12, wherein R is . 14. The composition of any one of claims 11-13, wherein R1 is hydroxyl. 15. The composition of any one of claims 11-14, wherein R2 is a C2 diamine, N-substituted with one or more R3. 16. The composition of any one of claims 11-14, wherein
wherein p is an integer from 1 to 6. 17. The composition of any one of claims 11-16, wherein the second macromolecule structure comprises a polymer comprising one or more units represented by Formula (C):
Formula (C) wherein, R3 is each independently hydrogen or C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl; q is an integer from 1 to 6; and p is an integer from 1 to 6. 18. The composition of any one of claims 16-17, wherein p is an integer of 1. 19. The composition of any one of claims 16-18, wherein at least one R3 is C1-C8 alkyl optionally substituted with one or more oxo, hydroxyl, C1-C8 alkyl, C1-C8 alkenyl, and C1-C8 alkynyl.
WSGR Docket No.53344-792.601 20. The composition of any one of claims 16-19, wherein at least one R3 is C1-C8 alkyl substituted with at least one of oxo, hydroxyl, and C1-C8 alkenyl. 21. The composition of any one of claims 11-20, wherein the structure of Formula (A) is represented by Formula (A-A):
Formula (A-A) wherein, R5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. 22. The composition of any one of claims 11-20, wherein the structure of Formula (A) is represented by Formula (A-B):
Formula (A-B) wherein, R5 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. 23. The composition of any one of claims 11-20, wherein the structure of Formula (A) is Formula (A-C):
WSGR Docket No.53344-792.601
Formula (A-C) wherein, R5 is each independently C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. 24. The composition of claim 23, wherein the structure of Formula (A-C) is:
. 25. The composition of any one of claims 11-16, wherein the structure of Formula (A) is represented by Formula (A-D):
Formula (A-D) 26. The composition of any one of claims 11-25, wherein q is an integer from 1 to 3. 27. The composition of any one of claims 11-26, wherein q is an integer of 1. 28. The composition of any one of claims 20-23, wherein R5 is C1-C10 alkenyl. 29. The composition of claim 11 or 12, wherein R is hydrogen. 30. The composition of claim 29, wherein the structure of Formula (A) is:
WSGR Docket No.53344-792.601
. 31. The composition of any one of claims 11-13, wherein R1 and R2 are taken together to form C2 heterocycloalkyl. 32. The composition of any one of claims 12-31, wherein m is an integer of 1. 33. The composition of any one of claims 12-32, wherein R4 is C1-C6 alkyl. 34. The composition of any one of claims 12-33, wherein the structure of Formula (B) is:
. 35. The composition of any one of claims 12-34, wherein the copolymer comprises the structure:
. 36. The composition of any one of claims 1-10, wherein the first macromolecule structure comprises a copolymer comprising two or more units represented by Formula (D) and Formula (E):
WSGR Docket No.53344-792.601
wherein, R4 is each independently hydrogen or C1-C6 alkyl; R6 is hydrogen or (CH2)pOR7; R7 is hydrogen or C1-C6 alkyl; m is an integer from 1 to 6; p is an integer from 1 to 6;
is a single bond or a double bond; and * is an attachment point to another unit of Formula (D) or Formula (E) when
single bond. 37. The composition of claim 36, wherein R6 is (CH2)pOR7. 38. The composition of claim 36 or 37, wherein the structure of Formula (E) is represented by Formula (E-A):
Formula (E-A) 39. The composition of any one of claims 36-38, wherein p is an integer of 2. 40. The composition of any one of claims 36-39, wherein R7 is H. 41. The composition of any one of claims 36-40, wherein R4 is C1-C6 alkyl. 42. The composition of any one of claims 36-41, wherein m is an integer of 1. 43. The composition of any one of claims 36-42, wherein the structure of Formula (E) is:
WSGR Docket No.53344-792.601
. 44. The composition of claim 34, wherein R6 is hydrogen. 45. The composition of claim 44, wherein R4 is C1-C6 alkyl. 46. The composition of claim 44 or 45, wherein the structure of Formula (E) is:
. 47. The composition of any one of claims 34-43, wherein the structure of Formula (D) is:
. 48. The composition of any one of claims 36-44, wherein the copolymer comprises the structure:
. 49. The composition of any one of claims 36-48, wherein the first macromolecule structure comprises a copolymer comprising three or more units represented by:
WSGR Docket No.53344-792.601
50. The composition of claim 49, wherein the unit represented by
is present in the first macromolecule structure in an amount of less than 5 wt%. 51. The composition of any one of the preceding claims, wherein the two or more particles are nanoparticles. 52. The composition of any one of the preceding claims, wherein the two or more particles each individually have a diameter of from about 100 nm to about 750 nm. 53. The composition of any one of the preceding claims, wherein the two or more particles each individually have a diameter of from about 100 nm to about 500 nm. 54. The composition of any one of the preceding claims, wherein the two or more particles each individually have a polydispersity index (PDI) of from about 0.01 to about 0.2. 55. The composition of any one of the preceding claims, wherein the two or more particles each individually have a PDI of from about 0.1 to about 0.2. 56. The composition of any one of the preceding claims, wherein the two or more particles comprises iron oxide. 57. The composition of any one of the preceding claims, wherein the two or more particles comprises a superparamagnetic iron oxide nanoparticle. 58. The composition of any one of the preceding claims, wherein the two or more particles comprises a core-shell structure. 59. The composition of any claim 58, wherein the core of the core-shell structure is paramagnetic.
WSGR Docket No.53344-792.601 60. The composition of any one of the preceding claims, wherein the two or more particles comprise an iron oxide core and a silica shell. 61. The composition of any one of claims 11-60, wherein the polymer or the copolymer is covalently coupled to a surface of the particle. 62. The composition of any one of claims 11-60, wherein the polymer is non-covalently coupled to a surface of the particle. 63. The composition of any one of claims 11-61, wherein the polymer or copolymer is covalently coupled to a surface of the particle via a linker. 64. The composition of any one of the preceding claims, wherein the first particle comprises the structure:
wherein,
is a surface of the first particle; L is a linker; and A is the copolymer of any one of claims 36-49. 65. The composition of any one of the preceding claims, wherein the second particle comprises the structure:
wherein,
is a surface of the second particle; L is a linker; and B is the polymer or copolymer of any one of claims 11-35. 66. The composition of any one of claims 63-65, wherein the linker comprises an alkylene, esteralkylene, or aralkylene.
WSGR Docket No.53344-792.601 67. The composition of any one of claims 12-66, wherein the copolymer is a random copolymer. 68. The composition of any one of claims 12-66, wherein the copolymer is a block copolymer. 69. The composition of any one of claims 11-68, wherein the composition comprises at least 1 wt% of the polymer or copolymer. 70. The composition of any one of claims 11-69, wherein the composition comprises from about 1 wt% to about 30 wt% of the polymer or copolymer. 71. The composition of any one of claims 11-70, wherein the polymer or copolymer comprises a molecular weight of from about 0.5 kDa to about 25 kDa. 72. The composition of any one of claims 11-71, wherein the polymer or copolymer comprises a molecular weight of from about 0.5 kDa to about 10 kDa. 73. A method of isolating one or more biomolecules from a biological sample, the method comprising: (a) contacting the biological sample comprising one or more biomolecules with a composition of any one of claims 1-72 to bind the one or more biomolecules to the at least two particles, thereby forming at least two biomolecule corona; and (b) eluting the one or more biomolecules from the at least two particles, thereby providing one or more isolated biomolecules. 74. A method of assaying a biological sample, the method comprising: (a) contacting the biological sample with a composition of any one of claims 1-72 to form at least two biomolecule corona; (b) assaying the at least two biomolecule corona to detect one or more biomolecules in the biological sample, wherein the assaying detects at least 5% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle; or wherein the assaying detects at least 50% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle.
WSGR Docket No.53344-792.601 75. The method of claim 73, wherein assaying detects at least 10% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the second particle in absence of the first particle. 76. The method of claim 74, wherein assaying detects at least 60% more unique biomolecules than a method comprising contacting the biological sample with a composition comprising the first particle in absence of the second particle. 77. The method of any one of claims 73-76, wherein the method further comprises separating the one or more biomolecules and the at least two particles from the biological sample. 78. The method of any one of claims 73-78, wherein the one or more biomolecules comprises proteins, peptides, or a combination thereof. 79. The method of any one of claims 73-78, wherein the biological sample comprises plasma, serum, or blood. 80. The method of any one of claims 74-79, further comprising eluting the one or more biomolecules from the two or more particles. 81. The method of claim 80, wherein eluting is in the presence of buffer or an aqueous solution. 82. The method of any one of claims 73-81, wherein the contacting is in the presence of a buffer. 83. The method of claim 82, wherein the buffer comprise a pH of from about 7 to about 8. 84. The method of claim 82 or 83, wherein the buffer comprises a pH of from about 7.4 to 7.6. 85. The method of any one of claims 83 or 84, wherein the buffer comprises HEPES. 86. The method of any one of claims 73-85, wherein one of the first particle or second particle is contacted with the one or more biomolecules at a concentration of 0.1 mg/mL to 0.2 mg/mL.
WSGR Docket No.53344-792.601 87. The method of any one of claims 73-86, wherein one of the first particle or second particle is contacted with the one or more biomolecules at a concentration of 0.5 mg/mL to 0.6 mg/mL. 88. The method of any one of claims 73-87, wherein the first particle and second particle are contacted with the one or more biomolecules at a concentration of 0.6 mg/mL to 0.8 mg/mL. 89. The method of any one of claims 73-88, wherein the method further comprises contacting the one or more biomolecules with the at least two particles in the presence of an organic solvent. 90. The method of any one of claims 73-77, wherein the method further comprises optionally digesting, alkylating, and/or lysing the one or more biomolecules to provide one or more digested biomolecules. 91. The method of claim 90, wherein the method comprises purifying the one or more digested biomolecules. 92. The method of claim 91, wherein purifying the one or more digested biomolecules comprises contacting the one or more digested biomolecules with a third particle in an organic solvent to form a biomolecule corona. 93. The method of any one of claims 90-92, wherein the organic solvent comprises an alcohol, acetonitrile, dichloromethane, dimethylformamide (DMF), dimethylsulfoxide (DMSO), ethyl acetate, hexamethylphosphoramide (HMPA), or tetrahydrofuran. 94. The method of claim 93, wherein the organic solvent comprises acetonitrile. 95. The method of any one of claims 92-94, wherein the method comprises eluting the one or more digested biomolecules from the third particle. 96. The method of claim 95, wherein eluting comprises contacting the one or more digested biomolecules and third particle with an aqueous solution. 97. The method of any one of claims 73-96, wherein eluting comprises contacting the one or more biomolecules and two or more particles with an aqueous solution. 98. The method of claim 96 or 97, wherein the aqueous solution comprises an organic solvent.
WSGR Docket No.53344-792.601 99. The method of claim 98, wherein the aqueous solution comprises an organic solvent in an amount of no more than 50 wt% (e.g., 40 wt%, 30 wt%, 20 wt%, 10 wt%, or no more than 5 wt%). 100. The method of any one of claims 73-99, wherein the method is capable of isolating from about 100 to about 20,000 biomolecules. 101. The method of any one of claims 73-100, wherein the method is capable of isolating at least 1,000 biomolecules. 102. The method of claim 101, wherein each of the 1,000 biomolecules comprise a different structure. 103. The method of any one of claims 73-102, wherein an amount of an acid or a base in a composition comprising the population of biomolecules is greater than the amount of the acid or the base in a composition comprising the one or more isolated biomolecules. 104. The method of any one of claims 73-103, wherein an amount of a surfactant(s) in a composition comprising the population of biomolecules is greater than the amount of the surfactant(s) in a composition comprising the one or more isolated biomolecules. 105. The method of any one of claims 73-104, wherein the method further comprises washing the one or more biomolecules and at least two particles with a wash solution. 106. The method of claim 105, wherein the wash solution comprises an organic solvent. 107. The method of any one of claims 75-106, wherein the method further comprises identifying the one or more biomolecules. 108. The method of any one of claims 73-106, wherein the method further comprises assaying the one or more digested biomolecules to identify the one or more biomolecules. 109. The method of claim 108, wherein the assaying or identifying comprises performing mass spectrometry (MS), liquid chromatography-mass spectrometry (LC-MS), protein sequencing, or a combination thereof. 110. The method of any one of claims 74-109, wherein when repeated, the assaying yields a percent quantile normalized coefficient (QNCV) of variation of 30% or less.
WSGR Docket No.53344-792.601 111. The method of any one of claims 74-110, wherein when repeated, the assaying yields a percent quantile normalized coefficient (QNCV) of variation of 20% or less. 112. The method of any one of claims 74-111, wherein the method is capable of identifying from about 100 to about 10,000 biomolecules. 113. The method of any one of claims 74-111, wherein the method is capable of identifying at least 100 biomolecules. 114. The method of any one of claims 74-113, wherein the method is capable of identifying biomolecules over a dynamic range of at least 7, at least 8, at least 9, or at least 10. 115. The method of any one of claims 90-114, wherein the digesting comprises contacting the one or more biomolecules with trypsin, lysin, serine protease, or any combination thereof. 116. The method of any one of claims 90-115, wherein the digesting comprises contacting the one or more biomolecules with a denaturing agent, a reduction agent, an alkylating agent, or any combination thereof. 117. The method of claim 116, wherein the denaturing agent comprises sodium dodecyl sulfate, acetic acid, trichloroacetic acid, sulfosalicylic acid, sodium bicarbonate, ethanol, formaldehyde, glutaraldehyde, urea, guanidium chloride, lithium perchlorate, 2- mercaptoethanol, dithiothreitol, tris(2-carboxyethyl)phosphine (TCEP), or any combination thereof. 118. The method of claim 116, wherein the reduction agent comprises TCEP, dithiothreitol, beta-mercaptoethanol, glutathione, cysteine, or any combination thereof. 119. The method of claim 116, wherein the alkylating agent comprises iodoacetamide, iodoacetic acid, acrylamide, chloroacetamide, or any combination thereof. 120. A system for isolating one or more biomolecules from a biological sample, the system comprising: (a) a composition of any one of claims 1-72; (b) a suspension solution configured to suspend the at least two particles; (c) a biological sample comprising one or more biomolecules; and
WSGR Docket No.53344-792.601 (d) an automated system comprising a network of units with differentiated functions configured to isolate one or more biomolecules from the biological sample using the at least two particles. 121. The system of claim 120, wherein the network of units comprises: (a) a first unit comprising a multichannel fluid transfer instrument for transferring fluids between units within the system; (b) a second unit comprising a support for storing a plurality of biological samples; and (c) a third unit comprising a support for an array plate possessing partitions that comprise the two or more particles for binding of the one or more biomolecules with the two or more particles. 122. The system of any one of claims 120-121, wherein the automated system is configured to perform the method of any one of claims 73-119. 123. A kit for isolating one or more biomolecules from a biological sample, the kit comprising a composition of any one of claims 1-72. 124. A method of preparing a mixture of at least two particles, the at least two particles comprising recurring units of a first monomer and a second monomer or a first monomer and a third monomer, the method comprising: (a) obtaining a first particle comprising a neutral to negative surface charge; (b) obtaining a second particle comprising a greater negative surface charge than the first particles; and (c) forming a mixture comprising the first and second particles. 125. The method of claim 124 wherein the first particle comprises the composition of any one of claims 1-72. 126. The method of any one of claims 124-125, wherein the second particle comprises the composition of any one of claims 1-72. 127. A method of preparing a macromolecule structure comprising recurring units of a first component and a second component, the method comprising: (a) providing a mixture of monomers in a solvent comprising a first monomer and a second monomer, wherein the first monomer comprises:
WSGR Docket No.53344-792.601
wherein q is an integer from 1 to 6; and the second monomer comprises:
wherein m is an integer from 1 to 6; (b) contacting a surface and the mixture of monomers, thereby producing a reaction mixture; (c) polymerizing the mixture of monomers to produce a macromolecule immobilized to the surface of a particle; (d) contacting the macromolecule immobilized to the surface and an amine, thereby producing an aminated macromolecule; and (e) optionally, contacting the aminated macromolecule with an anhydride optionally substituted with R2, wherein R2 is C1-C10 alkyl, C1-C10 alkenyl, or C1-C10 alkynyl. 128. Use of a macromolecule structure comprising 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units for binding proteins in a biological sample. 129. Use of a particle comprising a macromolecule structure comprising the structure of Formula (A-D) and the structure of Formula (A-A) as recurring units for binding proteins in a biological sample. 130. Use of a particle comprising a macromolecule structure comprising the structure of Formula (A-C) and the structure of Formula (A-B) as recurring units for binding proteins in a biological sample. 131. Use of the composition of any one of claim 1-72 for binding proteins in a biological sample.
WSGR Docket No.53344-792.601 132. A composition comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid as monomer units. 133. A composition comprising a plurality of particles, wherein the particles comprise an outer polymer surface and a magnetic core, wherein the outer polymer surface comprises ethylene glycol dimethacrylate, monomer 6, and at least one of: monomer 7, monomer 8, monomer 9, and glycidyl methacrylate. 134. A composition obtained by a method comprising polymerizing 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles. 135. A composition obtained by a method comprising: (i) polymerizing glycidyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl- functionalized magnetic particles to form polymer-coated particles; (ii) reacting the polymer-coated magnetic particles with an alkylene diamine to form amine-modified magnetic particles; and (iii) reacting the amine-modified magnetic particles with an optionally substituted succinic acid anhydride. 136. A method comprising: (a) contacting a plasma or serum sample comprising one or more proteins with the magnetic particles in the composition of any one of claims 1-72, thereby adsorbing at least a portion of the proteins to the magnetic particles; (b) separating the adsorbed proteins and the magnetic particles from the plasma or serum; (c) eluting and optionally digesting the adsorbed proteins from the magnetic particles, thereby providing one or more isolated proteins; (d) optionally purifying the isolated proteins using solid phase extraction; and (e) analyzing the isolated proteins using mass spectrometry. 137. A method of making polymer-coated magnetic particles, the method comprising polymerizing 2-hydroxyethyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles.
WSGR Docket No.53344-792.601 138. A method of making polymer-coated magnetic particles, the method comprising: (i) polymerizing glycidyl methacrylate, ethylene glycol dimethacrylate, and methacrylic acid in the presence of vinyl-functionalized magnetic particles to form polymer-coated particles; (ii) reacting the polymer-coated magnetic particles with an alkylene diamine to form amine-modified magnetic particles; and (iii) reacting the amine-modified magnetic particles with an optionally substituted succinic acid anhydride.
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| WO2023245075A2 (en) * | 2022-06-15 | 2023-12-21 | Seer, Inc. | Systems and methods for biomolecule assays |
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| WO1993012184A1 (en) * | 1991-12-03 | 1993-06-24 | Rohm And Haas Company | Process for particle adsorption |
| US20050009002A1 (en) * | 2001-03-20 | 2005-01-13 | Depu Chen | Processes for producing coated magnetic microparticles and uses thereof |
| US7713627B2 (en) * | 2006-03-24 | 2010-05-11 | Jsr Corporation | Magnetic particles comprising an organic polymer layer and method for producing the same |
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