WO2025159980A1 - Ratchet-chelators as unique barcodes for nanopore sequencing - Google Patents

Abstract

In one aspect, the disclosed technology relates to nanopore sequencing with a polynucleotide comprising a plurality of nucleotides, wherein each nucleotide comprises a chelating moiety bound to a metal ion. In some embodiments, the chelating moieties are configured for slowing or halting the polynucleotide translocation through a nanopore until a specific stimulus is achieved. In some embodiments, the chelating moieties, as well as any bound metal ions, can serve as reporters for specific nucleotides.

Description

RATCHET-CHELATORS AS UNIQUE BARCODES FOR NANOPORE SEQUENCING

INCORPORATION BY REFERENCE TO RELATED APPLICATION

[0001] This PCT application claims priority to U.S. Provisional Application 63/624011, filed January 23, 2024, the entirety of which is incorporated herein for any and all purposes.

BACKGROUND

[0002] Some polynucleotide sequencing techniques involve performing a large number of controlled reactions on support surfaces or within predefined reaction chambers. The controlled reactions may then be observed or detected, and subsequent analysis may help identify properties of the polynucleotide involved in the reaction. Examples of such sequencing techniques include next-generation sequencing or massive parallel sequencing involving sequencing-by-ligation, sequencing-by-synthesis, reversible terminator chemistry, or pyrosequencing approaches.

[0003] Some polynucleotide sequencing techniques utilize a nanopore, which can provide a path for an ionic electrical current. For example, as the polynucleotide traverses through the nanopore, it influences the electrical current through the nanopore. Each passing nucleotide, or series of nucleotides, that passes through the nanopore yields a characteristic blockage current. These characteristic electrical currents of the traversing polynucleotide can be recorded to determine the sequence of the polynucleotide.

SUMMARY

[0004] The readhead of nanopores (e.g., the constriction region of nanopores) usually reports the summation of all bases residing in the readhead concurrently along the sample DNA strand, increasing the challenge of accurate nanopore sequencing due to many permutations of signals arising from different sequences. For example, the MspA pore reads about 4 bases at a time, giving rise to at least 4⁴ = 256 different signals that need to be deconvoluted and resolved. [0005] In one aspect, the disclosed technology provides a method of directly sequencing a native strand of nucleic acids modified with various chemical moieties, including chelating moieties capable of binding to metal ions, linked to the nucleic acids via chemical/enzymatic means to attenuate translocation and enhance any signal generated as a consequence of the nucleotide passing through the readhead. In another aspect, the disclosed technology provides a method that instead of directly sequencing the sample DNA, a daughter strand is synthesized using natural or synthetic nucleotides, the daughter strand being generated from a template polynucleotide sequence, wherein the resulting daughter strand (“target polynucleotide”) further features the addition of various chemical moieties, including chelating moieties, linked to nucleotides via chemical/enzymatic means to attenuate translocation, or to provide a signal as a consequence of the chelating moiety and the nucleotide passing through the readhead. Generally, a metal ion can be introduced to each nucleotide/base by covalently attaching chelating moieties that can subsequently chelate to metal ions. Chelating moieties can have linear, branched, or cyclic structures, and serve to arrest (e.g., slow or halt) translocation through a nanopore. Moreover, chelating moieties along with metal ions can serve as identifier “barcodes” for identifying attached nucleotides. The metal ion in the modification can modulate the blockage current to further increase the signal resolution between each k-mer, thus enhancing accuracy in base calling.

[0006] In some aspects, the techniques described herein relate to a compound having one of the following structures:

wherein: n is 0 or a positive integer; Y is -O-, -S-, or -NH-; X is -O-, -NH-, or -CH2-; Li includes a linking group; and M is a modification including a chelating moiety. [0007] In some aspects, the techniques described herein relate to compounds 1(a) to VIII(a), wherein the modification further includes a metal ion complexed to the chelating moiety.

[0008] In some aspects, the techniques described herein relate to compounds 1(a) to VIII(a), wherein the metal ion is selected from the group consisting of Zn²⁺, Cd²⁺, Co²⁺, NI²⁺, Pb²⁺, Au³⁺, Hg²⁺, Ba²⁺, Cu²⁺, Fe²⁺, Al³⁺, Mn²⁺ and Mg²⁺.

[0009] In some aspects, the techniques described herein relate to compounds 1(a) to VIII(a), wherein the chelating moiety is selected from the group consisting of: Polyhistidine tag (His-tag), HQ-tag, HN-tag, HAT-tag, Zn finger (Zif268), DNA hairpins, G-quadruplex, porphyrins, crown-ethers, cyclodextrins, cucurbiturils, EDTA, tetraxetan (DOTA), NOTA, TETA, and HEHA.

[0010] In some aspects, the techniques described herein relate to compounds 1(a) to VIII(a), wherein LI includes a linking group selected from the group consisting of amine- NHS ester, amine-imidoester, amine-pentafluorophenyl ester, amine-hydroxymethyl phosphine, carboxyl-carbodiimide, thiol-maleimide, thiol-haloacetyl, thiol-pyridyl disulfide, thiol-thiosulfonate, thiol-vinyl sulfone, aldehyde-hydrazide, aldehyde-alkoxyamine, hydroxyisocyanate, azide-alkyne, azide-phosphine, transcyclooctene-tetrazine, norbornene-tetrazine, azide-cyclooctyne, and azide-norbornene.

[0011] In some aspects, the techniques described herein relate to a method for determining a sequence of a target polynucleotide in a nanopore-based sequencing system, the method including: providing a target polynucleotide including a modification covalently attached to each of nucleotides in the target polynucleotide, wherein the modification includes a chelating moiety-metal ion complex; applying a voltage bias to cause the target polynucleotide to translocate through a constriction of a nanopore; during a first arresting event, applying a reading voltage measuring an electrical response at the constriction of the nanopore; and identify the nucleotide or a combination of nucleotides passing through the constriction of the nanopore based on the electrical response.

[0012] In some aspects, the techniques described herein relate to a method, wherein the step of providing a target polynucleotide includes: conjugating each type of nucleotide with a chelating moiety to form modified nucleotides; incubating the modified nucleotides with different metal ions to form modified nucleotide-metal ion conjugates, wherein each of the different metal ions is configured to complex with each type of the modified nucleotides; and forming the target polynucleotide by synthesizing a daughter strand of a template polynucleotide using the modified nucleotide-metal conjugates.

[0013] In some aspects, the techniques described herein relate to a method, wherein the chelating moieties on each type of the modified nucleotides are the same, and each type of the modified nucleotides is separately incubated with different metal ions.

[0014] In some aspects, the techniques described herein relate to a method, wherein the chelating moieties on each type of the modified nucleotides are different, and each type of the modified nucleotides are separately incubated separately with different metal ions prior to the forming of the target polynucleotide.

[0015] In some aspects, the techniques described herein relate to a method, wherein the chelating moieties on each type of the modified nucleotides are different, and each type of the modified nucleotides are incubated together with at least four different metals prior to the forming of the target polynucleotide.

[0016] In some aspects, the techniques described herein relate to a method, wherein the chelating moieties on each type of nucleotides are different, and each type of the modified nucleotides is incubated together with at least four different metals after the forming of the target polynucleotide.

[0017] In some aspects, the techniques described herein relate to a method, wherein the step of providing a target polynucleotide includes: conjugating each type of nucleotides with a different chelating moiety to form modified nucleotides; synthesizing a daughter strand of a template polynucleotide using the modified nucleotides; and forming the target polynucleotide by incubating the daughter strand with different metal ions.

[0018] In some aspects, the techniques described herein relate to a method, wherein the chelating moiety-metal ion complex includes a chelating moiety selected from the group consisting of: Polyhistidine tag (His-tag), HQ-tag, HN-tag, HAT-tag, Zn finger (Zif268), DNA hairpins, G-quadruplex, porphyrins, crown-ethers, cyclodextrins, cucurbiturils, EDTA, tetraxetan (DOTA), NOTA, TETA, and HEHA.

[0019] In some aspects, the techniques described herein relate to a method, wherein the chelating moiety-metal ion complex includes a metal ion selected from the group consisting of Zn²⁺, Cd²⁺, Co²⁺, NI²⁺, Pb²⁺, Au³⁺, Hg²⁺, Ba²⁺, Cu²⁺, Fe²⁺, Al³⁺, Mn²⁺ and Mg²⁺. [0020] In some aspects, the techniques described herein relate to a method, wherein the modifications are covalently attached to each nucleotide in the target polynucleotide via a linker construct including a first linking group.

[0021] In some aspects, the techniques described herein relate to a method, wherein the first linking group includes a conjugating moiety selected from the group consisting of amine-NHS ester, amine- imidoester, amine-pentafluorophenyl ester, amine-hydroxymethyl phosphine, carboxyl-carbodiimide, thiol-maleimide, thiol-haloacetyl, thiol-pyridyl disulfide, thiol-thiosulfonate, thiol-vinyl sulfone, aldehyde-hydrazide, aldehyde-alkoxyamine, hydroxyisocyanate, azide-alkyne, azide-phosphine, transcyclooctene-tetrazine, norbornene-tetrazine, azide-cyclooctyne, and azide-norbornene.

[0022] In some aspects, the techniques described herein relate to a kit for performing a method for determining a sequence of a polynucleotide in a nanopore-based sequencing system according to any of the methods disclosed herein, the kit including a compound selected from:

wherein: n is 0 or a positive integer; Y is -O-, -S-, or -NH-; X is -O-, -NH-, or -CH2-; LI includes a linking group; and M is a modification including a chelating moiety. [0023] In some aspects, the techniques described herein relate to a kit, wherein M includes the chelating moiety-metal ion complex.

[0024] In some aspects, the techniques described herein relate to a kit, wherein M includes the chelating moiety, and the kit further includes a solution including four different metal ions, wherein the different metal ions are configured to complex with a predetermined chelating moiety.

[0025] It should be appreciated that all combinations of the foregoing concepts and additional concepts discussed in greater detail below are contemplated as being part of the inventive subject matter disclosed herein and may be used to achieve the benefits and advantages described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

[0026] Features of examples of the present disclosure will become apparent by reference to the following detailed description and drawings, in which like reference numerals correspond to similar, though perhaps not identical, components. For the sake of brevity, reference numerals or features having a previously described function may or may not be described in connection with other drawings in which they appear.

[0027] Figure 1 schematically illustrates an example of interactions of macromolecular blocks with residues of a nanopore or with the translocating polymer.

[0028] Figure 2 schematically illustrates a scheme for incorporation of a nucleotide into a polymer chain.

[0029] Figures 3-6 schematically illustrate steps for generating a modified nucleotide and a resulting daughter strand.

DETAILED DESCRIPTION

[0030] All patents, applications, published applications and other publications referred to herein are incorporated herein by reference to the referenced material and in their entireties. If a term or phrase is used herein in a way that is contrary to or otherwise inconsistent with a definition set forth in the patents, applications, published applications and other publications that are herein incorporated by reference, the use herein prevails over the definition that is incorporated herein by reference. Overview

[0031] Nanopore sequencing of nucleic acids typically involves the movement of a polynucleotide, or a polymeric chain corresponding to a polynucleotide, through an embedded nanopore. The movement of the nucleotides or associated moieties therefore generates an attenuated electrical signal, which can be processed in silico to instantiate any underlying nucleotide sequence. However, nanopore sequencers are sensitive to multiple bases of a polynucleotide strand resident in the nanopore. As opposed to reading a single base one at a time, multiple nucleotides can generate multiple signals, which are indistinct and require complex signal deconvolution. For example, the MspA nanopore possesses a constriction region which serves as a readhead of at least 4 nucleotides (a “k-mer”), resulting in minimally 256 (4⁴) different permutation of 4-mer sequences that need to be deconvoluted. For a k-mer of 5 bases, the number of possible signals increases to 4⁵ = 1,024 possible signals. A longer readhead will result in an exponential increase in the number of signals to be differentiated, which complicates the sequencing readout and increases the complexity of base calling, thus reducing accuracy. Another issue with nanopore sequencers is that the speed of translocation of natural single stranded DNA is in the order of >10 million nucleotides per second, far above the rate that is compatible with electronics and detectors.

[0032] In order to improve the accuracy of the base calling, a modification comprising a chelating moiety complexed to a metal ion may be conjugated to a polynucleotide to form a modified polynucleotide. The modification may arrest the translocation to achieve a controlled reading of the polynucleotide strand. The inclusion of a metal ion can also further enhance the signal resolution between the k-mer, instead of solely depending on the bases for signal generation. Disclosed herein include modified nucleotides, modified polynucleotides, and methods for making modified nucleotides and modified polynucleotides. Disclosed herein also includes a method of sequencing a polynucleotide.

Modified Nucleotides

[0033] In some embodiments a modified nucleotide comprising a modification covalently attached to its nucleobase or its sugar, wherein the modification comprises a chelating moiety. In some embodiments, the modification further comprises a metal ion complexed to the chelating moiety. [0034] In some embodiments, the chelating moiety has a linear, branched, or cyclic structure. In some embodiments, the chelating moiety may comprise a macromolecular block. In some embodiments, the macromolecular blocks are associated with the target polynucleotide via hydrogen bonding, Van-der-Waals interactions, ionic interactions, or hydrophobic interactions. In some embodiments, the chelating moiety is configured to slow, pause, or halt translocation through a nanopore. In some embodiments, the chelating moiety binds or chelates to one or more or a plurality of metal ions. In some embodiments, the chelating moiety is selected from the group consisting of: Polyhistidine tag (His-tag), HQ-tag, HN-tag, HAT-tag, Zn finger (Zif268), DNA hairpins, G-quadruplex, porphyrins, crown-ethers, cyclodextrins, cucurbiturils, EDTA, tetraxetan (DOTA), NOTA, TETA, and HEHA. In some embodiments, the modification further comprises a metal ion complexed to the chelating moiety. In some embodiments, the metal ion is selected from the group consisting of Zn²⁺, Cd²⁺, Co²⁺, NI²⁺, Pb²⁺, Au³⁺, Hg²⁺, Ba²⁺, Cu²⁺, Fe²⁺, Al³⁺, Mn²⁺ and Mg²⁺.

[0035] In some embodiments, the modified nucleotide further comprises a covalent coupling (which is a part of the “linking group”) between the chelating moiety and the nucleotide, wherein the covalent coupling comprises a moiety selected from the group consisting of amine-NHS ester, amine-imidoester, amine-pentafluorophenyl ester, aminehydroxymethyl phosphine, carboxyl-carbodiimide, thiol-maleimide, thiol-haloacetyl, thiolpyridyl disulfide, thiol-thiosulfonate, thiol-vinyl sulfone, aldehyde-hydrazide, aldehydealkoxyamine, hydroxy-isocyanate, azide-alkyne, azide-phosphine, transcyclooctene-tetrazine, norbornene-tetrazine, azide-cyclooctyne, and azide-norbornene. In some embodiments, the modification further comprise one or more covalently linked moieties selected from the group consisting of dyes, synthetic polymers, and small molecules.

[0036] In some embodiments, the modified nucleotide includes a compound having one of the following structures:

wherein: Y is -0-, -S-, or -NH-; X is -O-, -NH-, or -CH2-; n is 0 or a positive integer; Li comprises a linking group; and M is a modification comprising a chelating moiety.

[0037] In some embodiments, the modified nucleotide further comprises a covalent coupling (Li or “linking group”) between the chelating moiety and the modified nucleotide, wherein the covalent coupling comprises a moiety selected from the group consisting of amine- NHS ester, alkene, amine- imidoester, amine-pentafluorophenyl ester, amine-hydroxymethyl phosphine, carboxyl-carbodiimide, thiol-maleimide, thiol-haloacetyl, thiol-pyridyl disulfide, thiol-thiosulfonate, thiol-vinyl sulfone, aldehyde-hydrazide, aldehyde-alkoxyamine, hydroxyisocyanate, azide-alkyne, azide-phosphine, transcyclooctene-tetrazine, norbornene-tetrazine, azide-cyclooctyne, and azide-norbornene. In some embodiments, the modification further comprises one or more covalently linked moieties selected from the group consisting of dyes, synthetic polymers, and small molecules. In some embodiments, an oligonucleotide comprising one or more of the modified nucleotides is provided.

[0038] In some embodiments the nucleotide is a ribonucleotide with a hydroxide at the 2’ location, which is lacking in deoxyribonucleotides. In some embodiments the polynucleotide strand may be a mixture of deoxyribonucleotides and ribonucleotides.

[0039] In some embodiments, a modification, M, further comprises one or more metal ions complexed to the chelating moiety. In some embodiments, the metal ion is selected from the group consisting of Zn²⁺, Cd²⁺, Co²⁺, NI²⁺, Pb²⁺, Au³⁺, Hg²⁺, Ba²⁺, Cu²⁺, Fe²⁺, Al³⁺, Mn²⁺ and Mg²⁺. In some embodiments, the chelating moiety is selected from the group consisting of: Polyhistidine tag (His-tag), HQ-tag, HN-tag , HAT-tag , Zn finger (Zif268), DNA hairpins, G-quadruplex, porphyrins, crown-ethers, cyclodextrins, cucurbiturils, EDTA, tetraxetan (DOTA), NOTA, TETA, and HEHA.

[0040] In some embodiments, a method for determining a sequence of a target polynucleotide in a nanopore-based sequencing system is also provided, the method comprising: providing a daughter strand comprising one or more modified nucleotides, reading the modified nucleotides by applying a reading voltage across a read head to identify a first reporter element in a constriction of a nanopore based on a first electrical response in the system, wherein one or more nucleotides translocate through a nanopore. In some embodiments, the daughter strand is derived from a template polynucleotide. In some embodiments, the daughter strand is a target polynucleotide.

[0041] In some embodiments, a method for determining a sequence of a target polynucleotide in a nanopore-based sequencing system is provided, the method comprising: providing a target polynucleotide comprising a modification covalently attached to each of nucleotides in the target polynucleotide, wherein the modification comprises a chelating moiety-metal ion complex. In some embodiments, the method further comprises applying a voltage bias to cause the target polynucleotide to translocate through a constriction of a nanopore. The method further comprises that during a first arresting event, applying a reading voltage measuring an electrical response at the constriction of the nanopore. The method further comprises identifying the nucleotide or a combination of nucleotides passing through the constriction of the nanopore based on the electrical response.

[0042] In some embodiments, the step of providing a target polynucleotide comprises conjugating each type of nucleotide with a chelating moiety to form modified nucleotides, then incubating the modified nucleotides with different metal ions to form modified nucleotide-metal ion conjugates, wherein each different metal ion complexes with each type of the modified nucleotide. In some embodiments, the target polynucleotide is formed by synthesizing a daughter strand of a template polynucleotide using the modified nucleotide-metal conjugates. In some embodiments, the chelating moieties on each type of nucleotide is the same, and each type of modified nucleotide is separately incubated with different metal ions. In some embodiments, the chelating moieties on each type of nucleotide is different, and each type of modified nucleotide is incubated with a different metal separately or together. In some embodiments, the step of providing a target polynucleotide comprises conjugating each type of nucleotide with a different chelating moiety to form modified nucleotides, synthesizing a daughter strand of a template polynucleotide using the modified nucleotides; and forming the target polynucleotide by incubating the daughter strand with different metal ions. In some embodiments, the chelating moiety-metal ion complex comprises a chelating moiety selected from the group consisting of: Polyhistidine tag (His-tag), HQ-tag , HN-tag, HAT-tag, Zn finger (Zif268), DNA hairpins, G-quadruplex, porphyrins, crown-ethers, cyclodextrins, cucurbiturils, EDTA, tetraxetan (DOTA), NOTA, TETA, and HEHA. In some embodiments, the chelating moiety-metal ion complex comprises a metal ion selected from the group consisting of Zn²⁺, Cd²⁺, Co²⁺, NI²⁺, Pb²⁺, Au³⁺, Hg²⁺, Ba²⁺, Cu²⁺, Fe²⁺, Al³⁺, Mn²⁺ and Mg²⁺. In some embodiments, the modifications are covalently attached to each nucleotide in the target polynucleotide via a linker construct comprising a first linking group. In some embodiments, the first linking group comprises a conjugating moiety selected from the group consisting of amine-NHS ester, amine-imidoester, amine-pentafluorophenyl ester, aminehydroxymethyl phosphine, carboxyl-carbodiimide, thiol-maleimide, thiol-haloacetyl, thiolpyridyl disulfide, thiol-thiosulfonate, thiol-vinyl sulfone, aldehyde-hydrazide, aldehydealkoxyamine, hydroxy-isocyanate, azide-alkyne, azide-phosphine, transcyclooctene-tetrazine, norbornene-tetrazine, azide-cyclooctyne, and azide-norbornene.

[0043] Disclosed herein further includes a kit for performing a method for determining a sequence of a polynucleotide in a nanopore-based sequencing system, the kit comprising the modified nucleotides, chelating moieties, metal ions, or complexes disclosed herein.

[0044] In some embodiments, during sequencing of a polynucleotide, a system can “read” elements associated with each nucleotide sequence, as each nucleotide passes through the nanopore readhead to generate an output. The output being a signal that can be used to identify a particular base. In some embodiments, chelating moieties chemically linked to a polynucleotide strand or translocating polymer are designed to occupy and interact non- covalently with chemical or amino acid residues within the inner environment of a nanopore, thereby arresting translocation until certain external conditions are met. These interactions include, but are not limited to, electrostatic interactions, ion-dipole interactions, dipole-dipole (e.g. hydrogen bonding) interactions, induced-dipole interactions, hydrophobic interactions, London dispersion forces interactions, Van-der-Waals interactions, hydrophobic interactions, cation-pi, anion-pi, and pi-pi interactions. In some embodiments, the ratchet chelator or chelating moiety, as well as any bound metal ions, can modulate signal generation, thereby producing a distinguishable signal or signal break. In some embodiments, the ratchet chelator, as well as any bound metal ions, can serve as a barcode for identifying attached nucleotides. In some embodiments, the ratchet chelator’s ratchet function allows for situations wherein an associated nucleotide translocates only upon application of a voltage past a certain threshold, or a current over a certain timing, or a combination of voltages and timings therein. In some embodiments, the metal ion attached to a ratchet chelator can modulate translocation of a residue across a readhead, thereby producing a distinguishable signal or signal break. As a consequence, the ratchet chelator can serve to attenuate translocation or modulate any signal generated when an associated nucleotide passes through a readhead. In some embodiments, the chelating moiety can be any macromolecular structure capable of binding or coordinating to metal ions. In some embodiments, the chelation moiety can be a peptide based structure capable of binding or coordination to metal ions.

[0045] In another aspect, the disclosed technology provides systems, devices, kits, and methods which allow for the attachment of a ratchet chelator to a nucleotide, nucleotide backbone, translocating polymer, or other chemical group associated or attached to a sequence of nucleotides. Systems may be prepared to allow parallel reads in multiple nanopores, such as thousands or millions of nanopores. Accordingly, components of any system may be functionally duplicated to multiply sequencing throughput. Any system may also be adapted with microfluidics or automation. Any system may add one or multiple combinations of ratchet chelator to any of nucleotides, nucleotide backbones, or structures correlating to nucleotide sequences.

[0046] The systems, devices, kits, and methods disclosed herein each have several aspects, no single one of which is solely responsible for their desirable attributes. Without limiting the scope of the claims, some prominent features are discussed herein. Numerous other examples are also contemplated, including examples that have fewer, additional, and/or different components, steps, features, objects, benefits, and advantages. The components, aspects, and steps may also be arranged and ordered differently. After considering this discussion, and particularly after reading the section entitled “Detailed Description,” one will understand how the features of the devices and methods disclosed herein provide advantages over other known devices and methods.

[0047] Additional details of exemplary nanopore sequencing devices which can be used with the disclosed technology, and methods of operating the devices, can be found in U.S. Provisional Patent Application Numbers 63/200868 and 63/169041, the entirety of each of the disclosures is incorporated herein by reference.

[0048] Disclosed herein is a modified nucleotide comprising a modification covalently attached to its nucleobase or its sugar, wherein the modification comprises a ratchet chelator, the ratchet chelator comprising linear, branched, or cyclic structures. [0049] Further, disclosed herein is a nucleotide with a chelator moiety attached at any suitable location on the nucleotide. The nucleotide may constitute a portion of a polynucleotide or oligonucleotide having a plurality of chelator moieties. The chelator moiety may include a branched, cyclic, or linear compound, for example, polyhistidine tag (His-tag), HQ-tag, HN-tag, HAT-tag, Zn finger (Zif268), DNA hairpins, G-quadruplex, macrocycles such as porphyrins (porphin, tetraphenylporphyrin), crown-ethers, cyclodextrins, cucurbiturils, EDTA, tetraxetan (DOTA) and other analogous macrocycles such as NOTA, TETA, HEHA (See structures below). The polynucleotide or oligonucleotide may include a compound having one of the following structures:

(Villa) wherein: Y is -0-, -S-, or -NH-; X is -O-, -NH-, or -CH2-; n is 0 or a positive integer; Li comprises a linking group; and M is a modification comprising a chelating moiety.

Exemplary Ratchet-Chelators:

[0050] Exemplary ratchet chelators are shown in the structures below. More than one type of chelating moiety may be used with a single nucleotide, or different types of chelating moieties may be used in conjunction with each other. In some embodiments a single chelating moiety is used with a single nucleotide as a characteristic signal for the nucleotide.

[0051] In some embodiments, the modified nucleotide further comprises a covalent coupling between the chelating moiety and the nucleotide, wherein the covalent coupling comprises a moiety selected from or selected from the group consisting of amine-NHS ester, amine-imidoester, amine-pentafluorophenyl ester, amine-hydroxymethyl phosphine, carboxyl-carbodiimide, thiol-maleimide, thiol-haloacetyl, thiol-pyridyl disulfide, thiolthiosulfonate, thiol-vinyl sulfone, aldehyde-hydrazide, aldehyde-alkoxyamine, hydroxyisocyanate, azide-alkyne, azide-phosphine, transcyclooctene-tetrazine, norbornene-tetrazine, azide-cyclooctyne, and azide-norbornene. In some embodiments, the modification further comprise one or more covalently linked moiety selected from the group consisting of dyes, synthetic polymers, and small molecules. In some embodiments, an oligonucleotide comprising one or more of the modified nucleotides is provided.

[0052] In some embodiments, a method for determining a sequence of a target polynucleotide in a nanopore-based sequencing system is also provided, the method comprising: providing a daughter strand of a target polynucleotide comprising one or more modified nucleotides, reading the modified nucleotides by applying a reading voltage across a read head to identify a first reporter element in a constriction of a nanopore based on a first electrical response in the system, wherein one or more nucleotides translocate through a nanopore.

[0053] In some embodiments, an additional method for determining a sequence of a target polynucleotide in a nanopore-based sequencing system is provided. The method comprising providing the target polynucleotide and a plurality of the chelating moieties in an electrolyte for the nanopore-based sequencing system; applying a voltage bias to cause the target polynucleotide to translocate through a constriction of a nanopore, wherein one or more chelating moieties are covalently or non-covalently associated with the target polynucleotide; and detecting and identifying one or more nucleotides as the nucleotides pass through the constriction based on an electrical response in the system.

[0054] Disclosed herein further includes a kit for performing a method for determining a sequence of a polynucleotide in a nanopore-based sequencing system, the kit comprising the compound disclosed herein.

System and Method

[0055] FIG. 1 schematically illustrates examples of the interaction of chelating moieties with residues of the MspA nanopore. A nanopore 101 is deposited in a lipid bilayer 102. An elongated polymer/polynucleotide 103 translocates through the nanopore 101. The elongated polymer/polynucleotide 103 includes bound chelating moieties 104. By introducing a macromolecular block, such as a chelating moiety, the signal can be attenuated due to interactions of the metal ion, nucleotide, and/or chelating moiety with residues located within the nanopore, resulting in fewer and more isolated signals (for A, T, C and G). For example, Figure 1 shows that the chelating moiety may interact with amine groups in the nanopore. The various interactions of the chelating agents with the nanopore are not limited to amine interactions and may be dependent upon the metal that is chelated by the chelating agent and the type of nanopore used for sequencing. For example, the interactions may take the form of a cation-pi interactions, pi-pi interactions, hydrogen bonding, salt bridge, Van der Waals interactions, etc.

[0056] One of the primary purposes of the chelated metal ion is to modulate the blockage current to improve the signal resolution of the k-mer. The interaction of the chelating agent and/or metal ion with the interior surface of the nanopore can reduce the complexity of base calling and improve the fidelity of the readout. In some embodiments a characteristic linker/barcode may be used in addition to each of the chelator moieties and/or metal ions to achieve base recognition.

[0057] FIG. 2 schematically illustrates the incorporation of a single dNTP (deoxyribonucleoside triphosphate) bound to a linker and ratchet (“chelating moiety”) into a chain of nucleotides, wherein each nucleotide is also bound to a linker and ratchet, the resulting polymer chain being capable of translocating across a nanopore.

[0058] By “translocation,” it is meant that an analyte (e.g., DNA) enters one side of an opening of a nanopore and moves to and out of the other side of the opening. It is contemplated that any embodiment herein comprising translocation may refer to electrophoretic translocation or non-electrophoretic translocation, unless specifically noted. An electric field may move an analyte (e.g., a polynucleotide) or modified analyte. By “interacts,” it is meant that the analyte (e.g., DNA) or modified analyte moves into and, optionally, through the opening, where “through the opening” (or “translocates”) means to enter one side of the opening and move to and out of the other side of the opening. Optionally, methods that do not employ electrophoretic translocation are contemplated. In some embodiments, physical pressure causes a modified analyte to interact with, enter, or translocate (after alteration) through the opening. In some embodiments, a magnetic bead is attached to an analyte or modified analyte on the trans side, and the magnetic force causes the modified analyte to interact with, enter, or translocate (after alteration) through the opening. Other methods for translocation include but not limited to gravity, osmotic forces, temperature, and other physical forces such as centripetal force. [0059] In some embodiments, the nanopore may comprise a solid-state material, such as silicon nitride, modified silicon nitride, silicon, silicon oxide, or graphene, or a combination thereof. In some embodiments, the nanopore is protein that forms a tunnel upon insertion into a bilayer, membrane, thin film, or solid-state aperture. In some embodiments, the nanopore is comprised in a lipid bilayer. In some embodiments, the nanopore is comprised in an artificial membrane comprising a mycolic acid. The nanopore may be a Mycobacterium smegmatis porin (Msp) having a vestibule and a constriction zone that define the tunnel. The Msp porin may be a mutant MspA porin. In some embodiments, amino acids at positions 90, 91, and 93 of the mutant MspA porin are each substituted with asparagine. Some embodiments may comprise altering the translocation velocity or sequencing sensitivity by removing, adding, or replacing at least one amino acid of an Msp porin. A “mutant MspA porin” is a multimer complex that has at least or at most 70, 75, 80, 85, 90, 95, 98, or 99 percent or more identity, or any range derivable therein, but less than 100%, to its corresponding wild-type MspA porin and retains tunnel-forming capability. A mutant MspA porin may be a recombinant protein. Optionally, a mutant MspA porin is one having a mutation in the constriction zone or the vestibule of a wild-type MspA porin. Optionally, a mutation may occur in the rim or the outside of the periplasmic loops of a wild-type MspA porin. A mutant MspA porin may be employed in any embodiment described herein.

[0060] A “vestibule” refers to the cone-shaped portion of the interior of an Msp porin whose diameter generally decreases from one end to the other along a central axis, where the narrowest portion of the vestibule is connected to the constriction zone. A vestibule may also be referred to as a “goblet.” The vestibule and the constriction zone together define the tunnel of an Msp porin. A “constriction zone” or the “readhead” refers to the narrowest portion of the tunnel of an Msp porin, in terms of diameter, that is connected to the vestibule. The length of the constriction zone may range from about 0.3 nm to about 2 nm. Optionally, the length is about, at most about, or at least about 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, or 3 nm, or any range derivable therein. The diameter of the constriction zone may range from about 0.3 nm to about 2 nm. Optionally, the diameter is about, at most about, or at least about 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, or 3 nm, or any range derivable therein. A “tunnel” refers to the central, empty portion of an Msp porin that is defined by the vestibule and the constriction zone, through which a gas, liquid, ion, or analyte may pass. A tunnel is an example of an opening of a nanopore.

[0061] In some embodiments, the disclosed system for nanopore sequencing comprises an Msp porin having a vestibule and a constriction zone that define a tunnel, wherein the tunnel is positioned between a first liquid medium and a second liquid medium, wherein at least one liquid medium comprises an analyte polynucleotide, and wherein the system is operative to detect a property of the analyte. The system may be operative to detect a property of any analyte comprising subjecting an Msp porin to an electric field such that the analyte interacts with the Msp porin. The system may be operative to detect a property of the analyte comprising subjecting the Msp porin to an electric field such that the analyte electrophoretically translocates through the tunnel of the Msp porin. In some embodiments, the system comprises an Msp porin having a vestibule and a constriction zone that define a tunnel, wherein the tunnel is positioned in a lipid bilayer between a first liquid medium and a second liquid medium, and wherein the only point of liquid communication between the first and second liquid media occurs in the tunnel. Moreover, any Msp porin described herein may be comprised in any system described herein. In some embodiments, the system may further comprise an amplifier or a data acquisition device. The system may further comprise one or more temperature regulating devices in communication with the first liquid medium, the second liquid medium, or both. The system described herein may be operative to translocate an analyte through an Msp porin tunnel either electrophoretically or otherwise.

[0062] In some embodiments, chelating moieties can also modulate enzymatic synthesis through steric hindrance to tune incorporation kinetics or limit the processivity of an incorporating enzyme, including polymerase. Various polymerases exist generally for joining 3'-OH 5 '-triphosphate nucleotides, oligomers, and their analogs. Polymerases include, but are not limited to, DNA-dependent DNA polymerases, DNA-dependent RNA polymerases, RNA- dependent DNA polymerases, RNA-dependent RNA polymerases, T7 DNA polymerase, T3 DNA polymerase, T4 DNA polymerase, T7 RNA polymerase, T3 RNA polymerase, SP6 RNA polymerase, DNA polymerase I, Klenow fragment, Thermophilus aquaticus DNA polymerase, Tth DNA polymerase, VentR® DNA polymerase (New England Biolabs), Deep VentR® DNA polymerase (New England Biolabs), Bst DNA Polymerase Large Fragment, Stoeffel Fragment, 90N DNA Polymerase, 90N DNA polymerase, Pfu DNA Polymerase, Tfl DNA Polymerase, Tth DNA Polymerase, RepliPHI Phi29 Polymerase, Hi DNA polymerase, eukaryotic DNA polymerase beta, telomerase, Therminator™ polymerase (New England Biolabs), KOD HiFi™ DNA polymerase (Novagen), K0D1 DNA polymerase, Q-beta replicase, terminal transferase, AMV reverse transcriptase, M-MLV reverse transcriptase, Phi6 reverse transcriptase, HIV-1 reverse transcriptase, novel polymerases discovered by bioprospecting, and polymerases cited in US 2007/0048748, US 6,329,178, US 6,602,695, and US 6,395,524 (incorporated by reference). These polymerases include wild-type, mutant isoforms, and genetically engineered variants. "Encode" or "parse" are verbs referring to transferring from one format to another, and refers to transferring the genetic information of target template base sequence into an arrangement of reporters.

Daughter Strand Synthesis and dNTP Preparation Order of Operations

[0063] The formation of dNTP-chelator- metal conjugates (modified nucleotides) and resulting daughter strands can be accomplished through a variety of methods. Varying the chelator moiety identity, whether the metal ions are associated only with specific or broad classes of nucleotides, or any other aspect in the generation of modified nucleotides can be tuned to affect the resulting signal, kinetics, or efficacy of any resulting sequencing assay.

[0064] FIG. 3 illustrates an embodiment disclosed herein, wherein each dNTP is separately conjugated to the same chelator moiety (marked with a “1”), but incubated with four different metal ions (signified as “A”, “B”, “C”, or “D”), wherein metal ions are associated with specific nucleotides. In this embodiment, the metal ions are each associated with a specific nucleotide not due to the specificity of the chelating moiety but because each of the four different metal ions are incubated with a nucleotide that has been predetermined to correspond with the metal ion. For example, in this embodiment a chelating moiety may be chosen that is not selective as to metal binding and may bind with any of the metal ions, A, B, C, or D. In such a scenario the chelation may run to completion so as to not leave nucleotides that have not been chelated with metal ions. Additionally or alternatively, a washing or separating step may be used to separate any unreacted metal ions prior to combining the nucleotides with other types of nucleotides.

[0065] The bound nucleotide complexes are then pooled and used to synthesize a daughter strand from a template to be sequenced. The daughter strand is then sequenced through a nanopore. Enhanced signal arising from the metal ions during translocation through the nanopore provides signal discrimination in order to aid in differentiating the polynucleotide sequence. For example, the chelated metal ions may provide distinct levels of signals to aid in base and signal resolution. The signal from the metal ions may be read in conjunction with the signal from each different nucleotide, providing a combined signal of the metal ions with the corresponding nucleotide. In some embodiments additional modifications, such as cyclic loops or barcodes may be provided on the nucleotide in order to enhance resolution and discrimination between nucleotides.

[0066] FIG. 4 illustrates an embodiment disclosed herein, wherein each dNTP is separately conjugated to different chelators (marked with a “1” “2” “3” and “4”), and incubated with four different metal ions (signified as “A”, “B”, “C”, or “D”). In this embodiment the four different nucleotides are incubated with metal ions separately prior to the formation of the daughter strand, as with Figure 3. However, here different chelating moieties (1, 2, 3, 4) are provided on each corresponding nucleotide. The different chelating moieties may have a unique affinity to each of the metal ions A, B, C, or D, or the chelating moieties may be nonspecific and have a binding affinity for each of A, B, C, or D. In the case where the chelating moieties are non-specific to each of the metal ions (A, B, C, D), there are still advantages to the process shown in FIG. 4 where the chelating moiety itself may provide a different signal that can be used in conjunction with the unique signal of the metal ion itself. After incubating with metal ions, the dNTP-chelator-metal-conjugates are then pooled (as shown in FIG. 4) and used to synthesize a daughter strand. The daughter strand is sequenced through a nanopore, and each unique signature (nucleotide with metal-ion complex) may be associated with a particular nucleotide in the daughter strand. The daughter strand may be read out as a function of each unique chelating moiety, metal ion complexed to the chelating moiety, and/or nucleotide signal. In some embodiments additional modifications, such as cyclic loops or barcodes may be provided on the nucleotide in order to enhance resolution and discrimination between nucleotides.

[0067] FIG. 5 illustrates an additional embodiment disclosed herein where each dNTP is separately conjugated to different chelators (1, 2, 3, 4). However, instead of incubating the different chelators separately, the different chelators are pooled together (as shown in FIG. 5) and incubated with a mixture of four different metal ions. [0068] In this embodiment, each chelator has a specific binding affinity with one of the metal ions, which allows pooling of the different chelators. The resulting dNTP-chelator- metal conjugates (modified nucleotides) are then used to synthesize the daughter strand. Finally, the daughter strand is sequenced through a nanopore and each unique signature (nucleotide with metal-ion complex) may be associated with a particular nucleotide in the daughter strand. The daughter strand may be read out as a function of each unique chelating moiety, metal ion complexed to the chelating moiety, and/or nucleotide signal. In some embodiments additional modifications, such as cyclic loops or barcodes may be provided on the nucleotide in order to enhance resolution and discrimination between nucleotides.

[0069] FIG. 6 illustrates an additional embodiment where each dNTP is separately conjugated to different chelating moieties (1, 2, 3, 4). However, instead of incubating the different chelating moieties with metals prior to incorporating the nucleotides on a daughter strand, as with FIGS. 3-5, the nucleotides with their associated chelating moieties are first incorporated into a daughter strand as shown in FIG. 6. Subsequently, the daughter strand, which incorporates different chelators associated with each unique nucleotide, is incubated with a mixture of four different metal ions (A, B, C, D). This is possible because each chelator has a specific binding affinity with one of the metal ions (chelator “1” has a specific affinity for metal ion “A” for example). Thereafter the daughter strand with the several chelating moiety-metal complexes is sequenced in a nanopore. The daughter strand may be read out as a function of each unique chelating moiety, metal ion complexed to the chelating moiety, and/or nucleotide signal. In some embodiments additional modifications, such as cyclic loops or barcodes may be provided on the nucleotide in order to enhance resolution and discrimination between nucleotides.

Peptides as Metal Chelators

[0070] Modifications for chelating moieties include various peptides capable of chelating metal ions. Peptide- based chelating moieties are chemical groups designed to contain one or a series of derivative amino acid structures that can interact with a polymer sequence or residues comprising a nanopore, and they may chelate and bind to metal ions as well. Peptide- based chelating moieties for use in nanopore sequencing can be designed to contain side chains that exhibit favorable interactions with the exposed residues of a nanopore, including MspA. For example, oppositely charged amino acid side chains interact via H-bonding and electrostatic forces to form salt bridges. Amino acids with polar side chains interact via hydrogen bonding and the bond strengths depend on the nature of H-donors and acceptors. Hydrophobic amino acids such as tyrosine and phenylalanine are also known to engage in OH- pi and CH-0 type H-bonding. Peptide-based chelating moieties for controlling translocation, controlling signal generation, and controlling enzymatic synthesis can be homogeneous in composition or contain a mixture of either naturally-occurring or synthetic amino acids. The geometry of the peptide-based chelating moieties can be modified to provide additional steric and conformational effects, which can affect the rate of translocation through the nanopore. For instance, increasing the degree of branching in peptide blocks can increase their cross- sectional area while circularizing a linear sequence can provide a rigid block.

[0071] Peptides can undergo conformation shift in response to stimuli, including electric current, or binding of certain substituent groups, including metal ions. For example, a Zinc finger is capable of binding to Zn(II), which induces a conformation shift and inability to translocate through various nanopores (e.g. aHL). Metal ions also can bind with different affinities to one or more peptide groups acting as chelating moieties. The AB1-16 peptide fragment (His at 6, 13, 14) coordinates to metal ions with selective affinity, (e.g. Cu²⁺ > Zn²⁺ > Fe³⁺ > Al³⁺).

[0072] Various peptide chelators that may be used in embodiments of this application are shown below:

HAT-tag

Macromolecules as Metal Chelators

[0073] Modifications for chelating moieties can also include various macromolecules capable of chelating metal ions. For example, a DNA hairpin with a pair of thymine residues at the pinhead is capable of interacting strongly with Hg²⁺ to form a stable hairpin complex. Macromolecules can undergo conformation shift in response to stimuli, including electric current, or binding of certain substituent groups, including metal ions. Without Hg²⁺, the hairpin is unzipped at the nanopore. An Hg-bound hairpin is illustrated below:

Exemplary Macromolecules:

[0074] Various different macromolecules may be incorporated with or associated with a specific nucleotide (such as A, T, C, G, or U in the case of RNA). The macrocycles shown below are only exemplary, and additional macrocycles or macrocycle analogues may be used, such as analogues of tetraxetan (DOTA) like NOTA, TETA, or HEHA.

Porphin Tetraphenylporphyrin 18-crown-6

[0075] Cyclodextrins:

[0076] Cucurbiturils:

[0078] For MspA, the positively charged arginine and lysine residues can electrostatically and sterically affect translocation speed. Chelating moieties, in addition to arresting translocation, can also affect translocation speed including for example, amide and cationic nitrogen moieties as well as aromatic and aliphatic carbon moieties. Chelating moieties can also affect signal generation by methods including but not limited to interactions with residues at or near the constriction of the nanopore, interactions with the translocating polymer, or a combination of both.

Definitions

[0079] All technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which this disclosure belongs unless clearly indicated otherwise. [0080] As used herein, the singular forms “a”, “and”, and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a sequence” may include a plurality of such sequences, and so forth.

[0081] The terms comprising, including, containing and various forms of these terms are synonymous with each other and are meant to be equally broad. Moreover, unless explicitly stated to the contrary, examples comprising, including, or having an element or a plurality of elements having a particular property may include additional elements, whether or not the additional elements have that property.

[0082] As used herein, the term “nanopore” is intended to mean a hollow structure discrete from, or defined in, and extending across the membrane. The nanopore permits ions, electric current, and/or fluids to cross from one side of the membrane to the other side of the membrane. For example, a membrane that inhibits the passage of ions or water-soluble molecules can include a nanopore structure that extends across the membrane to permit the passage (through a nanoscale opening extending through the nanopore structure) of the ions or water-soluble molecules from one side of the membrane to the other side of the membrane. The diameter of the nanoscale opening extending through the nanopore structure can vary along its length (i.e., from one side of the membrane to the other side of the membrane), but at any point is on the nanoscale (i.e., from about 1 nm to about 100 nm, or to less than 1000 nm). Examples of the nanopore include, for example, biological nanopores, solid-state nanopores, and biological and solid-state hybrid nanopores. In some embodiments, a nanopore refers to a pore having an opening with a diameter at its most narrow point of about 0.3 nm to about 2 nm. For example, a nanopore may be a solid-state nanopore, a graphene nanopore, an elastomer nanopore, or may be a naturally-occurring or recombinant protein that forms a tunnel upon insertion into a bilayer, thin film, membrane, or solid-state aperture, also referred to as a protein pore or protein nanopore herein (e.g., a transmembrane pore). If the protein inserts into the membrane, then the protein is a tunnel-forming protein.

[0083] As used herein, the term “diameter” is intended to mean a longest straight line inscribable in a cross-section of a nanoscale opening through a centroid of the crosssection of the nanoscale opening. It is to be understood that the nanoscale opening may or may not have a circular or substantially circular cross-section (the cross-section of the nanoscale opening being substantially parallel with the cis/trans electrodes). Further, the cross-section may be regularly or irregularly shaped.

[0084] As used herein, “cis” refers to the side of a nanopore opening through which an analyte or modified analyte enters the opening or across the face of which the analyte or modified analyte moves.

[0085] As used herein, “trans” refers to the side of a nanopore opening through which an analyte or modified analyte (or fragments thereof) exits the opening or across the face of which the analyte or modified analyte does not move.

[0086] As used herein, the term “biological nanopore” is intended to mean a nanopore whose structure portion is made from materials of biological origin. Biological origin refers to a material derived from or isolated from a biological environment such as an organism or cell, or a synthetically manufactured version of a biologically available structure. Biological nanopores include, for example, polypeptide nanopores and polynucleotide nanopores.

[0087] As used herein, a “moiety” is one of two or more parts into which something may be divided, such as, for example, the various parts of a tether, a molecule or a probe.

[0088] As used herein, a “reporter” is composed of one or more reporter elements. Reporters include what are known as “tags” and “labels.” A linker construct (when including a reporter moiety) or a nucleobase residue of the elongated polymer can be considered a reporter. Reporters serve to parse the genetic information of the target nucleic acid.

[0089] As used herein, a “linker” is a molecule or moiety that joins two molecules or moieties and provides spacing between the two molecules or moieties such that they are able to function in their intended manner. For example, a linker can comprise a diamine hydrocarbon chain that is covalently bound through a reactive group on one end to an oligonucleotide analog molecule and through a reactive group on another end to a solid support, such as, for example, a bead surface. Coupling of linkers to nucleotides and substrate constructs of interest can be accomplished through the use of coupling reagents that are known in the art (see, e.g., Efimov et al., Nucleic Acids Res. 27: 4416-4426, 1999). Methods of derivatizing and coupling organic molecules are well known in the arts of organic and bioorganic chemistry. A linker may also be cleavable or reversible. [0090] As used herein, the term “polypeptide nanopore” is intended to mean a protein/polypeptide that extends across the membrane, and permits ions, electric current, polymers such as DNA or peptides, or other molecules of appropriate dimension and charge, and/or fluids to flow therethrough from one side of the membrane to the other side of the membrane. A polypeptide nanopore can be a monomer, a homopolymer, or a heteropolymer. Structures of polypeptide nanopores include, for example, an a-helix bundle nanopore and a 0-barrel nanopore. Example polypeptide nanopores include a-hemolysin, Mycobacterium smegmatis porin A (MspA), gramicidin A, maltoporin, OmpF, OmpC, PhoE, Tsx, F-pilus, etc. The protein a-hemolysin is found naturally in cell membranes, where it acts as a pore for ions or molecules to be transported in and out of cells. Mycobacterium smegmatis porin A (MspA) is a membrane porin produced by Mycobacteria, which allows hydrophilic molecules to enter the bacterium. MspA forms a tightly interconnected octamer and transmembrane beta-barrel that resembles a goblet and contains a central pore.

[0091] As used herein, a “peptide” refers to two or more amino acids joined together by an amide bond (that is, a “peptide bond”). Peptides may be linear or cyclic. Peptides may be a, 0, y, 8, or higher, or mixed. Peptides may comprise any mixture of amino acids as defined herein, such as comprising any combination of D, L, a, 0, y, 8, or higher amino acids.

[0092] As used herein, a “protein” refers to an amino acid sequence having multiple linked amino acids.

[0093] A polypeptide nanopore can be synthetic. A synthetic polypeptide nanopore includes a protein-like amino acid sequence that does not occur in nature. The protein-like amino acid sequence may include some of the amino acids that are known to exist but do not form the basis of proteins (i.e., non-proteinogenic amino acids). The protein-like amino acid sequence may be artificially synthesized rather than expressed in an organism and then purified/isolated.

[0094] The nanopores disclosed herein may be hybrid nanopores. A “hybrid nanopore” refers to a nanopore including materials of both biological and non-biological origins. An example of a hybrid nanopore includes a polypeptide-solid-state hybrid nanopore and a polynucleotide-solid-state nanopore.

[0095] The application of the electric potential difference across a nanopore may force the translocation of a nucleic acid through the nanopore. One or more signals are generated that correspond to the translocation of the nucleotide through the nanopore. Accordingly, as a target polynucleotide, or as a mononucleotide or a probe derived from the target polynucleotide or mononucleotide, transits through the nanopore, the current across the membrane changes due to base-dependent (or probe dependent) blockage of the constriction, for example. The signal from that change in current can be measured using any of a variety of methods. Each signal is unique to the species of nucleotide(s) (or linker constructs with a reporter moiety region) in the nanopore, such that the resultant signal can be used to determine a characteristic of the polynucleotide. For example, the identity of one or more species of nucleotide(s) (or probe) that produces a characteristic signal can be determined.

[0096] As used herein, a “nucleotide” includes a nitrogen containing heterocyclic base, a sugar, and one or more phosphate groups. Nucleotides are monomeric units of a nucleic acid sequence. Examples of nucleotides include, for example, ribonucleotides or deoxyribonucleotides. In ribonucleotides (RNA), the sugar is a ribose, and in deoxyribonucleotides (DNA), the sugar is a deoxyribose, i.e., a sugar lacking a hydroxyl group that is present at the 2' position in ribose. The nitrogen containing heterocyclic base can be a purine base or a pyrimidine base. Purine bases include adenine (A) and guanine (G), and modified derivatives or analogs thereof. Pyrimidine bases include cytosine (C), thymine (T), and uracil (U), and modified derivatives or analogs thereof. The C-l atom of deoxyribose is bonded to N-l of a pyrimidine or N-9 of a purine. The phosphate groups may be in the mono- , di-, or tri-phosphate form. These nucleotides are natural nucleotides, but it is to be further understood that non-natural nucleotides, modified nucleotides or analogs of the aforementioned nucleotides can also be used.

[0097] As used herein, “nucleobase” is a heterocyclic base such as adenine, guanine, cytosine, thymine, uracil, inosine, xanthine, hypoxanthine, or a heterocyclic derivative, analog, or tautomer thereof. A nucleobase can be naturally occurring or synthetic. Non-limiting examples of nucleobases are adenine, guanine, thymine, cytosine, uracil, xanthine, hypoxanthine, 8-azapurine, purines substituted at the 8 position with methyl or bromine, 9-oxo-N6-methyladenine, 2-aminoadenine, 7-deazaxanthine, 7-deazaguanine, 7- deaza-adenine, N4-ethanocytosine, 2,6- diaminopurine, N6-ethano-2,6-diaminopurine, 5- methylcytosine, 5-(C3-C6)- alkynylcytosine, 5-fluorouracil, 5-bromouracil, thiouracil, pseudoisocytosine, 2-hydroxy-5-methyl-4-triazolopyridine, isocytosine, isoguanine, inosine, 7,8-dimethylalloxazine, 6-dihydrothymine, 5,6-dihydrouracil, 4-methyl-indole, ethenoadenine and the non-naturally occurring nucleobases described in U.S. Pat. Nos. 5,432,272 and 6,150,510 and PCT applications WO 92/002258, WO 93/10820, WO 94/22892, and WO 94/24144, and Fasman ("Practical Handbook of Biochemistry and Molecular Biology", pp. 385-394, 1989, CRC Press, Boca Raton, LO), all herein incorporated by reference in their entireties.

[0098] The term “nucleic acid” or “polynucleotide” refers to a deoxyribonucleotide or ribonucleotide polymer in either single- or double-stranded form, and unless otherwise limited, encompasses known analogs of natural nucleotides that hybridize to nucleic acids in manner similar to naturally occurring nucleotides, such as peptide nucleic acids (PNAs) and phosphorothiolate DNA. Unless otherwise indicated, a particular nucleic acid sequence includes the complementary sequence thereof. Nucleotides include, but are not limited to, ATP, dATP, CTP, dCTP, GTP, dGTP, UTP, TTP, dUTP, 5-methyl-CTP, 5-methyl-dCTP, ITP, diTP, 2-amino-adenosine-TP, 2-amino-deoxyadenosine-TP, 2-thiothymidine triphosphate, pyrrolo-pyrimidine triphosphate, and 2-thiocytidine, as well as the alphathiotriphosphates for all of the above, and 2'-O-methyl-ribonucleotide triphosphates for all the above bases. Modified bases include, but are not limited to, 5-Br-UTP, 5-Br-dUTP, 5-F-UTP, 5-F-dUTP, 5-propynyl dCTP, and 5-propynyl-dUTP.

[0099] As used herein, the term “signal” is intended to mean an indicator that represents information. Signals include, for example, an electrical signal and an optical signal. The term “electrical signal” refers to an indicator of an electrical quality that represents information. The indicator can be, for example, current, voltage, tunneling, resistance, potential, voltage, conductance, or a transverse electrical effect. An “electronic current” or “electric current” refers to a flow of electric charge. In an example, an electrical signal may be an electric current passing through a nanopore, and the electric current may flow when an electric potential difference is applied across the nanopore.

[0100] As used herein, the term “driving force” is intended to mean an electrical current that allows a polynucleotide to translocate through the nanopore. In some embodiments, the electrical current electric current may flow when an electric potential difference is applied across the nanopore. [0101] As used herein, the term “holding force” is intended to mean a resistance that slows and/or stops a polynucleotide to translocate through the nanopore. In some embodiments, the holding force is overcome by the application of a driving force. Thus, the driving force overcomes/overrides the resistance that slows and/or stops a polynucleotide, thereby allowing the polynucleotide to translocate through the nanopore.

[0102] As used herein, the term “modification” is intended to refer to any group or moiety attached to or interacting with a nucleotide or polymer backbone. A modification can be covalently attached to a nucleotide to arrest (e.g., slow or halt) translocation, thereby achieve controlled reading of each individual bases. The resistance provided by the modification is due to inherent chemical and physical properties, (e.g., size, geometry, and/or non-covalent interactions with residues comprising the nanopore). The modification can operate as a ratchet or a brake for the polypeptide translocation through a nanopore, and can be attached to any part of the nucleotide and can also be attached to the nucleotide at two locations forming a loop. A chelating moiety may be referred to as a modification or visa versa.

[0103] As used herein, a “chelating moiety” is intended to refer to a molecule or structure that binds to or sequesters a metal ion. Chelating moieties may be macromolecules and may be monodentate, bidentate, tridentate, or multidentate. The chelating may interact or bond with the metal ion in various locations. For example, EDTA is a chelating moiety that is a multidentate chelating molecule that is hexadentate, with six potential binding or coordination sites.

[0104] The aspects and examples set forth herein and recited in the claims can be understood in view of the above definitions.

Additional Notes

[0105] It should be appreciated that all combinations of the foregoing concepts and additional concepts discussed in greater detail below (provided such concepts are not mutually inconsistent) are contemplated as being part of the inventive subject matter disclosed herein. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are contemplated as being part of the inventive subject matter disclosed herein. It should also be appreciated that terminology explicitly employed herein that also may appear in any disclosure incorporated by reference should be accorded a meaning most consistent with the particular concepts disclosed herein. [0106] Reference throughout the specification to “one example”, “another example”, “an example”, and so forth, means that a particular element (e.g., feature, structure, and/or characteristic) described in connection with the example is included in at least one example described herein, and may or may not be present in other examples. In addition, it is to be understood that the described elements for any example may be combined in any suitable manner in the various examples unless the context clearly dictates otherwise.

[0107] It is to be understood that the ranges provided herein include the stated range and any value or sub-range within the stated range, as if such value or sub-range were explicitly recited. For example, a range from about 2 nm to about 20 nm should be interpreted to include not only the explicitly recited limits of from about 2 nm to about 20 nm, but also to include individual values, such as about 3.5 nm, about 8 nm, about 18.2 nm, etc., and sub-ranges, such as from about 5 nm to about 10 nm, etc. Furthermore, when “about” and/or “substantially” are/is utilized to describe a value, this is meant to encompass minor variations (up to +/- 10%) from the stated value.

[0108] While several examples have been described in detail, it is to be understood that the disclosed examples may be modified. Therefore, the foregoing description is to be considered non-limiting.

[0109] While certain examples have been described, these examples have been presented by way of example only and are not intended to limit the scope of the disclosure. Indeed, the novel methods and systems described herein may be embodied in a variety of other forms. Furthermore, various omissions, substitutions and changes in the systems and methods described herein may be made without departing from the spirit of the disclosure. The accompanying claims and their equivalents are intended to cover such forms or modifications as would fall within the scope and spirit of the disclosure.

[0110] Features, materials, characteristics, or groups described in conjunction with a particular aspect, or example are to be understood to be applicable to any other aspect or example described in this section or elsewhere in this specification unless incompatible therewith. All of the features disclosed in this specification (including any accompanying claims, abstract and drawings), and/or all of the steps of any method or process so disclosed, may be combined in any combination, except combinations where at least some of such features and/or steps are mutually exclusive. The protection is not restricted to the details of any foregoing examples. The protection extends to any novel one, or any novel combination, of the features disclosed in this specification (including any accompanying claims, abstract and drawings), or to any novel one, or any novel combination, of the steps of any method or process so disclosed.

[0111] Furthermore, certain features that are described in this disclosure in the context of separate implementations can also be implemented in combination in a single implementation. Conversely, various features that are described in the context of a single implementation can also be implemented in multiple implementations separately or in any suitable sub-combination. Moreover, although features may be described above as acting in certain combinations, one or more features from a claimed combination can, in some cases, be excised from the combination, and the combination may be claimed as a sub-combination or variation of a sub-combination.

[0112] Moreover, while operations may be depicted in the drawings or described in the specification in a particular order, such operations need not be performed in the particular order shown or in sequential order, or that all operations be performed, to achieve desirable results. Other operations that are not depicted or described can be incorporated in the example methods and processes. For example, one or more additional operations can be performed before, after, simultaneously, or between any of the described operations. Further, the operations may be rearranged or reordered in other implementations. Those skilled in the art will appreciate that in some examples, the actual steps taken in the processes illustrated and/or disclosed may differ from those shown in the figures. Depending on the example, certain of the steps described above may be removed or others may be added. Furthermore, the features and attributes of the specific examples disclosed above may be combined in different ways to form additional examples, all of which fall within the scope of the present disclosure. Also, the separation of various system components in the implementations described above should not be understood as requiring such separation in all implementations, and it should be understood that the described components and systems can generally be integrated together in a single product or packaged into multiple products. For example, any of the components for an energy storage system described herein can be provided separately, or integrated together (e.g., packaged together, or attached together) to form an energy storage system. [0113] For purposes of this disclosure, certain aspects, advantages, and novel features are described herein. Not necessarily all such advantages may be achieved in accordance with any particular example. Thus, for example, those skilled in the art will recognize that the disclosure may be embodied or carried out in a manner that achieves one advantage or a group of advantages as taught herein without necessarily achieving other advantages as may be taught or suggested herein.

[0114] Conditional language, such as “can,” “could,” “might,” or “may,” unless specifically stated otherwise, or otherwise understood within the context as used, is generally intended to convey that certain examples include, while other examples do not include, certain features, elements, and/or steps. Thus, such conditional language is not generally intended to imply that features, elements, and/or steps are in any way required for one or more examples or that one or more examples necessarily include logic for deciding, with or without user input or prompting, whether these features, elements, and/or steps are included or are to be performed in any particular example.

[0115] Conjunctive language such as the phrase “at least one of X, Y, and Z,” unless specifically stated otherwise, is otherwise understood with the context as used in general to convey that an item, term, etc. may be either X, Y, or Z. Thus, such conjunctive language is not generally intended to imply that certain examples require the presence of at least one of X, at least one of Y, and at least one of Z.

[0116] Language of degree used herein, such as the terms “approximately,” “about,” “generally,” and “substantially” represent a value, amount, or characteristic close to the stated value, amount, or characteristic that still performs a desired function or achieves a desired result.

[0117] The scope of the present disclosure is not intended to be limited by the specific disclosures of preferred examples in this section or elsewhere in this specification, and may be defined by claims as presented in this section or elsewhere in this specification or as presented in the future. The language of the claims is to be interpreted broadly based on the language employed in the claims and not limited to the examples described in the present specification or during the prosecution of the application, which examples are to be construed as non-exclusive. [0118] Although the foregoing invention has been described in terms of certain preferred embodiments, other embodiments will be apparent to those of ordinary skill in the art. Additionally, other combinations, omissions, substitutions and modification will be apparent to the skilled artisan, in view of the disclosure herein. Accordingly, the present invention is not intended to be limited by the recitation of the preferred embodiments, but is instead to be defined by reference to the appended claims.

[0119] The terminology used in the description presented herein is not intended to be interpreted in any limited or restrictive manner and unless otherwise indicated refers to the ordinary meaning as would be understood by one of ordinary skill in the art in view of the specification. Furthermore, embodiments may comprise, consist of, consist essentially of, several novel features, no single one of which is solely responsible for its desirable attributes or is believed to be essential to practicing the embodiments herein described. As used herein, the section headings are for organizational purposes only and are not to be construed as limiting the described subject matter in any way. All literature and similar materials cited in this application, including but not limited to, patents, patent applications, articles, books, treatises, and internet web pages are expressly incorporated by reference for any purpose. When definitions of terms in incorporated references appear to differ from the definitions provided in the present teachings, the definition provided in the present teachings shall control. It will be appreciated that there is an implied “about” prior to the temperatures, concentrations, times, etc. discussed in the present teachings, such that slight and insubstantial deviations are within the scope of the present teachings herein.

[0120] Although this disclosure is in the context of certain embodiments and examples, those of ordinary skill in the art will understand that the present disclosure extends beyond the specifically disclosed embodiments to other alternative embodiments and/or uses of the embodiments and obvious modifications and equivalents thereof. In addition, while several variations of the embodiments have been shown and described in detail, other modifications, which are within the scope of this disclosure, will be readily apparent to those of ordinary skill in the art based upon this disclosure. It is also contemplated that various combinations or sub-combinations of the specific features and aspects of the embodiments may be made and still fall within the scope of the disclosure. It should be understood that various features and aspects of the disclosed embodiments can be combined with, or substituted for, one another in order to form varying modes or embodiments of the disclosure. Thus, it is intended that the scope of the present disclosure herein disclosed should not be limited by the particular disclosed embodiments described above.

Claims

WHAT IS CLAIMED IS:

1. A compound having one of the following structures: wherein: n is 0 or a positive integer;

Y is -O-, -S-, or -NH-;

X is -O-, -NH-, or -CH2-;

L₁ comprises a linking group; and M is a modification comprising a chelating moiety.

2. The compound of claim 1, wherein the modification further comprises a metal ion complexed to the chelating moiety.

3. The compound of claim 2, wherein the metal ion is selected from the group consisting of Zn²⁺, Cd²⁺, Co²⁺, NI²⁺, Pb²⁺, Au³⁺, Hg²⁺, Ba²⁺, Cu²⁺, Fe²⁺, Al³⁺, Mn²⁺ and Mg²⁺.

4. The compound of claim 1, wherein the chelating moiety is selected from the group consisting of: Polyhistidine tag (His-tag), HQ-tag, HN-tag, HAT-tag, Zn finger (Zif268), DNA hairpins, G-quadruplex, porphyrins, crown-ethers, cyclodextrins, cucurbiturils, EDTA, tetraxetan (DOTA), NOTA, TETA, and HEHA.

5. The compound of any one of claims 1 to 4, wherein Li comprises a linking group selected from the group consisting of amine-NHS ester, amine-imidoester, aminepentafluorophenyl ester, amine-hydroxymethyl phosphine, carboxyl-carbodiimide, thiol- maleimide, thiol-haloacetyl, thiol-pyridyl disulfide, thiol-thiosulfonate, thiol-vinyl sulfone, aldehyde-hydrazide, aldehyde-alkoxyamine, hydroxy-isocyanate, azide-alkyne, azidephosphine, transcyclooctene-tetrazine, norbornene-tetrazine, azide-cyclooctyne, and azidenorbornene.

6. A method for determining a sequence of a target polynucleotide in a nanoporebased sequencing system, the method comprising: providing a target polynucleotide comprising a modification covalently attached to each of nucleotides in the target polynucleotide, wherein the modification comprises a chelating moiety-metal ion complex; applying a voltage bias to cause the target polynucleotide to translocate through a constriction of a nanopore; during a first arresting event, applying a reading voltage measuring an electrical response at the constriction of the nanopore; and identify the nucleotide or a combination of nucleotides passing through the constriction of the nanopore based on the electrical response.

7. The method of claim 6, wherein the step of providing a target polynucleotide comprises: conjugating each type of nucleotide with a chelating moiety to form modified nucleotides; incubating the modified nucleotides with different metal ions to form modified nucleotide-metal ion conjugates, wherein each of the different metal ions is configured to complex with each type of the modified nucleotides; and forming the target polynucleotide by synthesizing a daughter strand of a template polynucleotide using the modified nucleotide-metal conjugates.

8. The method of claim 7, wherein the chelating moieties on each type of the modified nucleotides are the same, and each type of the modified nucleotides are separately incubated with different metal ions.

9. The method of claim 7, wherein the chelating moieties on each type of the modified nucleotides are different, and each type of the modified nucleotides are separately incubated separately with different metal ions prior to the forming of the target polynucleotide.

10. The method of claim 7, wherein the chelating moieties on each type of the modified nucleotides are different, and each type of the modified nucleotides are incubated together with at least four different metals prior to the forming of the target polynucleotide.

11. The method of claim 7, wherein the chelating moieties on each type of nucleotides are different, and each type of the modified nucleotides are incubated together with at least four different metals after the forming of the target polynucleotide.

12. The method of claim 6, wherein the step of providing a target polynucleotide comprises: conjugating each type of nucleotides with a different chelating moiety to form modified nucleotides; synthesizing a daughter strand of a template polynucleotide using the modified nucleotides; and forming the target polynucleotide by incubating the daughter strand with different metal ions.

13. The method of claim 6, wherein the chelating moiety-metal ion complex comprises a chelating moiety selected from the group consisting of: Polyhistidine tag (His- tag), HQ-tag, HN-tag, HAT-tag, Zn finger (Zif268), DNA hairpins, G-quadruplex, porphyrins, crown-ethers, cyclodextrins, cucurbiturils, EDTA, tetraxetan (DOTA), NOTA, TETA, and HEHA.

14. The method of claim 6, wherein the chelating moiety-metal ion complex comprises a metal ion selected from the group consisting of Zn²⁺, Cd²⁺, Co²⁺, Ni²⁺, Pb²⁺, Au³⁺, Hg²⁺, Ba²⁺, Cu²⁺, Fe²⁺, Al³⁺, Mn²⁺ and Mg²⁺.

15. The method of claim 6, wherein the modifications are covalently attached to each nucleotide in the target polynucleotide via a linker construct comprising a first linking group.

16. The method of claim 15, wherein the first linking group comprises a conjugating moiety selected from the group consisting of amine-NHS ester, amine- imidoester, amine-pentafluorophenyl ester, amine-hydroxymethyl phosphine, carboxyl-carbodiimide, thiol-maleimide, thiol-haloacetyl, thiol-pyridyl disulfide, thiol-thiosulfonate, thiol-vinyl sulfone, aldehyde-hydrazide, aldehyde-alkoxyamine, hydroxy-isocyanate, azide-alkyne, azide-phosphine, transcyclooctene-tetrazine, norbornene-tetrazine, azide-cyclooctyne, and azide-norbornene.

17. A kit for performing a method for determining a sequence of a polynucleotide in a nanopore-based sequencing system according to any one of claims 6 to 16, the kit comprising a compound selected from:

wherein: n is 0 or a positive integer;

Y is -O-, -S-, or -NH-;

X is -O-, -NH-, or -CH2-;

Li comprises a linking group; and

M is a modification comprising a chelating moiety.

18. The kit of claim 17, wherein M comprises a chelating moiety-metal ion complex.

19. The kit of claim 17, wherein M comprises the chelating moiety, and the kit further comprising a solution comprising four different metal ions, wherein the different metal ions are configured to complex with a predetermined chelating moiety.