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WO2025080691A1 - Colorants fluorescents et compositions comprenant des dendrimères pour détecter la présence d'un analyte dans un échantillon - Google Patents

Colorants fluorescents et compositions comprenant des dendrimères pour détecter la présence d'un analyte dans un échantillon Download PDF

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WO2025080691A1
WO2025080691A1 PCT/US2024/050544 US2024050544W WO2025080691A1 WO 2025080691 A1 WO2025080691 A1 WO 2025080691A1 US 2024050544 W US2024050544 W US 2024050544W WO 2025080691 A1 WO2025080691 A1 WO 2025080691A1
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compound
optionally
dendrimer
linkage
rule
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Shulin WAN
Matthew YEROU
Teng CHI
Wenjuan HOU
Nan Jiang
Jing Wang
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Biolegend Inc
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Biolegend Inc
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    • CCHEMISTRY; METALLURGY
    • C09DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
    • C09BORGANIC DYES OR CLOSELY-RELATED COMPOUNDS FOR PRODUCING DYES, e.g. PIGMENTS; MORDANTS; LAKES
    • C09B57/00Other synthetic dyes of known constitution
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07CACYCLIC OR CARBOCYCLIC COMPOUNDS
    • C07C215/00Compounds containing amino and hydroxy groups bound to the same carbon skeleton
    • C07C215/02Compounds containing amino and hydroxy groups bound to the same carbon skeleton having hydroxy groups and amino groups bound to acyclic carbon atoms of the same carbon skeleton
    • C07C215/04Compounds containing amino and hydroxy groups bound to the same carbon skeleton having hydroxy groups and amino groups bound to acyclic carbon atoms of the same carbon skeleton the carbon skeleton being saturated
    • C07C215/06Compounds containing amino and hydroxy groups bound to the same carbon skeleton having hydroxy groups and amino groups bound to acyclic carbon atoms of the same carbon skeleton the carbon skeleton being saturated and acyclic
    • C07C215/10Compounds containing amino and hydroxy groups bound to the same carbon skeleton having hydroxy groups and amino groups bound to acyclic carbon atoms of the same carbon skeleton the carbon skeleton being saturated and acyclic with one amino group and at least two hydroxy groups bound to the carbon skeleton
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07CACYCLIC OR CARBOCYCLIC COMPOUNDS
    • C07C59/00Compounds having carboxyl groups bound to acyclic carbon atoms and containing any of the groups OH, O—metal, —CHO, keto, ether, groups, groups, or groups
    • C07C59/40Unsaturated compounds
    • C07C59/58Unsaturated compounds containing ether groups, groups, groups, or groups
    • C07C59/72Unsaturated compounds containing ether groups, groups, groups, or groups containing six-membered aromatic rings and other rings
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D207/00Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom
    • C07D207/46Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with hetero atoms directly attached to the ring nitrogen atom
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07DHETEROCYCLIC COMPOUNDS
    • C07D487/00Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00
    • C07D487/12Heterocyclic compounds containing nitrogen atoms as the only ring hetero atoms in the condensed system, not provided for by groups C07D451/00 - C07D477/00 in which the condensed system contains three hetero rings
    • C07D487/16Peri-condensed systems
    • CCHEMISTRY; METALLURGY
    • C09DYES; PAINTS; POLISHES; NATURAL RESINS; ADHESIVES; COMPOSITIONS NOT OTHERWISE PROVIDED FOR; APPLICATIONS OF MATERIALS NOT OTHERWISE PROVIDED FOR
    • C09KMATERIALS FOR MISCELLANEOUS APPLICATIONS, NOT PROVIDED FOR ELSEWHERE
    • C09K11/00Luminescent, e.g. electroluminescent, chemiluminescent materials
    • C09K11/06Luminescent, e.g. electroluminescent, chemiluminescent materials containing organic luminescent materials
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/531Production of immunochemical test materials
    • G01N33/532Production of labelled immunochemicals
    • G01N33/533Production of labelled immunochemicals with fluorescent label
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/58Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances
    • G01N33/582Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving labelled substances with fluorescent label
    • CCHEMISTRY; METALLURGY
    • C07ORGANIC CHEMISTRY
    • C07CACYCLIC OR CARBOCYCLIC COMPOUNDS
    • C07C2603/00Systems containing at least three condensed rings
    • C07C2603/02Ortho- or ortho- and peri-condensed systems
    • C07C2603/52Ortho- or ortho- and peri-condensed systems containing five condensed rings

Definitions

  • the present description relates to compounds having desirable fluorescence properties, methods of making, and methods of using.
  • compositions having tunable excitation and emission profiles and/or increased brightness there is a continuing need for improved compositions having tunable excitation and emission profiles and/or increased brightness, and methods of using such compositions.
  • a and B are linked to one or more B groups by an electron conducting conjugated bond configured to delocalize one or more electrons between A and B; where A is an electron receiving group, an electron donating group, or a fluorophore; where B is an electron receiving group, an electron donating group, or a fluorophore; and wherein said compound is free of repeat units of A, B, or combinations thereof, and optionally wherein A and B are not identical in structure.
  • the electron conducting conjugated bond is a conjugated single bond.
  • A is a conjugated ring structure dye.
  • B is a conjugated ring structure dye.
  • the compound optionally has a maximum absorption at a wavelength between 300 nm and 450 nm, optionally between 365 nm and 830 nm. In any aspect of any of the foregoing, the compound optionally has a maximum emission at a wavelength between 365 nm and 830 nm.
  • A has a maximum absorption at a wavelength between 300 nm and 450 nm, optionally between 300 nm and 600 nm.
  • absent conjugation to A, B has a maximum absorption at a wavelength between 150 nm and 450 nm, optionally absent conjugation to A, B has a maximum emission at a wavelength between 150 nm and 830 nm.
  • the compound optionally is a structure comprising or consisting of A linked to 1 to 10 B groups, optionally having the formula:
  • the dendrimer further comprises a functional group.
  • the dendrimer optionally comprises a compound of formula wherein: each n is independently an integer from 10 to 300; R63, R64, R65, R66, R67, R68, R69, and R70 are independently selected from an amine, an azide, a linkage A or B, a linkage to a probe, and one or more additional dendrimers, optionally 1 to 10 additional dendrimer structures.
  • the probe is a protein or fragment thereof optionally including but not limited to an antibody or fragment thereof, a nucleic acid, a phospholipid, a polysaccharide, a triglyceride, aptamer, avidin, streptavidin, neutravidin, avidinDN, avidinD, or a cell.
  • the linkage is selected from the group consisting of amide, thiol, succimidylester, maleimide, azide, carboxylate, carboxy/EDC (l-Ethyl-3-[3-imethylaminopropyl]carbodiimide Hydrochloride), Sulfo-SMCC, BMPH, Sulfo-SBED, transcyclooctene/tetrazine, and amine/epoxide.
  • a or B are selected from the group consisting of fluorescein, 6-FAM, rhodamine, Texas Red, tetramethylrhodamine, a carb oxy rhodamine, carboxyrhodamine 6G, carboxyrhodol, carb oxy rhodamine 110, Cascade Blue, Cascade Yellow, coumarin, 2-[3-[3-[6-[(2,5-dioxo-l- pyrrolidinyl)oxy]-6-oxohexyl]-2(3H)-benzoxazolylidene]-l-propen-l-yl]-3-ethyl- benzoxazolium, monoiodide (Cy2), Sulfo-Cyanine3 (Cy3), Cyanine 3.5 (Cy3.5), Sulfo-Cyanine5
  • SUBSTITUTE SHEET (RULE 26) (3- ⁇ 2-[(3,5-Dimethyl-lH-pyrrol-2-yl-kappaN)methylene]-2H-pyrrol-5-yl- kappaN ⁇ propanoato)(difluoro)boron (BODIPY® FL), BODIPY FL-Br2, CAS No. 216961-93-2 (BODIPY ® 530/550), 12-(2,2-difluoro- 12-thiophen-2-yl-3 -aza- 1 -azonia-2- boranuidatricyclo[7.3.0.03,7]dodeca-l(12),4,6,8,10-pentaen-4-yl)dodecanoate;hydron
  • FIG. 1 depicts an excitation and emission profile of a compound, according to one aspect
  • FIG. 2 depicts a flow cytometry plot of mean fluorescence intensity (MFI) (y-axis) as a function of detector for a compound according to one aspect, and a comparative example;
  • MFI mean fluorescence intensity
  • FIG. 4A depicts flow cytometry plots of a comparative example
  • FIG. 4C depicts flow cytometry plots of an example, according to one aspect
  • florescent detection technologies include the ability to absorb light of a particular wavelength that is itself able to penetrate complex backgrounds, emit at readily detectable and valuable wavelengths, and provide a robust fluorescent signal.
  • unique structures that enable not only specific binding of a target molecule, but also are able to more fully saturate that target with fluorophores to improve detectability, which is particularly useful for low quantity analytes.
  • Unique florescent dendrimer structures are also disclosed that may be linked or linkable to a probe such as an antibody, peptide, nucleic acid or other, and provide multiple florescent molecules to that probe, thereby improving localization of fluorescent molecules to the target when present.
  • the dendrimer structures provide the ability to not only
  • SUBSTITUTE SHEET (RULE 26) present multiple probes, but also a large number of fluorophores capable of providing a desired signal.
  • (Ci-C2o)hydrocarbyl means a hydrocarbon radical of from 1 to 20 carbon atoms, in which each hydrocarbon radical is aromatic or non-aromatic, saturated or unsaturated,
  • SUBSTITUTE SHEET (RULE 26) straight chain or branched chain, cyclic (including mono- and poly-cyclic, fused and non-fused polycyclic, including bicyclic; 3 carbon atoms or more) or acyclic and is unsubstituted or substituted by one or more substituents.
  • the compounds disclosed herein have utility, for example, as molecules for florescent imaging, and/or as fluorescent dyes, with increased extinction coefficients and tunable excitation and emission.
  • fluorophores such as the compositions disclosed herein, may be coupled with a dendrimer to form compositions having improved solubility in aqueous solvent systems and decreased quenching, both of which may increase utility for improved analytical detection methods.
  • Dendrimer compositions may also be formed by conjugating a targeting molecule to the disclosed compositions.
  • the compositions described and disclosed herein may have utility as ultraviolet (UV) dyes having tunable emissions and/or increased brightness.
  • UV ultraviolet
  • n may be greater than or equal to 2.
  • the electron conducting conjugated bond may be a conjugated single bond.
  • A, B, or both may be a conjugated ring structure dye.
  • a conjugated ring structure dye optionally is formed of 1, 2, 3, or more ring structures with conjugation within one or more of such ring structures and optionally between ring structures.
  • a conjugated ring structure dye includes at least one 6-membered ring.
  • a conjugated ring structure dye includes at least one 5-membered ring.
  • a conjugated ring structure dye includes at least one 6-membered ring and at least one 5-membered ring.
  • a conjugated ring structured dye includes 1, 2, 3, 4, 5, 6, 7 or more ring structures within the conjugated ring structured dye.
  • a compound including A and B may be characterized as having a maximum absorption at a wavelength and a maximum emission at a wavelength. Tuning of the absorption and emission properties of the compound may be provided in part by structural variations in A and B.
  • a compound may have a maximum absorption at a wavelength greater than or equal to 300 nm.
  • a compound has a maximum absorption wavelength in the range of 300 nm to 830 nm.
  • a compound has a maximum absorption wavelength of 300 nm to 400 nm, and optionally 300 nm and 450 nm.
  • a compound has a maximum absorption wavelength of 365 nm to 400 nm.
  • the A unit of a compound as disclosed herein may have a maximum absorption at a wavelength greater than or equal to 300 nm, or a wavelength of less than or equal to 450 nm, or both, wherein the maximum absorption is measured absent conjugation to B.
  • A may have a maximum absorption at a wavelength greater than or equal to 325 nm, greater than or equal to 350 nm, or greater than or equal to 375 nm, absent conjugation to B.
  • A may have a maximum absorption at a wavelength less than or equal to 425 nm, less than or equal to 400 nm, or less than or equal to 475 nm, absent conjugation to B.
  • the B unit of a compound as disclosed herein may have a maximum emission at a wavelength greater than or equal to 150 nm, or less than or equal to 830 nm, or both, wherein the maximum emission is measured absent conjugation to A.
  • B may have a maximum emission at a wavelength greater than or equal to 150 nm, 200 nm, 250 nm, 300 nm, 350 nm, 400 nm, 450 nm, or 500 nm, absent conjugation to A.
  • B may have a maximum emission at a wavelength less than or equal to 830 nm, 800 nm, 750 nm, 700 nm, 650 nm, 600 nm, 550 nm, or 500 nm, , absent conjugation to A.
  • a water-soluble group is a linear or branched (Ci- C2o)hydrocarbyl, a (Ci-C2o)heterohydrocarbyl, or combinations thereof, wherein a heteroatom comprises optionally an 0, N, or S, optionally wherein said heterocycle comprises -SO3, -NH2, - OH, or other.
  • SUBSTITUTE SHEET (RULE 26) linked to two or more of A, or both.
  • A may be linked to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more of B, or B may be linked to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more of A, or both.
  • R56, R58, and R60 are a linkage to A; and R57, R59, R61, and R62 are independently a water-soluble group, optionally a (Ci-C5o)heterohydrocarbyl, a (Ci-C4o)heterohydrocarbyl, a (Cs- C4o)heterohydrocarbyl, (Cio-C4o)heterohydrocarbyl, a (Ci-C3o)heterohydrocarbyl, a (C5-C30- )heterohydrocarbyl, or a (Cio-C3o)heterohydrocarbyl.
  • n is an integer from 1 to 15
  • m is an integer from 1 to 5
  • R71 is independently selected from the group consisting of-H and a linkage to a second structure, optionally a dendrimer or a probe.
  • each n may be 10 or 11.
  • R57, R59, R61, and R62 may be independently selected from the group consisting of a (Ci-Csojheterohydrocarbyl and a linkage to the second structure.
  • SUBSTITUTE SHEET (RULE 26) and/or R62 may be independently selected to increase a solubility of the compound in water, optionally wherein the R3, R4, R5, R6 R10, R11, R12, R16, R17, R18, R21, R22, R25, R26, R27, R28, R31, R33, R35, R37, R39, R40, R42, R44, R46, R47, R48, R50, R51, R54, R55, R57, R59, R61, and/or R62 may be where n is an integer from 1 to 15, m is an integer from 1 to 5, and R71 is independently selected from the group consisting of-H and a linkage to a second structure, optionally a dendrimer or a probe. In some aspects, each n may be 10 or 11.
  • a group, a B group, or both are a compound as described in U.S. Patent No: 10,053,484 or US Patent Application Publication No: 2021/0102873.
  • a probe may be an antibody fragment such as single chain antibodies (scFv), Fab and scFv antibodies, single domain antibodies (VHH), or chimeric antibodies.
  • the probe may be derived from a naturally occurring protein or polypeptide; it may be designed de novo, or it may be selected from a library.
  • a probe may be derived from an antibody, a single chain
  • SUBSTITUTE SHEET (RULE 26) antibody (scFv), a single domain antibody (VHH), a lipocalin, a single chain MHC molecule, an AnticalinTM (Pieris), an AffibodyTM, a nanobody (Ablynx) or a TrinectinTM (Phylos).
  • conjugation of such a compound comprising A and B to a dendrimer may reduce dye-to-dye interactions by distancing each compound comprising A and B from a plurality of the compounds comprising A and B.
  • a dendrimer composition may have an F/P ratio of from 5 to 100, such as from 10 to 30, where the F/P ratio is defined as the total number of molecules of the compound present in the
  • SUBSTITUTE SHEET (RULE 26) fluorescein, 6-FAM, rhodamine, Texas Red, tetramethylrhodamine, a carboxyrhodamine, carb oxy rhodamine 6G, carboxyrhodol, carboxyrhodamine 110, Cascade Blue, Cascade Yellow, coumarin, Cy2®, Cy3®, Cy3.5®, Cy5®, Cy5.5®, Cy-Chrome, phycoerythrin, PerCP (peridinin chlorophyll-a Protein), allophycocyanin, PerCP-Cy5.5, JOE (6-carboxy-4',5'-dichloro-2',7'- dimethoxyfluorescein), NED, ROX (5-(and -6)-carboxy-X-rhodamine), HEX, Lucifer Yellow, Marina Blue, Oregon Green 488, Oregon Green 500, Oregon Green 514, Alexa Fluor® 350, Alexa Fluor® 430,
  • Methods of detecting the presence or absence of an analyte in the sample or the organism may include use of a dendrimer linked to a fluorophore as disclosed herein.
  • the dendrimer of the method of detecting the presence or absence of an analyte in a sample or an organism may include any dendrimer described herein and any compound as described herein.
  • SUBSTITUTE SHEET (RULE 26) dendrimer with the one or more functional groups with a fluorophore, optionally using well understood conditions in the art, a targeted dendrimer composition may be formed.
  • Any dendrimer disclosed herein may be formed from the methods of forming a targeted dendrimer composition described herein, and optionally include one or more fluorescent compounds disclosed herein, or another fluorophore.
  • Step 1 100-300 mL acetic acid, 10-100 mL toluene, 10-100 mL 48% aqueous HBr was added to the 500 mL pressure round bottom vessel. The vessel was capped immediately and tightly with a specific press vessel plastic cap. Then 1-20 grams (g) 6,6’, 12, 12’-tetrakis(3- phenoxypropyl) indeno[l,2-b]fluorine was added to the 500 mL pressure round bottom vessel. The reaction was stirred overnight under reflux and crystals Fr-4Br after reaction were collected by filtration.
  • Step 4 is performed by adding 3.6 g FR-2Br-4PEG10 to the 24/40 100 mL and 1.152 g 4-(2-Carboxyethyl)phenylboronic acid, pinacol ester to two neck round bottom flask, and dissolve by 18 mL anhydrous dimethylformamide (DMF). Freeze the mixture with liquid N2. Add 2M K2CO3 (1.73 g in 6 mL) and [l,l'-Bis(diphenylphosphino)ferrocene]dichloropalladium(II), complex with dichloromethane 58 mg to the container. Freeze and thaw three times then heat to 100 °C for 6 hours.
  • DMF dimethylformamide
  • SUBSTITUTE SHEET (RULE 26) mL anhydrous DMF is added. TSTU and DIPEA are then added to the vial, that is shaken at room temperature for 15 min. Acetic acid to the vial is then added and the mixture shaken to mix followed by removal of solvent by lyophilization. The product is isolated using a C18 HPLC column, dried and subjected to analyses by HPLC and NMR. The resulting compound formed from Step 5 is identified herein as Compound IF.
  • FIG. 5 depicts flow cytometry plots of fluorescein isothiocyanate area (FITC-A) as a function of side scattering area (SSC-A) and counts per FITC-A for the samples of Example 7.
  • FITC-A fluorescein isothiocyanate area
  • SSC-A side scattering area
  • Example 5A which had a staining index of 68.
  • Example 5C increased the staining index by approximately 7.1 times that of Comparative Example 5B, which included the same dye, but did not include the dendrimer.
  • Comparative Example 5B and Example 5C had an F/P ratio of approximately 14.
  • the inclusion of the dendrimer reduced the quenching effect of the dye.
  • SUBSTITUTE SHEET (RULE 26) 9. The compound of any one of aspects 1-8, wherein the compound has a maximum absorption at a wavelength between 300 nm and 450 nm.
  • R32, R34, R36, R38, R41, R43, R45, and R49 are a linkage to B; and wherein X is C, Si, 0, S, P, N, Se, or Te.
  • R57, R59, R61, and R62 are independently a water soluble group, optionally a (Ci-C- 5o)heterohy drocarbyl .
  • SUBSTITUTE SHEET (RULE 26) 42 The compound of any one of any of aspects 31-41, wherein said dendrimer further comprises a functional group.
  • SUBSTITUTE SHEET (RULE 26) 51 The method of aspect 50, wherein said detecting is by flow cytometry.
  • polyethylene glycol chain comprises at least 3 repeating units of ethylene glycol.
  • fluorophore is selected from the group consisting of fluorescein, 6-FAM, rhodamine, Texas Red, tetramethylrhodamine, a carboxyrhodamine, carboxyrhodamine 6G, carboxyrhodol, carboxyrhodamine 110, Cascade Blue, Cascade Yellow, coumarin, Cy2®, Cy3®, Cy3.5®, Cy5®, Cy5.5®, Cy-Chrome, phycoerythrin, PerCP (peridinin chlorophyll-a Protein), allophycocyanin, PerCP-Cy5.5, JOE (6-carboxy-4',5'- dichloro-2',7'-dimethoxyfluorescein), NED, ROX (5-(and -6)-carboxy-X-rhodamine), HEX, Lucifer Yellow, Marina Blue, Oregon Green 488, Oregon Green 500, Oregon Green 514, Alexa Fluor®
  • polyethylene glycol chain comprises at least 3 repeating units of ethylene glycol.
  • R63, R64, R65, R66, R67, R68, R69, and R70 are independently selected from an amine, an azide, a linkage to the fluorophore, a linkage to the probe, and one or more additional dendrimers, optionally 1 to 10 additional dendrimer structures.

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Abstract

La présente invention concerne un composé comprenant A et B, où un ou plusieurs groupes A étant liés à un ou plusieurs groupes B par une liaison conjuguée conductrice d'électrons configurée pour délocaliser un ou plusieurs électrons entre A et B ; un procédé de détection de la présence ou de l'absence d'un analyte dans un échantillon ou un organisme, le procédé comprenant les opérations consistant à mettre en contact un échantillon avec une composition comprenant une structure de dendrimère et un composé tel que décrit ici ; exposer l'échantillon à de la lumière d'une longueur d'onde de lumière qui excite le composé de la composition ; et détecter la présence ou l'absence de lumière émise par la composition ; et un procédé de formation d'une composition de dendrimère comprenant les opérations consistant à mettre en contact un dendrimère avec un composé comprenant un composé tel que décrit ici, formant ainsi une composition de dendrimère ; et mettre en contact la composition de dendrimère avec une sonde dans des conditions où la composition de dendrimère se lie à la sonde.
PCT/US2024/050544 2023-10-09 2024-10-09 Colorants fluorescents et compositions comprenant des dendrimères pour détecter la présence d'un analyte dans un échantillon Pending WO2025080691A1 (fr)

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