Conjugated polymers or polymer dots as fluorescent labels

Patent metadata

Field	Value
Publication number	US-2025163505-A1
Application number	US-202418947955-A
Country	US
Kind code	A1
Filing date	Nov 14, 2024
Priority date	Nov 17, 2023
Publication date	May 22, 2025
Grant date	—

Abstract

Embodiments of the present disclosure relate to compositions and methods for labeling of nucleotides, oligonucleotides, or polynucleotides with conjugated polymers or polymer dots. In particular, conjugated polymers or polymer dots can be used as detectable labels for nucleotides, oligonucleotides, or polynucleotides in sequencing by synthesis.

First claim

1 . A nucleotide, oligonucleotide or polynucleotide comprising a water-soluble conjugated polymer or a water-dispersible polymer dot attached thereto as a detectable label.

2 . The nucleotide, oligonucleotide or polynucleotide of claim 1 , wherein the water-soluble conjugated polymer comprise one or more repeating unit moieties selected from the group consisting of:

a five membered heteroarylene containing one, two or three heteroatoms selected from the group consisting of N, O and S,

and combinations thereof;
wherein each of R 1a , R 1b , R 1c , R 1d , R 1e and R 1f is independently H, unsubstituted C 1 -C 12 alkyl, C 1 -C 12 alkyl substituted with one or more water solubilizing groups, or 2 to 20 membered heteroalkyl;
ring A is a five or six membered heteroaryl containing one, two or three heteroatoms selected from the group consisting of N, O and S, and
wherein each structure is optionally substituted with one or more electron donating groups, one or more electron withdrawing groups, one or more functional moiety R F , or one or more water solubilizing group R S , or combinations thereof.

3 . The nucleotide, oligonucleotide or polynucleotide of claim 2 , wherein the water solubilizing groups are selected from the group consisting of phosphate;

wherein each C 1 -C 6 alkyl is optionally substituted with one or more substituents selected from phosphate,

4 . The nucleotide, oligonucleotide or polynucleotide of claim 2 , wherein the conjugated polymer is covalently bounded to the nucleotide, oligonucleotide or polynucleotide through reaction of the functional moiety R F of the conjugated polymer with a reactive moiety of the oligonucleotide or polynucleotide.

5 . The nucleotide, oligonucleotide or polynucleotide of claim 4 , wherein the conjugated polymer comprises the structure:

wherein each of R 2a , R 2b and R 2c is independently H, R F or C 1 -C 12 alkyl substituted with R F ;
X is O, S, an alkylene linker, or a heteroalkylene linker;
each R F is independently azido, amino, a reactive ester,

 unsubstituted or substituted 1,2,4,5-tetrazinyl,

 unsubstituted or substituted dibenzocyclooctyne (DBCO),

 unsubstituted or substituted bicyclo[6.1.0]nonynyl (BCN),

 unsubstituted or substituted transcyclooctenyl (TCO), or

 and
each of m and n is independently an integer from 1 to 100,000.

6 . The nucleotide, oligonucleotide or polynucleotide of claim 1 , comprising the water-dispersible polymer dot covalently bounded thereto, wherein the water-dispersible polymer dot comprises a conjugated polymer nanoparticle and one or more functionalized surfactants attached to the surface of the nanoparticle.

7 .- 9 . (canceled)

10 . The nucleotide, oligonucleotide or polynucleotide of claim 6 , wherein the water-dispersible polymer dot is covalently bounded to the nucleotide, oligonucleotide or polynucleotide through reaction of a functional moiety of the conjugated polymer or a functional moiety of the one or more functionalized surfactants with a reactive moiety of the nucleotide, oligonucleotide or polynucleotide.

11 . The nucleotide, oligonucleotide or polynucleotide of claim 10 , wherein the functional moiety of the conjugated polymer or one or more functionalized surfactants is selected from the group consisting of azido, amino, a reactive ester,

unsubstituted or substituted 1,2,4,5-tetrazinyl,

unsubstituted or substituted DBCO,

unsubstituted or substituted BCN,

unsubstituted or substituted TCO, and

12 . The nucleotide, oligonucleotide or polynucleotide of claim 10 , wherein the one or more functionalized surfactants comprises an amphiphilic block copolymer or a water soluble nonionic emulsifier (e.g., Polysorbate 80 (Tween® 80)), or a combination thereof.

13 . The nucleotide, oligonucleotide or polynucleotide of claim 12 , wherein the amphiphilic block copolymer comprises

each of s and k is independently an integer from 1 to 10,000.

14 . The nucleotide, oligonucleotide or polynucleotide of claim 1 , comprising a core-shell water-dispersible polymer dot covalently bounded thereto, wherein the core-shell water-dispersible polymer dot comprises a conjugated polymer nanoparticle core, and a hydrogel shell.

15 . The nucleotide, oligonucleotide or polynucleotide of claim 14 , wherein the core-shell water-dispersible polymer dot further comprises one or more surfactants on the surface of the conjugated polymer nanoparticle core.

16 . The nucleotide, oligonucleotide or polynucleotide of claim 15 , wherein the one or more surfactants comprises a water soluble nonionic emulsifier (e.g., Polysorbate 80 (Tween® 80)) or an anionic surfactant (e.g., sodium dodecyl sulfate (SDS)), or a combination thereof.

17 . The nucleotide, oligonucleotide or polynucleotide of claim 14 , wherein the core-shell water-dispersible polymer dot is covalently bounded to the oligonucleotide or polynucleotide through reaction of a functional moiety of the hydrogel shell with a reactive moiety of the nucleotide, oligonucleotide or polynucleotide.

18 . (canceled)

19 . The nucleotide, oligonucleotide or polynucleotide of claim 14 , wherein the hydrogel shell comprises an acrylamide hydrogel.

20 . (canceled)

21 . The nucleotide, oligonucleotide or polynucleotide of claim 1 , comprising a core-shell water-dispersible polymer dot covalently bounded thereto, wherein the core-shell water-dispersible polymer dot comprises a conjugated polymer coated on a supporting particle matrix core, and wherein the conjugated polymer is water-soluble, water-swellable, or hydrophilic.

22 . The nucleotide, oligonucleotide or polynucleotide of claim 21 , wherein the core-shell water-dispersible polymer dot is covalently bounded to the nucleotide, oligonucleotide or polynucleotide through reaction

Assignees

• Illumina Inc

Inventors

• Nguyen Nam
• Maria Iuliana Petruta
• Brown Andrew A
• George Wayne N
• Wu Xiaolin
• Von Hatten Xavier
• Dharmarwardana Madushani

Classifications

• G01N33/582

  with fluorescent label · CPC title

• C08F134/04

  in a ring containing sulfur · CPC title

• C07H19/16

  Purine radicals · CPC title

• C07H19/06

  Pyrimidine radicals · CPC title

• C07H21/00

  Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids · CPC title