Polymer coatings

• US 9,752,186 B2
• Filed: 04/06/2015
• Issued: 09/05/2017
• Est. Priority Date: 06/08/2012
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: George, Wayne N., Brown, Andrew A., Bratton, Daniel, Ren, Hongji, Smith, Ryan C.
• Primary Examiner(s): Peng, Kuo-Liang
• Application Number:
  US14/679,760
• Publication Number:
  US 20150259735A1
• Time in Patent Office: 883 Days
• CPC Class Codes: B05D 3/06 by exposure to radiation B05D3/02 takes precedence ; plasma treatment B05D3/141
• CPC Class Codes: B05D 3/065 After-treatment
• CPC Class Codes: C09D 133/26 Homopolymers or copolymers of acrylamide or methacrylamide
• CPC Class Codes: C09D 135/00 Coating compositions based on homopolymers or copolymers of compounds having one or more unsaturated aliphatic radicals, each having only one carbon-to-carbon double bond, and at least one being terminated by a carboxyl radical, and containing at least another carboxyl radical in the molecule, or of salts, anhydrides, esters, amides, imides or nitriles thereof; Coating compositions based on derivatives of such polymers
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: Y10T 428/24802 Discontinuous or differential coating, impregnation or bond [e.g., artwork, printing, retouched photograph, etc.]
• CPC Class Codes: Y10T 428/24917 including metal layer
• CPC Class Codes: Y10T 428/24926 including ceramic, glass, porcelain or quartz layer
• CPC Class Codes: Y10T 428/2998 including synthetic resin or polymer
• CPC Class Codes: Y10T 428/31536 Including interfacial reaction product of adjacent layers
• CPC Class Codes: Y10T 428/31935 Ester, halide or nitrile of addition polymer

Abstract

The present disclosure relates to polymer coatings covalently attached to the surface of a substrate and the preparation of the polymer coatings, such as poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) (PAZAM), in the formation and manipulation of substrates, such as molecular arrays and flow cells. The present disclosure also relates to methods of preparing a substrate surface by using beads coated with a covalently attached polymer, such as PAZAM, and the method of determining a nucleotide sequence of a polynucleotide attached to a substrate surface described herein.

Claims

1. A method of preparing an array of polynucleotides, said method comprising:

providing a substrate comprising a polymer coating present on a surface of the substrate, the polymer coating comprising a recurring unit of Formula (Ia) and a recurring unit of Formula (II);

2. The method of claim 1, further comprising contacting the plurality of first oligonucleotides attached to the polymer coating with templates to be amplified, each template comprising at the 3′

end a sequence capable of hybridizing to the first oligonucleotides and at the 5′

end a sequence the complement of which is capable of hybridizing to the second oligonucleotides.

3. The method of claim 2, further comprising amplifying the templates using the first oligonucleotides and the second oligonucleotides, thereby generating a clustered array of polynucleotides.

4. The method of claim 1, wherein R^A is azido.

5. The method of claim 4, wherein R¹ is H or alkyl.

6. The method of claim 5, wherein R¹ is hydrogen and wherein o is 5.

7. The method of claim 1, wherein the polymer coating comprises a polymer of Formula (III) or (III′

);

8. The method of claim 7, wherein the polymer of Formula (III) or (III′

) is also represented by Formula (IIIa) or (IIIb);

9. The method of claim 1, wherein the first oligonucleotides or the second oligonucleotides comprise one or more functional groups selected from the group consisting of:

alkyne, amine, and aldehyde.

10. A method of preparing an array of polynucleotides, said method comprising:

providing a substrate having a polymer coating present on a surface of the substrate, the polymer coating comprising a recurring unit of Formula (Ia) and a recurring unit of Formula (II);

11. The method of claim 10, further comprising contacting the plurality of first oligonucleotides attached to the polymer coating with templates to be amplified, each template comprising at the 3′

end a sequence capable of hybridizing to the first oligonucleotides.

12. The method of claim 11, further comprising amplifying the templates using the first oligonucleotides, thereby generating an array of polynucleotides.

13. The method of claim 10, wherein R^A is azido.

14. The method of claim 13, wherein R¹ is H or alkyl.

15. The method of claim 14, wherein R¹ is hydrogen and wherein o is 5.

16. The method of claim 10, wherein the polymer coating comprises a polymer of Formula (III) or (III′

) ;

17. The method of claim 16, wherein the polymer of Formula (III) or (III′

) is also represented by Formula (IIIa) or (IIIb);

18. The method of claim 12, further comprising reacting a plurality of the second oligonucleotides with reactive sites of the polymer coating, thereby producing a plurality of second oligonucleotides attached to the polymer coating.

19. The method of claim 11, wherein each template further comprises, at the 5′

end, a sequence the complement of which is capable of hybridizing to a plurality of second oligonucleotides and wherein the amplifying comprises amplifying the templates using the first oligonucleotides and the second oligonucleotides, thereby generating an array of polynucleotides.

20. The method of claim 18, wherein the first oligonucleotides or the second oligonucleotides comprise aldehyde or alkyne groups.

21. A flow cell comprising a substrate, said substrate having a surface comprising a polymer coating covalently attached thereto, wherein the polymer coating comprises a recurring unit of Formula (Ia) and a recurring unit of Formula (II):

22. The flow cell of claim 21, wherein R^A is azido.

23. The flow cell of claim 22, wherein R¹ is H or alkyl.

24. The flow cell of claim 23, wherein R¹ is hydrogen and wherein o is 5.

25. The flow cell of claim 21, wherein the polymer coating comprises a polymer of Formula (III) or (III′

);

26. The flow cell of claim 25, wherein the polymer of Formula (III) or (III′

) is also represented by Formula (IIIa) or (IIIb);

27. The flow cell of claim 21, further comprising polynucleotides attached to the surface of the substrate via the polymer coating.

28. The flow cell of claim 27, wherein the polynucleotides are present in polynucleotide clusters.

29. The flow cell of claim 28, wherein polynucleotides within a single polynucleotide cluster have the same nucleotide sequence.

30. The flow cell of claim 28, wherein polynucleotides of different polynucleotide clusters have different nucleotide sequences.

31. A method of determining a nucleotide sequence of a polynucleotide, said method comprising the steps of:

(a) contacting a polynucleotide polymerase with polynucleotide clusters attached to a surface of a substrate via a polymer coating present on the surface of the substrate;

wherein the polymer coating comprises a recurring unit of Formula (Ia) and a recurring unit of Formula (II);

32. The method of claim 31, wherein R^A is azido.

33. The method of claim 32, wherein R^l is H or alkyl.

34. The method of claim 33, wherein R^l is hydrogen and wherein o is 5.

35. The method of claim 31, wherein the polymer coating comprises a polymer of Formula (III) or (III′

);

36. The method of claim 35, wherein the polymer of Formula (III) or (III′

) is also represented by Formula (IIIa) or (IIIb);

37. The method of claim 31, wherein the surface of the substrate is present within a flow cell.

38. The method of claim 31, wherein the detectable signal comprises an optical signal.

39. The method of claim 31, wherein the detectable signal comprises a non-optical signal.

40. The method of claim 39, wherein the non-optical signal is a change in pH.