Modified molecular arrays

• US 8,563,477 B2
• Filed: 07/13/2012
• Issued: 10/22/2013
• Est. Priority Date: 01/07/2004
• Status: Active Grant

• Current Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Inventors: Smith, Mark Edward Brennan, Sabot, Andrea, Horgan, Adrian Martin, Swerdlow, Harold Philip, Rasalonjatovo, Isabelle Marie Julia, Sohna Sohna, Jean-Ernest
• Primary Examiner(s): Bradley, Christina
• Assistant Examiner(s): GARYU, LIANKO G
• Application Number:
  US13/548,558
• Publication Number:
  US 20130085084A1
• Time in Patent Office: 466 Days
• Field of Search: None
• US Class Current: 506/16
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00351 Means for dispensing and evacuation of reagents
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00639 the compounds being trapped in or bound to a porous medium
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00716 Heat activated synthesis
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C08F 222/38 Amides
• 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 1/6834 : Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6876 : Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/18 : using a particular method of attachment to the solid support
• CPC Class Codes: Y10T 428/265 : 1 mil or less

Abstract

A composition including (a) a solid support having a surface; (b) a first plurality of nucleic acids immobilized on the surface, wherein the nucleic acids in the first plurality each include the P7 primer sequence (5′-CAAGCAGAAGACGGCATACGA-3′; SEQ ID NO: 3); and (c) a second plurality of nucleic acids immobilized on the surface, wherein the nucleic acids in the second plurality each include the P5 primer sequence (5′-AATGATACGGCGACCACCGA-3′; SEQ ID NO: 4).

Claims

1. A composition comprising:

(a) a solid support comprising a surface;

(b) a first plurality of nucleic acids immobilized on the surface, wherein the nucleic acids in the first plurality each comprise the sequence 5′

-CAAGCAGAAGACGGCATACGA-3′

(SEQ ID NO;

     3); and

(c) a second plurality of nucleic acids immobilized on the surface, wherein the nucleic acids in the second plurality each comprise the sequence 5′

-AATGATACGGCGACCACCGA-3′

(SEQ ID NO;

     4).

2. The composition of claim 1, wherein the nucleic acids are covalently attached to a hydrogel that is immobilized on the surface.

3. The composition of claim 2, wherein the thickness of the hydrogel is less than 100 nm.

4. The composition of claim 2, wherein the 5′

ends of the nucleic acids are covalently attached to the hydrogel.

5. The composition of claim 2, wherein the hydrogel is the product of polymerizing a first comonomer with a second comonomer, wherein the first comonomer is selected from the group consisting of acrylamide, methacrylamide, hydroxyethyl methacrylate and N-vinyl pyrrolidinone, and wherein the second comonomer is selected from the group consisting of a functionalized acrylamide, acrylate, methacrylate and methacrylamide.

6. The composition of claim 2, wherein the hydrogel is the product of polymerizing acrylamide with N-(5-bromoacetamidylpentyl)acrylamide (BRAPA).

7. The composition of claim 1, wherein the nucleic acids are covalently attached to a polyelectrolyte multilayer that is immobilized on the surface.

8. The composition of claim 1, wherein the nucleic acids are covalently attached directly to the surface.

9. The composition of claim 1, wherein the nucleic acids in the first plurality each comprise the sequence 5′

-CAAGCAGAAGACGGCATACGA (SEQ ID NO;

     3)-template-TCGGTGGTCGCCGTATCATT-3′

(SEQ ID NO;

     5), wherein the template comprises a nucleotide sequence that is longer than 300 nucleotides.

10. The composition of claim 1, wherein the nucleic acids in the second plurality each comprise the sequence 5′

-AATGATCGGCGACCACCGA (SEQ ID NO;

     4)-template-TCGTATGCCGTCTTCTGCTTG (SEQ ID NO;

     11)-3′

, wherein the template comprises a nucleotide sequence that is longer than 300 nucleotides.

11. The composition of claim 1, wherein the nucleic acids in the first plurality each comprise the sequence 5′

-polyT-CAAGCAGAAGACGGCATACGA (SEQ ID NO;

     3)-3′

, wherein the polyT comprises from 2 to 10 thymine nucleotides.

12. The composition of claim 1, wherein the nucleic acids in the second plurality each comprise the sequence 5′

-polyT-AATGATACGGCGACCACCGA (SEQ ID NO;

     4)-3′

, wherein the polyT comprises from 2 to 10 thymine nucleotides.

13. The composition of claim 1, wherein the composition comprises an array of nucleic acid clusters, wherein each of the clusters comprises nucleic acids in the first plurality and nucleic acids in the second plurality.

14. The composition of claim 13, wherein each of the clusters comprises nucleic acids in the first plurality that are hybridized to nucleic acids in the second plurality.

15. The composition of claim 1, wherein the solid support comprises a silica-based substrate, plastic, gold, titanium dioxide or silicon.

16. The composition of claim 1, wherein the nucleic acids in the first plurality are hybridized to target nucleic acids comprising the sequence 5′

-TCGGTGGTCGCCGTATCATT-3′

(SEQ ID NO;

     5).

17. The composition of claim 1, wherein the nucleic acids in the second plurality are hybridized to target nucleic acids comprising the sequence 5′

-TCGTATGCCGTCTTCTGCTTG-3′

(SEQ ID NO;

     11).

18. The composition of claim 1, wherein the sequence 5′

-CAAGCAGAAGACGGCATACGA-3′

(SEQ ID NO;

     3) is at the 3′

end of the nucleic acids in the first plurality.

19. The composition of claim 1, wherein the sequence 5′

-AATGATACGGCGACCACCGA-3′

(SEQ ID NO;

     4) is at the 3′

end of the nucleic acids in the second plurality.

20. The composition of claim 1, wherein the nucleic acids in the first plurality further comprise a fluorescent label.

21. The composition of claim 20, wherein the nucleic acids in the first plurality further comprise a 3′

blocking group.

22. The composition of claim 1, wherein the nucleic acids in the second plurality further comprise a fluorescent label.

23. The composition of claim 22, wherein the nucleic acids in the second plurality further comprise a 3′

blocking group.

24. The composition of claim 1, wherein the surface comprises a polyacrylamide based polymer.

25. The composition of claim 1, wherein the surface does not comprise silane.

26. The composition of claim 1, wherein the surface comprises polymethylmethacrylate.

27. The composition of claim 1, wherein the surface comprises a polymer comprising N-(5-bromoacetamidyl pentyl)acrylamide (BRAPA).

28. The composition of claim 1, wherein the surface has a thickness of less than 50 nm.

29. The composition of claim 1, wherein the solid support comprises glass.

30. The composition of claim 1, wherein the solid support comprises a polyelectrolyte.

31. A method of determining the sequence of a polynucleic acid comprising the steps of contacting said polynucleic acid with the composition of claim 1 and thereafter determining the sequence of the polynucleic acid.