Methods of localizing nucleic acids to arrays

• US 8,969,258 B2
• Filed: 10/14/2013
• Issued: 03/03/2015
• Est. Priority Date: 01/07/2004
• Status: Active Grant

• Current Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Inventors: Smith, Mark Edward Brennan, Sabot, Andrea, Rasolonjatovo, Isabelle Marie Julia, Sohna Sohna, Jean-Ernest, Horgan, Adrian Martin, Swerdlow, Harold Philip
• Primary Examiner(s): Skowronek, Karlheinz R
• Assistant Examiner(s): GARYU, LIANKO G
• Application Number:
  US14/053,333
• Publication Number:
  US 20140100140A1
• Time in Patent Office: 505 Days
• US Class Current: 506/32
• 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

Methods are disclosed relating to localizing nucleic acids to arrays such as silane-free arrays, and of sequencing the nucleic acids localized thereby.

Claims

1. A method of localizing a nucleic acid molecule to a solid support comprising:

providing a solid support comprising;

a surface;

a first plurality of nucleic acids immobilized on the surface, wherein the nucleic acids in the first plurality each comprises the sequence 5′

-CAAGCAGAAGACGGCATACGA-3′

(SEQ ID NO;

     3); and

a second plurality of nucleic acids immobilized on the surface, wherein the nucleic acids in the second plurality each comprises the sequence 5′

-AATGATACGGCGACCACCGA-3′

(SEQ ID NO;

     4);

providing a nucleic acid molecule comprising a sequence that hybridizes to SEQ ID NO;

3; and

hybridizing the nucleic acid molecule to at least one of the first plurality of nucleic acids immobilized on the surface, thereby localizing the nucleic acid molecule to the solid support.

2. The method of claim 1, further comprising contacting the nucleic acid molecule hybridized to at least one of the first plurality of nucleic acids immobilized on the surface with reagents necessary to synthesize a complement of at least part of the nucleic acid molecule, wherein the complement to at least part of the nucleic acid molecule is covalently bound to the 3′

end of at least one of the nucleic acids immobilized on the surface.

3. The method of claim 2, further comprising separating said nucleic acid molecule from said solid support.

4. The method of claim 2, further comprising hybridizing said complement of at least part of the nucleic acid molecule to at least one of the second plurality of nucleic acids immobilized on the surface.

5. The method of claim 4, further comprising determining the sequence of the nucleic acid molecule.

6. A method of localizing a nucleic acid molecule to a solid support comprising:

providing a solid support comprising;

a surface;

a first plurality of nucleic acids immobilized on the surface, wherein the nucleic acids in the first plurality each comprises the sequence 5′

-CAAGCAGAAGACGGCATACGA-3′

(SEQ ID NO;

     3); and

a second plurality of nucleic acids immobilized on the surface, wherein the nucleic acids in the second plurality each comprises the sequence 5′

-AATGATACGGCGACCACCGA-3′

(SEQ ID NO;

     4);

providing a nucleic acid molecule comprising a sequence that hybridizes to SEQ ID NO;

4; and

hybridizing the nucleic acid molecule to at least one of the second plurality of nucleic acids immobilized on the surface, thereby localizing the nucleic acid molecule to the solid support.

7. The method of claim 6, further comprising contacting the nucleic acid molecule hybridized to at least one of the second plurality of nucleic acids immobilized on the surface with reagents necessary to synthesize a complement of at least part of the nucleic acid molecule, wherein the complement to at least part of the nucleic acid molecule is covalently bound to the 3′

end of at least one of the nucleic acids immobilized on the surface.

8. The method of claim 7, further comprising separating said nucleic acid molecule from said solid support.

9. The method of claim 7, further comprising hybridizing said complement of at least part of the nucleic acid molecule to at least one of the first plurality of nucleic acids immobilized on the surface.

10. The method of claim 9, further comprising determining the sequence of the nucleic acid molecule.

11. The method of claim 6, wherein the surface comprises a hydrogel.

12. The method of claim 11, wherein the thickness of the hydrogel is less than 100 nm.

13. The method of claim 11, 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 a functionalized comonomer selected from the group consisting of acrylamide, acrylate, methacrylate and methacrylamide.

14. The method of claim 11, wherein the hydrogel is the product of polymerizing acrylamide with N-(5-bromoacetamidylpentyl) acrylamide.

15. The method of claim 6, wherein the first plurality of nucleic acids are immobilized on the surface via a linkage at their 5′

ends.

16. The method of claim 6, wherein the second plurality of nucleic acids are immobilized on the surface via a linkage at their 5′

ends.

17. The method of claim 6, wherein the first plurality of nucleic acids are immobilized on the surface via a linkage at their 5′

ends, and wherein the second plurality of nucleic acids are immobilized on the surface via a linkage at their 5′

ends.