Methods of localizing nucleic acids to arrays

• US 9,889,422 B2
• Filed: 05/23/2016
• Issued: 02/13/2018
• 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): Garyu, Lianko G
• Application Number:
  US15/162,304
• Publication Number:
  US 20160256846A1
• Time in Patent Office: 631 Days
• Field of Search: None
• 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 and compositions are disclosed relating to the localization of nucleic acids to arrays such as silane-free arrays, and of sequencing the nucleic acids localized thereby.

Claims

1. A population of polynucleotides comprising template nucleic acids having a first end capable of hybridizing to SEQ ID NO:

3, a second end capable of hybridizing to SEQ ID NO;

5 and a remainder polynucleotide disposed between the first end and the second end, wherein the template nucleic acids are different from each other.

2. The population of claim 1, wherein the template nucleic acids comprise genomic DNA.

3. The population of claim 1, further comprising amplified template nucleic acids.

4. The population of claim 1, wherein the template nucleic acids comprise more than 300 base pairs of nucleotides.

5. The population of claim 1, wherein the first end comprises SEQ ID NO:

11, and the second end comprises SEQ ID NO;

4.

28. The population claim 1, wherein the first end and the second end are capable of hybridizing at 5×

SSC and 40°

C.

6. A composition comprising:

a solid support comprising a surface;

a plurality of immobilized nucleic acids bound to the surface, wherein the immobilized nucleic acids each comprise a primer sequence selected from SEQ ID NO;

3 and SEQ ID NO;

4; and

a population of template nucleic acids, wherein each template nucleic acid comprises a first end capable of hybridizing to SEQ ID NO;

3 and a second end capable of hybridizing to SEQ ID NO;

5, wherein at least one template nucleic acid is hybridized to an immobilized nucleic acid comprising SEQ ID NO;

3.

7. The composition of claim 6, wherein each first end of each template nucleic acid is hybridized to an immobilized nucleic acid comprising SEQ ID NO:

3.

8. The composition of claim 6, wherein the template nucleic acids are different from each other.

9. The composition of claim 6, wherein the template nucleic acids comprise genomic DNA.

10. The composition of claim 6, wherein the template nucleic acids comprise more than 300 base pairs of nucleotides.

11. The composition of claim 6, wherein the first end comprises SEQ ID NO:

11, and the second end comprises SEQ ID NO;

4.

12. The composition of claim 6, wherein the immobilized nucleic acids each comprise a polyT spacer 5′

of the primer sequence comprising from 2 to 10 thymine nucleotides.

13. The composition of claim 6, wherein the plurality of immobilized nucleic acids is covalently attached to a hydrogel on the surface.

14. The composition of claim 13, wherein the hydrogel is the product of polymerizing a first comonomer with a second comonomer.

15. The composition of claim 14, 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.

29. The composition of claim 6, wherein the first end and the second end are capable of hybridizing at 5×

SSC and 40°

C.

16. A method of localizing a population of template nucleic acids to a solid support comprising:

providing a solid support comprising;

a surface, and

a plurality of nucleic acids immobilized on the surface, wherein the nucleic acids in the plurality each comprise a primer sequence selected from SEQ ID NO;

3 and SEQ ID NO;

4; and

hybridizing a population of template nucleic acids having a first end capable of hybridizing to SEQ ID NO;

3 and a second end capable of hybridizing to SEQ ID NO;

5 to the plurality of nucleic acids comprising SEQ ID NO;

3 immobilized on the surface.

17. The method of claim 16, further comprising extending the nucleic acids immobilized on the surface and hybridized to a template nucleic acid.

18. The method of claim 17, further comprising determining the sequence of the extended nucleic acids.

19. The method of claim 16, further comprising amplifying the population of nucleic acids comprising template nucleic acids.

20. The method of claim 16, wherein the template nucleic acids are different from each other.

21. The method of claim 16, wherein the template nucleic acids comprise genomic DNA.

22. The method of claim 16, wherein the template nucleic acids comprise more than 300 base pairs of nucleotides.

23. The method of claim 16, wherein the first end comprises SEQ ID NO:

11, and the second end comprises SEQ ID NO;

4.

24. The method of claim 16, wherein the nucleic acids in the plurality each comprise a polyT spacer 5′

of the primer sequence comprising from 2 to 10 thymine nucleotides.

25. The method of claim 16, wherein the plurality of nucleic acids is covalently attached to a hydrogel immobilized on the surface.

26. The method of claim 25, wherein the hydrogel is the product of polymerizing a first comonomer with a second comonomer.

27. The method of claim 26, 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.

30. The method of claim 16, wherein the first end and the second end are capable of hybridization at 5×

SSC and 40°

C.