Methods and compositions of localizing nucleic acids to arrays

• US 10,525,437 B2
• Filed: 01/08/2018
• Issued: 01/07/2020
• 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:
  US15/864,384
• Publication Number:
  US 20180207606A1
• Time in Patent Office: 729 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 template nucleic acids, wherein each template nucleic acid comprises a first end capable of hybridizing to SEQ ID NO:

03, and a second end, wherein the template nucleic acids are different from each other and comprise genomic DNA.

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

11.

3. The population of claim 1, wherein the second end is capable of hybridizing to SEQ ID NO:

05.

4. The population of claim 1, wherein the second end comprises SEQ ID NO:

4.

5. The population of claim 1, wherein a remainder polynucleotide is disposed between the first end and the second end.

6. The population of claim 1, wherein the template nucleic acids have a length greater than 300 nucleotides.

7. The population claim 1, wherein the first end is capable of hybridizing at 5×

SSC and 40°

C.

16. A method of amplifying a population of template nucleic acids comprising:

hybridizing the population of template nucleic acids of claim 1 to a plurality of first oligonucleotides via the first ends of the template nucleic acids, wherein the plurality of first oligonucleotides are immobilized on a substrate;

extending the first oligonucleotides;

hybridizing the extended first oligonucleotides to a plurality of second oligonucleotides immobilized on the substrate; and

extending the hybridized second oligonucleotides.

17. The method of claim 16, wherein the plurality of first oligonucleotides comprise SEQ ID NO:

03.

18. The method of claim 16, wherein the second ends of the template nucleic acids are capable of hybridizing to SEQ ID NO:

05.

19. The method of claim 18, wherein the second ends comprise SEQ ID NO:

4.

20. The method of claim 16, wherein the plurality of second oligonucleotides comprise SEQ ID NO:

04.

21. The method of claim 16, further comprising removing the population of template nucleic acids from the extended first oligonucleotides.

22. The method of claim 16, further comprising sequencing the extended first oligonucleotides or the extended second oligonucleotides.

8. A composition comprising:

a population of template nucleic acids that are different from one another, and wherein each template nucleic acid comprises a first end capable of hybridizing to SEQ ID NO;

03 and a second end, wherein the population of template nucleic acids is hybridized to a plurality of first oligonucleotides via the first ends of the template nucleic acids, wherein the first oligonucleotides are immobilized on a substrate.

9. The composition of claim 8, wherein the first oligonucleotides comprise SEQ ID NO:

03.

10. The composition of claim 8, wherein the second ends of the template nucleic acids are capable of hybridizing to SEQ ID NO:

05.

11. The composition of claim 10, wherein the second ends of the template nucleic acids comprise SEQ ID NO:

4.

12. The composition of claim 8, further comprising a plurality of second oligonucleotides immobilized on a substrate.

13. The composition of claim 12, wherein the plurality of second oligonucleotides comprise SEQ ID NO:

04.

14. The composition of claim 8, wherein the immobilized first oligonucleotides each comprise a polyT spacer comprising from 2 to 10 thymine nucleotides, wherein the polyT spacer is at the 5′

end of the immobilized first oligonucleotides.

15. The composition of claim 8, wherein the plurality of first oligonucleotides is covalently attached to a hydrogel on the substrate.