Method of making an array of nucleic acid colonies

• US 8,709,729 B2
• Filed: 05/29/2013
• Issued: 04/29/2014
• Est. Priority Date: 12/23/2008
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Ronaghi, Mostafa, Eltoukhy, Helmy
• Primary Examiner(s): HORLICK, KENNETH R
• Application Number:
  US13/905,003
• Publication Number:
  US 20130338008A1
• Time in Patent Office: 335 Days
• Field of Search: 435/6.12, 435/91.2
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2565/543 characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification

Abstract

A method of making an array of nucleic acid colonies, including the steps of (a) providing a substrate having a patterned surface of features, wherein the features are spatially organized in a repeating pattern on the surface of the substrate; (b) contacting the substrate with a solution of different target nucleic acids to seed no more than a subset of the features that contact the solution; (c) amplifying the nucleic acids on the subset of features; and (d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of nucleic acid colonies.

Claims

1. A method of making an array of nucleic acid colonies, comprising

(a) providing a substrate comprising a patterned surface of features, wherein the features are spatially organized in a repeating pattern on the surface of the substrate;

(b) contacting the substrate with a solution of different target nucleic acids to seed no more than a subset of the features that contact the solution;

(c) amplifying the nucleic acids on the subset of features; and

(d) repeating steps (b) and (c) to increase the number of features that are seeded with a nucleic acid, thereby making an array of nucleic acid colonies.

2. The method of claim 1, further comprising detecting the array of nucleic acid colonies in a sequencing reaction.

3. The method of claim 2, wherein a subset of the colonies in the array comprise a first type of target nucleic acid and a second type of target nucleic acid.

4. The method of claim 3, wherein the amount of the second type of target nucleic acid does not adversely affect the signal-to-noise for the detecting of the first type of nucleic acid.

5. The method of claim 2, wherein the detecting comprises detecting a byproduct of incorporating a nucleotide into a nucleic acid.

6. The method of claim 5, wherein the byproduct is pyrophosphate.

7. The method of claim 2, wherein the sequencing reaction comprises extension of a nascent nucleic acid strand through iterative addition of nucleotides against templates in the nucleic acid colonies.

8. The method of claim 7, wherein the nucleotides comprise fluorescent labels that are detected in the sequencing reaction.

9. The method of claim 1, wherein the features comprise wells.

10. The method of claim 1, wherein the features comprise attached primer nucleic acids for the amplifying.

11. The method of claim 10, wherein each of the features comprises a pair of attached primer nucleic acids.

12. The method of claim 11, wherein the amplifying comprises bridge amplification.

13. The method of claim 10, wherein the amplifying comprises polymerase chain reaction amplification.

14. The method of claim 10, wherein the nucleic acid colonies are covalently attached to the features.

15. The method of claim 1, wherein the features comprise reactive pads on the surface.

16. The method of claim 1, wherein the features are spatially separated from each other on the surface of the substrate.

17. The method of claim 1, wherein the same solution of different target nucleic acids is contacted with the substrate in steps (b) and (d).

18. The method of claim 1, wherein the substrate comprises a CMOS detector.

19. The method of claim 1, wherein the substrate comprises a density of at least 1,000 features/cm².

20. The method of claim 1, wherein each feature in the subset is seeded with no more than a single nucleic acid from the solution during step (b).