Method of making an array of nucleic acid colonies
A method of making an array of nucleic acid colonies, by (a) providing a substrate having a patterned surface of features, wherein the features are spatially separated from each other on the surface of the substrate; (b) contacting the substrate with a solution of different target nucleic acids to seed a subset of the features that contact the solution, wherein each feature in the subset is seeded with a single nucleic acid from the solution, wherein a plurality of the features that contact the solution are not seeded with a nucleic acid from the solution; (c) amplifying the nucleic acids to form a nucleic acid colony at each of the features in the subset; and (d) repeating steps (b) and (c) to increase the number of the features on the surface that have a nucleic acid colony, thereby making an array of nucleic acid colonies.
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 separated from each other on the surface of the substrate;
(b) contacting the substrate with a solution of different target nucleic acids to seed a subset of the features that contact the solution, wherein each feature in the subset is seeded with a single nucleic acid from the solution, wherein a plurality of the features that contact the solution are not seeded with a nucleic acid from the solution;
(c) amplifying the nucleic acids to form a nucleic acid colony at each of the features in the subset; and
(d) repeating steps (b) and (c) to increase the number of the features on the surface that comprise a nucleic acid colony, 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 patterned surface comprises a repeated pattern of the features.
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/cm 2 .