Gel patterned surfaces

• US 9,512,422 B2
• Filed: 03/06/2013
• Issued: 12/06/2016
• Est. Priority Date: 02/26/2013
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Barnard, Steven M., Bowen, M. Shane, Rogert Bacigalupo, Maria Candelaria, George, Wayne N., Brown, Andrew A., Tsay, James
• Primary Examiner(s): Riggs, Larry
• Assistant Examiner(s): DINES, KARLA A
• Application Number:
  US13/787,396
• Publication Number:
  US 20140243224A1
• Time in Patent Office: 1,371 Days
• Field of Search: 506/9
• US Class Current: 1/1
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2563/159 Microreactors, e.g. emulsion PCR or sequencing, droplet PCR, microcapsules, i.e. non-liquid containers with a range of different permeability's for different reaction components

Abstract

Provided is an array including a solid support having a surface, the surface having a plurality of wells, the wells containing a gel material, the wells being separated from each other by interstitial regions on the surface, the interstitial regions segregating the gel material in each of the wells from the gel material in other wells of the plurality; and a library of target nucleic acids in the gel material, wherein the gel material in each of the wells comprises a single species of the target nucleic acids of the library. Methods for making and using the array are also provided.

Claims

1. An array, comprising

a solid support comprising a surface, the surface comprising a plurality of wells, the wells containing a gel material, the wells being separated from each other by interstitial regions on the surface, the interstitial regions segregating the gel material in each of the wells from the gel material in other wells of the plurality, wherein the volume of each of the wells is at most 1×

10⁴ μ

m³; and

a library of target nucleic acids in the gel material, wherein the gel material in each of the wells comprises a different species of the target nucleic acids of the library compared to species of the target nucleic acids in other wells of the solid support, and wherein the gel material comprises poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide).

2. The array of claim 1,

wherein the plurality of wells is in a flow cell that contains a solution and wherein the library of target nucleic acids that is in the plurality of wells has simultaneous fluidic access to the solution.

3. The array of claim 1, wherein the plurality of wells form an array having a repeating pattern.

4. The array of claim 3, wherein the wells in the pattern have a pitch of no more than 5 micrometers.

5. The array of claim 1, wherein the wells comprise a non-silanized surface.

6. The array of claim 1, wherein the gel material in each of the wells comprises multiple copies of a single species of target nucleic acid of the library.

7. The array of claim 6, wherein the multiple copies of the single species form a clonal population of nucleic acid molecules.

8. The array of claim 6, wherein the multiple copies of the single species are present as concatameric repeats in a nucleic acid molecule.

9. The array of claim 1, wherein the surface comprises a density of at least 1,000 of the wells per mm².

10. The array of claim 1, wherein the gel material is covalently attached to the surface of the wells.

11. The array of claim 1, wherein each of the wells comprises an opening in the surface that is at most 100 μ

m².

12. The array of claim 1, wherein a single species of a target nucleic acid of the library is present in each of the wells as no more than a single nucleic acid molecule.

13. The array of claim 12, wherein the single nucleic acid molecule comprises two complementary strands.

14. The array of claim 1, wherein the gel is non-covalently retained in the wells.

15. The array of claim 1, wherein the target nucleic acids are not attached to beads in the wells.

16. The array of claim 1, further comprising a concave feature that contains several different species of the target nucleic acids of the library.

17. The array of claim 16, wherein the concave feature comprises a fiducial.

18. The array of claim 16, wherein the concave feature is a well.

19. The array of claim 1, wherein the gel material in each of the wells fills part of the volume of the well where it resides.

20. A method of detecting nucleic acids, comprising

(a) providing the array of claim 2;

(b) contacting the solid support with at least one probe that binds to the target nucleic acids; and

(c) detecting the solid support to distinguish the wells having a target nucleic acid species that binds to the at least one probe.

21. The method of claim 20, wherein the at least one probe comprises at least one nucleic acid that is complementary to at least a portion of at least one of the target nucleic acids.

22. The method of claim 21, wherein the at least one probe further comprises a polymerase and a nucleotide.

23. The method of claim 20, wherein steps (b) and (c) are repeated several times in a sequencing procedure.

24. The method of claim 20, wherein the probe comprises a nucleic acid binding protein.

25. A method of detecting analytes, comprising

(a) providing the array of claim 2;

(b) contacting the solid support with probes under conditions wherein the target analytes interact specifically with the probes; and

(c) detecting the solid support to distinguish at least a subset of the target analytes that interact with one or more of the probes.