Gel patterned surfaces

• US 10,668,444 B2
• Filed: 11/22/2016
• Issued: 06/02/2020
• 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): Dines, Karla A
• Application Number:
  US15/358,846
• Publication Number:
  US 20170136434A1
• Time in Patent Office: 1,288 Days
• Field of Search: 506 9
• 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. A method comprising:

coating at least a portion of a support with a gel material, the support comprising a planar surface interrupted by a plurality of concave features bordered by one or more interstitial regions on the planar surface, wherein the portion comprises at least some of the concave features and at least some of the interstitial regions; and

polishing the gel material from the at least some of the interstitial regions while maintaining the gel material in the at least some of the concave features, including on bottom surfaces of the at least some of the concave features;

wherein the gel material comprises poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide) that non-covalently associates with the at least some of the concave features.

2. The method of claim 1 wherein

the support comprises glass, silicon, a plastic material, or a combination thereof.

3. The method of claim 1, wherein coating comprises contacting the support with a preformed gel material.

4. The method of claim 1, wherein coating comprises contacting the support with a liquid that subsequently forms the gel material.

5. The method of claim 1, wherein the concave features comprise a non-silanized surface.

6. The method of claim 1, wherein the gel material is further attached to nucleic acids.

7. The method of claim 6, wherein the nucleic acids comprise amplification primers.

8. The method of claim 6, wherein the nucleic acids comprise template nucleic acids and the method further comprises amplifying the template nucleic acids attached to the gel material in the concave features.

9. The method of claim 1, wherein polishing comprises mechanical abrasion with a slurry of beads.

10. The method of claim 1, wherein polishing comprises mechanical abrasion by wiping or scraping the surface of the support.

11. The method of claim 1, wherein polishing comprises chemical polishing.

12. The method of claim 1, wherein each of the concave features comprises an opening in the surface that is at most 100 μ

m².

13. The method of claim 1, wherein the concave features are spaced from one another with an average pitch of at most 10 μ

m.

14. The method of claim 13, wherein the concave features are spaced from one another with an average pitch of at most 1 μ

m.

15. The method of claim 1, wherein the concave features have a density of at least 2 million per mm².

16. The method of claim 1, wherein:

the support includes at least one fiducial marker having an alternating pattern of concave rings and interstitial rings;

the gel material is coated on the concave rings and the interstitial rings during coating; and

the gel material is removed from the interstitial rings during polishing.

17. The method of claim 1, wherein:

the support includes at least one fiducial marker;

the fiducial marker is a well that is larger than each of the plurality of concave features; and

the method further comprising introducing a fluorophore labeled bead into the well.

18. The method of claim 1, further comprising delivering a library of target nucleic acids to the support, whereby a different species of the target nucleic acids attaches to the gel material in each of the at least some of the concave features.

19. A biological sample array made by the method of claim 1.