Using populations of beads for the fabrication of arrays on surfaces

• US 9,079,148 B2
• Filed: 03/11/2014
• Issued: 07/14/2015
• Est. Priority Date: 07/02/2008
• Status: Active Grant

• Current Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Inventors: Rigatti, Roberto, Smith, Geoffrey Paul, Boutell, Jonathan Mark
• Primary Examiner(s): HORLICK, KENNETH R
• Application Number:
  US14/204,329
• Publication Number:
  US 20140296109A1
• Time in Patent Office: 490 Days
• Field of Search: 435/91.1, 435/91.2, 536/24.33
• 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 2219/00608 DNA chips
• 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 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads
• CPC Class Codes: C12Q 2563/161 Vesicles, e.g. liposome
• CPC Class Codes: C12Q 2565/537 characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C12Q 2565/543 characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification

Abstract

The present invention provides methods for creating an array of features on a surface based on content transferred from a plurality of beads to the surface. Nucleic acid content can be transferred using a method including the steps of (a) providing a surface having one or more primer oligonucleotides attached to the surface; (b) providing a pool of beads, wherein beads in the pool have a plurality of templates attached thereto, the plurality comprising multiple copies of a single nucleic acid template sequence; (c) arraying the beads onto the surface by hybridizing the templates to the primer oligonucleotides; and (d) extending the primers to produce copies of the templates attached to the surface.

Claims

1. An array comprising spatially discrete nucleic acid features on a surface, wherein each spatially discrete feature comprises two or more different amplification primers each having a different sequence attached to the surface, and wherein each spatially discrete feature is separated from any other discrete feature by a space which does not carry amplification primers, wherein the array of spatially discrete features comprises an average center-to-center distance that is less than two times the diameter of a feature.

2. The array of claim 1, wherein the surface is flat or planar.

3. The array of claim 1, wherein the surface comprises wells, depressions, pillars, ridges or channels.

4. The array of claim 1, wherein the surface comprises a hydrogel.

5. The array of claim 1, wherein the array further comprises amplified nucleic acids.

6. The array of claim 1, wherein the spatially discrete nucleic acid features on the surface are of similar size to each other.

7. The array of claim 1, wherein the array is fabricated by a method comprising:

(a) providing a plurality of beads, wherein each bead in the plurality of beads comprises nucleic acid content comprising two or more different amplification primers each having a different sequence;

(b) contacting the plurality of beads with a surface to produce a layer of beads on the surface, wherein the layer of beads comprises an average center-to-center distance that is less than two times the diameter of a bead;

(c) transferring the nucleic acid content from the beads to the surface to create an array of spatially discrete features on the surface, wherein each spatially discrete feature comprises nucleic acid content from a bead in the plurality of beads, the nucleic acid content comprising amplification primers and wherein each spatially discrete feature on the array is separated from any other discrete feature by a space which does not carry amplification primers;

(d) removing the plurality of beads from the surface.

8. The array of claim 7, wherein the array of spatially discrete features comprises an average center-to-center spacing that is equivalent to the diameter of the beads.

19. The array of claim 1, wherein at least one or more of the amplification primers comprise the sequence set forth in one or more of SEQ ID NOs:

1-4.

9. A method of creating an array comprising spatially discrete nucleic acid features on a surface, wherein each spatially discrete feature comprises two or more different amplification primers each having a different sequence attached to the surface, and wherein each spatially discrete is separated from any other discrete feature by a space which does not carry amplification primers, the method comprising:

(a) providing a plurality of beads, wherein each bead in the plurality of beads comprises nucleic acid content comprising two or more different amplification primers each having a different sequence;

(b) contacting the plurality of beads with a surface to produce a layer of beads on the surface, wherein the layer of beads comprises an average center-to-center distance that is less than two times the diameter of a bead;

(c) transferring the nucleic acid content from the beads to the surface to create an array of spatially discrete features on the surface, wherein each spatially discrete feature comprises nucleic acid content from a bead in the plurality of beads, the nucleic acid content comprising amplification primers and wherein each spatially discrete feature on the array is separated from any other discrete feature by a space which does not carry amplification primers;

(d) removing the plurality of beads from the surface.

10. The method of claim 9, wherein the transferring of the nucleic acid content comprises physically transferring nucleic acids from each of the beads to attach the nucleic acids to a feature on the surface.

11. The method of claim 9, wherein the transferring comprises covalently attaching the nucleic acid content from the beads to each of the spatially discrete features on the surface.

12. The method of claim 9, wherein the transferring comprises non-covalently attaching the nucleic acid content from the beads to each of the spatially discrete features on the surface.

13. The method of claim 9, wherein the transferring of the nucleic acids comprises replicating a nucleic acid from each of the beads to form a copy of the nucleic acid at each of the spatially discrete features.

14. The method of claim 9, wherein the transferring of the nucleic acids comprises physically transferring a nucleic acid molecule from each of the beads to attach the nucleic acid molecule to each of the spatially discrete features.

15. The method of claim 9, wherein the nucleic acids that are transferred from the beads to the surface are single stranded.

16. The method of claim 9, wherein the array of spatially discrete features comprises an average center-to-center spacing that is equivalent to the diameter of the beads.

17. The method of claim 9, wherein the surface is flat or planar.

18. The method of claim 9, wherein the surface comprises wells, depressions, pillars, ridges or channels.

20. The method of claim 9, wherein at least one or more of the amplification primers comprise the sequence set forth in one or more of SEQ ID NOs:

1-4.