Using populations of beads for the fabrication of arrays on surfaces

• US 8,399,192 B2
• Filed: 02/03/2012
• Issued: 03/19/2013
• 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:
  US13/365,562
• Publication Number:
  US 20120172259A1
• Time in Patent Office: 410 Days
• Field of Search: 435/6.1, 435/7, 435/6.12, 435/91.2
• US Class Current: 435/6.1
• 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 a method of creating an array of features. The method can include steps of (a) providing a plurality of beads, wherein each bead in the plurality of beads includes probe content; (b) contacting the plurality of beads with a surface to produce a layer of beads on the surface; and (c) transferring the probe content from the beads to the surface to create an array of spatially discrete features on the surface, wherein each spatially discrete feature includes probe content from a bead in the plurality of beads.

Claims

1. A method of creating an array of features, comprising

(a) providing a plurality of beads, wherein each bead in the plurality of beads comprises nucleic acid content;

(b) contacting the plurality of beads with a surface to produce a layer of beads on the surface;

(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; and

(d) performing an amplification reaction using the nucleic acid content at each of the discrete features on the surface, thereby producing a homogenous population of nucleic acids at each feature.

2. The method of claim 1, wherein the transferring comprises physically transferring nucleic acids from the beads to each of the spatially discrete features on the surface.

3. The method of claim 1, wherein the transferring comprises covalently attaching nucleic acids from the beads to each of the spatially discrete features on the surface.

4. The method of claim 1, wherein the transferring comprises non-covalently attaching nucleic acids from the beads to each of the spatially discrete features on the surface.

5. The method of claim 1, wherein a single nucleic acid molecule is transferred from each of the beads to each of the spatially discrete features.

6. The method of claim 1, wherein several copies of a single nucleic acid species are transferred from each of the beads to each of the spatially discrete features.

7. The method of claim 1, wherein the transferring 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.

8. The method of claim 1, wherein the transferring 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.

9. The method of claim 1, wherein the nucleic acids that are transferred from the beads to the surface are single stranded.

10. The method of claim 1, wherein the nucleic acids that are transferred from the beads to the surface are double stranded.

11. The method of claim 1, wherein the array of spatially discrete features comprises an average center-to-center spacing that is equivalent to the diameter of the beads.

12. The method of claim 1, wherein the array of spatially discrete features comprises an average center-to-center spacing that is less than 100 μ

m.

13. The method of claim 1, wherein the surface is flat or planar.

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

15. The method of claim 1, further comprising removing the beads from the surface after the transferring of the nucleic acid content from the beads to the surface.

16. The method of claim 15, further comprising obtaining an image of the surface after removing the beads from the surface.

17. The method of claim 1, wherein the nucleic acid content comprises nucleic acid primers that are transferred from the beads to the surface and used as primers in the amplification reaction.

18. The method of claim 17, wherein different beads in the plurality of beads comprise primers having the same sequence.

19. The method of claim 17, wherein different beads in the plurality of beads comprise primers having different sequences.

20. The method of claim 17, wherein each of the beads in the plurality of beads comprises two amplification primers each having a different sequence.

21. The method of claim 1, wherein the nucleic acid content comprises nucleic acid templates that are transferred from the beads to the surface and used as templates that are copied in the amplification reaction.

22. The method of claim 1, wherein nucleic acid content on each bead comprise a nucleic acid molecule having (i) a universal sequence that is the same as the universal sequence on other beads in the plurality of beads and (ii) a region of sequence that is different from a region of sequence on the other beads in the plurality of beads.

23. The method of claim 1, wherein the amplification reaction is performed using a universal primer that is complementary to a universal sequence that is the same as the universal sequence on other beads in the plurality of beads.

24. The method of claim 1, wherein the amplification reaction uses primers attached to the surface.

25. The method of claim 1, further comprising sequencing nucleic acids in the homogenous population of nucleic acids at each feature.

26. The method of claim 1, further comprising hybridizing nucleic acid probes to nucleic acids in the homogenous population of nucleic acids at each feature.

27. The method of claim 26, further comprising detecting a label at features on the surface, wherein the label is attached to the probes or attached to the nucleic acids in the homogeneous population of nucleic acids.