Nucleic acid arrays of spatially discrete features on a surface

• US 10,287,577 B2
• Filed: 06/12/2017
• Issued: 05/14/2019
• Est. Priority Date: 07/02/2008
• Status: Active Grant

• Current Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Original Assignee: Illumina Cambridge Ltd. (California) (Illumina Incorporated)
• Inventors: Rigatti, Roberto, Smith, Geoffrey Paul, Boutell, Jonathan Mark
• Primary Examiner(s): Horlick, Kenneth R
• Application Number:
  US15/620,668
• Publication Number:
  US 20170342406A1
• Time in Patent Office: 701 Days
• Field of Search: None
• 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. A composition comprising

(a) an array of beads positioned in spatially discrete features on a surface, wherein the beads are attached to template nucleic acids, wherein each discrete feature comprises the surface attached to two or more oligonucleotide primers each having a different sequence, wherein the beads are immobilized on the surface via hybridization of the template nucleic acids to the two or more of the oligonucleotide primers, wherein each spatially discrete feature is separated from another feature by a space that does not carry oligonucleotide primers, and wherein an average center-to-center distance between the spatially discrete features is less than two times the diameter of a feature;

and

(b) a nucleic acid polymerase that is bound to hybrids formed between the template nucleic acids and the oligonucleotide primers.

2. The composition of claim 1, wherein the average center-to-center distance between the spatially discrete features is equivalent to the diameter of the beads.

3. The composition of claim 1, wherein the average center-to-center distance between the spatially discrete features is less than 100 μ

m.

4. The composition of claim 1, wherein the surface is flat or planar.

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

6. The composition of claim 1, wherein the surface comprises wells.

7. The composition of claim 1, wherein the surface comprises a hydrogel.

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

9. The composition of claim 1, wherein the spatially discrete features are of similar size to each other.

10. The composition of claim 1, wherein at least one or more of the oligonucleotide primers comprise the sequence set forth in one or more of SEQ ID NOs:

1-4.

11. The composition of claim 1, wherein at least one or more of the oligonucleotide primers comprise the sequence set forth in SEQ ID NO:

1.

12. The composition of claim 1, wherein at least one or more of the oligonucleotide primers comprise the sequence set forth in SEQ ID NO:

2.

13. The composition of claim 1, wherein at least one or more of the oligonucleotide primers comprise the sequence set forth in SEQ ID NO:

3.

14. The composition of claim 1, wherein at least one or more of the oligonucleotide primers comprise the sequence set forth in SEQ ID NO:

4.