Cleavable oligonucleotide arrays

• US 7,291,471 B2
• Filed: 11/21/2005
• Issued: 11/06/2007
• Est. Priority Date: 11/21/2005
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Sampson, Jeffrey R., Myerson, Joel
• Primary Examiner(s): Whisenant; Ethan
• Application Number:
  US11/284,495
• Publication Number:
  US 20070117101A1
• Time in Patent Office: 715 Days
• Field of Search: 435/6, 435/287.2, 536/25.3
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2523/107 Chemical cleaving agents

Abstract

Oligonucleotide arrays having features that include cleavable oligonucleotides are disclosed, as well as methods of making such arrays. Methods of synthesizing an oligonucleotide on a surface of a substrate are described.

Claims

1. An oligonucleotide array comprising a substrate having a surface and a plurality of features on the substrate, each feature of the plurality of features comprising A) a first population of oligonucleotides bound via a cleavable linker moiety to the surface, and B) a second population of oligonucleotides bound to the surface other than through said cleavable linker moiety;

said first population of oligonucleotides defining an interior area of each feature;

said second population of oligonucleotides defining an edge area of each feature, the edge area substantially surrounding the interior area.

2. The oligonucleotide array of claim 1, wherein the first population of oligonucleotides has a lower percentage of failure sequences than the second population of oligonucleotides.

3. The oligonucleotide array of claim 1, wherein the second population of oligonucleotides has a percentage of failure sequences that is at least 120% of the percentage of failure sequences of the first population.

4. The oligonucleotide array of claim 1, wherein the plurality of features includes at least 50 features.

5. The oligonucleotide array of claim 1, wherein the plurality of features includes at least about 200 features.

6. The oligonucleotide array of claim 1, wherein, at a given feature, the interior area is at least about 70% of the area of the total defined area of the feature.

7. The oligonucleotide array of claim 1, wherein, at a given feature, the interior area is at least about 90% of the area of the total defined area of the feature.

8. The oligonucleotide array of claim 1, wherein the edge area of each feature completely surrounds the interior area of said each feature.

9. The oligonucleotide array of claim 1, wherein the cleavable linker moiety includes a cleavable moiety selected from a photocleavable moiety and a chemically cleavable moiety.

10. The oligonucleotide array of claim 1, wherein the cleavable linker moiety includes a chemically cleavable moiety selected from an acid-cleavable moiety, a base-cleavable moiety, and a nucleophile-cleavable moiety.

11. The oligonucleotide array of claim 1, wherein the cleavable linker moiety is bound to the surface via an oligonucleotide moiety.

12. A method of synthesizing an oligonucleotide on a surface of a substrate, the method comprising,

a) covalently binding a cleavable linker moiety to the surface, the cleavable linker moiety defining an interior area on the surface,

b) covalently binding a nucleotide moiety to the surface, the nucleotide moiety defining a combined area on the surface, wherein the combined area includes the interior area and an edge area substantially surrounding the interior area, wherein the nucleotide moiety in the interior area is bound to the surface via the cleavable linker moiety, wherein the nucleotide moiety in the edge area is bound to the surface other than via the cleavable linker moiety;

and

c) repeating b) as necessary to result in synthesis of the oligonucleotide on the surface.

13. The method of claim 12, wherein the interior area is at least 50% of the combined area.

14. The method of claim 12, wherein the interior area is at least 70% of the combined area.

15. The method of claim 12, wherein the method is performed at each site of a plurality of sites on the surface, wherein the method results in the synthesis of an oligonucleotide at each site of the plurality of sites.

16. The method of claim 15, wherein the plurality of sites comprises at least 50 sites, wherein the method results in synthesis of at least 50 different oligonucleotides.

17. The method of claim 15, wherein the method includes using a pulse jet to deposit reagents at each site of the plurality of sites.

18. The method of claim 12, further comprising contacting the surface with a cleavage agent effective to cleave the cleavable linker moiety, said contacting being for a time and under conditions sufficient to result in cleaving the oligonucleotides from the surface.

19. The method of claim 18, said conditions also being sufficient to concurrently deprotect the oligonucleotides.

20. The method of claim 18, further comprising, prior to contacting the surface with the cleavage agent, contacting the oligonucleotide with a deprotection agent to remove protecting groups from the oligonucleotide to result in a deprotected oligonucleotide bound to the surface.

21. The method of claim 18, further comprising recovering a solution phase mixture of oligonucleotides.