Parallel preparation of high fidelity probes in an array format

• US 8,338,585 B2
• Filed: 12/09/2011
• Issued: 12/25/2012
• Est. Priority Date: 12/31/2004
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: McGall, Glenn H., Kuimelis, Robert G.
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US13/316,254
• Publication Number:
  US 20120184467A1
• Time in Patent Office: 382 Days
• Field of Search: 536/25.3, 536/23.1, 536/24.3, 536/25.4, 536/26.6, 435/6.1
• US Class Current: 536/25.3
• 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 2219/00427 using masks
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/14 Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 80/00 Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers

Abstract

The present invention provides massively parallel oligonucleotide synthesis and purification for applications that utilize large collections of defined high-fidelity oligonucleotides (e.g., from about 10¹ to about 10⁵ different sequences, generally between 25-160 bases in length).

Claims

1. A method of synthesizing one or more oligonucleotides on a solid substrate, wherein the method comprises:

attaching to a solid substrate one or more ribonucleotides having the following structure;

2. The method according to claim 1, which further comprises transesterifying the one or more oligonucleotides synthesized on the solid substrate, thereby releasing the one or more oligonucleotides form the solid substrate.

3. The method according to claim 1, wherein the one or more oligonucleotides comprises sequences complimentary to an individual genomic library.

4. The method according to claim 3, wherein the one or more oligonucleotides are synthesized by a combinatorial synthesis strategy.

5. The method according to claim 3, wherein the individual is selected from the group consisting of:

mammals, plants, and bacteria.

6. The method according to claim 5, wherein the individual is human.

7. The method according to claim 3, wherein the one or more oligonucleotides are between 80 and 160 nucleotides in length.

8. The method according to claim 6, wherein sequences of the one or more oligonucleotides are complimentary to mRNA sequences in the genomic library.

9. The method according to claim 1, wherein synthesizing the one or more oligonucleotide by sequential addition of one or more additional nucleotides is accomplished by photolithography.

10. The method according to claim 1, wherein the substrate is glass.

11. The method according to claim 2, which further comprises attaching biotin to the one or more oligonucleotides.

12. The method according to claim 11, wherein attaching biotin to the one or more oligonucleotides occurs after transesterification.