Parallel preparation of high fidelity probes in an array format

• US 7,803,934 B2
• Filed: 01/28/2009
• Issued: 09/28/2010
• 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:
  US12/360,945
• Publication Number:
  US 20090192050A1
• Time in Patent Office: 608 Days
• Field of Search: 435/6, 536/23.1, 536/24.3, 536/25.3, 536/25.4, 536/26.6
• US Class Current: 536/25.4
• 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 purifying a set of oligonucleotides, comprising the steps of

a) providing a solid substrate comprising a plurality of ribonucleotides attached thereto at a density of 200 to 2000 pmoles per cm², one said ribonucleotide shown below

2. A method according to claim 1 wherein said PG₂ is selected from the group consisting of FPMP, CEE, TBDMS, TOM and a photo labile protective group.

3. A method according to claim 2 wherein said PG₂ is selected from the group consisting of FPMP and CEE.

4. A method according to claim 3 wherein PG₂ is removed with mild acid.

5. A method according to claim 2 wherein said PG₂ is selected from the group consisting of TBDMS and TOM.

6. A method according to claim 5 wherein PG₂ is removed by exposure to fluoride ions.

7. A method according to claim 2 wherein said PG₂ is a photo labile protecting group removed by exposure to electromagnetic radiation of about 310 nm and up.

8. A method according to claim 7 wherein said photolabile protecting group is selected from the group consisting of NNPOC and MBPMOC.