Methods and compositions for producing biopolymeric arrays

• US 6,346,423 B1
• Filed: 07/16/1999
• Issued: 02/12/2002
• Est. Priority Date: 07/16/1999
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Schembri, Carol T.
• Primary Examiner(s): Celsa, Bennett
• Assistant Examiner(s): FRIEND, TOMAS H F
• Application Number:
  US09/354,816
• Time in Patent Office: 942 Days
• Field of Search: 435/4, 435/6, 435/7.1, 435/283.1, 435/286.5, 435/288.4, 435/292.1, 435/DIG.1, 435/44-50, 436/94, 436/501, 436/516, 436/506, 436/518, 424/462, 424/482, 424/9.1, 530/334, 530/333, 530/300, 536/23.1, 536/25.3, 422/129, 422/131, 422/134
• US Class Current: 506/30
• 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 2219/00274 Sequential or parallel reactions; Apparatus and devices for combinatorial chemistry or for making arrays; Chemical library technology
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00531 essentially square
• CPC Class Codes: B01J 2219/00533 essentially rectangular
• CPC Class Codes: B01J 2219/00536 in the shape of disks
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00731 Saccharides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

Methods and compositions are provided for producing arrays of polymeric binding agents. In the subject methods, the individual polymers of the array are synthesized using solid phase synthesis techniques on the surface of a substrate. A critical feature of the invention is that one or more locations on the substrate surface are spatially and temporally protected by a protective bubble during the synthesis protocol, where the protective bubble may be produced using any convenient bubble producing means. The bubble producing means may be a component of either a substrate or a structure separate from the substrate. Also provided are the arrays produced by the subject methods, kits for use in practicing the subject methods, and methods of using the arrays in analyte detection assays, including hybridization assays, such as gene discovery, differential gene expression and gene sequencing assays.

Claims

1. A method for synthesizing a plurality of polymers on a substrate surface, said method comprising:

(a) producing a solvent layer on said substrate surface, where said substrate surface has a plurality of individually activatable resistors associated with it;

(b) performing at least two iterations of the following steps;

(1) selectively protecting at least one site on said substrate surface with a protective bubble by selective activation of said resistors;

(2) contacting said selectively protected substrate surface with a reactive agent under conditions sufficient for said reactive agent to react with unprotected susceptible moieties present on said substrate surface; and

(3) removing unreacted reactive agent from said substrate surface;

whereby a plurality of polymers are produced on said substrate surface.

2. The method according to claim 1, wherein said reactive agent is a deblocking agent.

3. The method according to claim 1, wherein said reactive agent is an activated monomer.

4. The method according to claim 1, wherein said polymers are nucleic acids.

5. A method for synthesizing a plurality of polymers on a substrate surface, said method comprising:

(a) producing a solvent layer on said substrate surface;

(b) performing at least two iterations of the following steps;

(1) selectively protecting at least one site on said substrate surface with a protective bubble, where said protective bubble is produced by activation of a resistor present on a structure apart from said substrate;

(2) contacting said selectively protected substrate surface with a reactive agent under conditions sufficient for said reactive agent to react with unprotected susceptible moieties present on said substrate surface; and

(3) removing unreacted reactive agent from said substrate surface;

whereby a plurality of polymers are produced on said substrate surface.

6. The method according to claim 5, wherein said reactive agent is a deblocking agent.

7. The method according to claim 5, wherein said reactive agent is an activated monomer.

8. The method according to claim 5, wherein said polymers are nucleic acids.

9. The method according to claim 5, wherein said polymers are peptides.