Chemical arrays and methods of using the same

• US 7,588,889 B2
• Filed: 12/08/2004
• Issued: 09/15/2009
• Est. Priority Date: 07/31/2000
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Atwell, Andrew S., Ilsley-Tyree, Diane, Amorese, Douglas, Kincaid, Robert H., Leproust, Eric M., Wolber, Paul K., Kronick, Mel N.
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US11/008,603
• Publication Number:
  US 20050148004A1
• Time in Patent Office: 1,742 Days
• Field of Search: None
• US Class Current: 435/6.12
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00572 Chemical means
• CPC Class Codes: B01J 2219/00574 radioactive
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• 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: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2525/131 incorporating a restriction site
• CPC Class Codes: C12Q 2525/161 : incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2565/525 : characterised by the capture oligonucleotide being double stranded
• CPC Class Codes: C12Q 2565/537 : characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C12Q 2600/158 : Expression markers
• 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 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes

Abstract

Methods and compositions for generating mixtures of product molecules from an initial chemical array are provided. In the subject methods, a chemical array of surface immobilized first moieties is subjected to cleavage conditions such that a composition of solution phase first moieties is produced. The resultant composition of solution phase first moieties is then contacted with one or more reactants to produce a mixture of product molecules that are different from the first moieties. Also provided are the arrays employed in the subject methods and kits for practicing the subject methods.

Claims

1. A method comprising:

(a) subjecting an array comprising a plurality of features, each comprising nucleic acids immobilized on a surface of a solid support via a cleavable domain having a cleavable region, to conditions sufficient to generate a solution phase composition of nucleic acids;

(b) contacting said solution phase composition of nucleic acids with one or more reactants to produce a mixture of product nucleic acids; and

(c) contacting said product nucleic acids with an addressable array of probe nucleic acids.

2. The method according to claim 1, wherein said cleavable region is recognized by a restriction endonuclease.

3. The method according to claim 1, wherein said one or more reactants comprises an enzymatic activity.

4. The method according to claim 3, wherein said one or more reactants make up a template dependent polymerase reaction system.

5. The method according to claim 4, wherein said template dependent polymerase reaction system is an amplification system.

6. The method according to claim 1, wherein said product nucleic acids are deoxyribonucleic acids.

7. The method according to claim 1, wherein said product nucleic acids are ribonucleic acids.

8. The method according to claim 1, wherein said method comprises cleaving said cleavable region prior to said contacting step.

9. The method according to claim 1, wherein said array comprising a plurality of features comprises surface immobilized single-stranded nucleic acids described by the formula:

surface-L-V

wherein;

L is a cleavable domain that includes a cleavable region; and

V is a variable domain;

wherein only said variable domain V of said surface immobilized single-stranded nucleic acids differs between features.