Long oligonucleotide arrays

• US 7,556,919 B2
• Filed: 11/09/2004
• Issued: 07/07/2009
• Est. Priority Date: 11/15/1999
• Status: Expired due to Fees

• Current Assignee: Takara Bio Usa, Inc. (Ningbo Junsheng Investment Group Co., Ltd.)
• Original Assignee: Clontech Laboratories Incorporated (Ningbo Junsheng Investment Group Co., Ltd.)
• Inventors: Chenchik, Alex, Simonenko, Peter, Munishkin, Alexander
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US10/985,372
• Publication Number:
  US 20060068403A1
• Time in Patent Office: 1,701 Days
• Field of Search: None
• US Class Current: 435/6.11
• 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 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 50/00 Methods of creating libraries, e.g. combinatorial synthesis

Abstract

Long oligonucleotide arrays, as well as methods for their preparation and use in hybridization assays, are provided. The subject arrays are characterized in that at least a portion of the probes of the array, and usually all of the probes of the array, are long oligonucleotides, e.g. oligonucleotides having a length of from about 50 to 120 nt. Each long oligonucleotide probe on the array is preferably chosen to exhibit substantially the same high target binding efficiency and substantially the same low non-specific binding under conditions in which the array is employed. The subject arrays find use in a number of different applications, e.g. differential gene expression analysis.

Claims

1. A nucleic acid hybridization assay comprising the steps of:

contacting at least one labeled target nucleic acid sample with an array under conditions sufficient to produce a hybridization pattern; and

detecting said hybridization pattern, wherein said array comprises at least one pattern of different probe oligonucleotide spots covalently attached to the surface of a solid support, wherein the spots on said array have a density of at least 10/cm2 and each probe oligonucleotide spot of said pattern comprises an oligonucleotide probe composition made up of long oligonucleotide probes ranging in length from 60 to about 100 nucleotides, and further wherein each oligonucleotide probe composition is made up of long oligonucleotide probes that have less than 50% homology with oligonucleotide probes of any other different probe composition of said array.

2. The method according to claim 1, wherein said method further comprises preparing said labeled target nucleic acid sample.

3. The method according to claim 2, wherein said preparing comprises conjugating a detectable label to a functionalized target nucleic acid.

4. The method according to claim 1, where said method further comprises:

generating a second hybridization pattern; and

comparing said hybridization patterns.

5. The method according to claim 1, wherein two or more different target nucleic acids hybridize to different probe oligonucleotide spots in said pattern.

6. The method according to claim 5, wherein each probe oligonucleotide spot in said pattern hybridizes to a different target nucleic acid.

7. The method according to claim 1, wherein the spots on said array do not exceed a density of 1000/cm².

8. The method according to claim 1, wherein the spots on said array do not exceed a density of 400/cm².

9. The method according to claim 1, wherein the spots on said array range from about 50 to 50,000 in number.

10. The method according to claim 1, wherein the spots on said array range from about 50 to 10,000 in number.

11. The method according to claim 1, wherein said solid support is glass.

12. The nucleic acid hybridization assay of claim 1, wherein said oligonucleotide probes are single-stranded.

13. The nucleic acid hybridization assay of claim 1, wherein said oligonucleotide probes range in length from 65 to 85 monomers.