Long oligonucleotide arrays

• US 7,041,445 B2
• Filed: 11/15/1999
• Issued: 05/09/2006
• 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
• Inventors: Chenchik, Alex, Simonenko, Peter, Munishkin, Alexander
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US09/440,829
• Publication Number:
  US 20020160360A1
• Time in Patent Office: 2,367 Days
• Field of Search: 422/50, 422/68.1, 422/161, 435/287.2, 435/288.3, 435/6, 435/283.1, 536/24.3, 536/23.1
• 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. An array comprising 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 that range in length from 60 to about 100 nucleotides and have less than 50% homology with oligonucleotide probes of any other different probe composition of said array.

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

3. The array according to claim 1, wherein each probe oligonucleotide spot In said pattern hybridizes to a different target nucleic acid.

4. The array according to claim 1, wherein each of said long oligonucleotide probes is cross-linked to the surface of said support.

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

6. The array according to claim 5, wherein the spots on said array do not exceed a density of 400/cm².

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

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