Method of identifying cis acting nucleic acid elements

• US 6,100,035 A
• Filed: 10/02/1998
• Issued: 08/08/2000
• Est. Priority Date: 07/14/1998
• Status: Expired due to Fees

• Current Assignee: Cistem Molecular Corporation
• Original Assignee: Cistem Molecular Corporation
• Inventors: Kauffman, Stuart A., Ballivet, Marc
• Primary Examiner(s): MCKELVEY, TERRY ALAN
• Application Number:
  US09/165,794
• Time in Patent Office: 676 Days
• Field of Search: 435/6
• US Class Current: 435/6.11
• CPC Class Codes: C12N 15/1034 Isolating an individual clone by screening libraries
• CPC Class Codes: C12Q 1/6804 Nucleic acid analysis using immunogens immunoassay G01N33/53
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 2521/507 Recombinase
• CPC Class Codes: C12Q 2522/101 Single or double stranded nucleic acid binding proteins
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences

Abstract

The invention provides a method of identifying nucleic acid molecules that contain cis acting nucleic acid elements. Also provided is a method of isolating nucleic acid binding factors. The invention also provides methods of identifying compounds that are cis acting nucleic acid element analogs, compounds that are nucleic acid binding factor analogs, compounds that selectively bind cis acting nucleic acid elements and compounds that selectively displace binding between a nucleic acid binding factor and a cis acting nucleic acid element or between nucleic acid binding factors. Also provided is a method of determining a binding state of a nucleic acid. Pluralities of isolated nucleic acid molecules containing cis acting nucleic acid elements, of isolated cis acting nucleic acid elements and of isolated nucleic acid binding factors are also provided. The invention further provides methods of treating pathological conditions using molecules of the invention to alter genetic activities of nucleic acids involved in pathological conditions.

Claims

1. A method of identifying a nucleic acid containing a cis acting nucleic acid element, comprising:

(a) contacting a preparation of nucleic acids bound to a diverse population of nucleic acid binding factors with a diverse population of isolated nucleic acid molecules under conditions wherein said nucleic acid binding factors selectively bind said isolated nucleic acid molecules; and

(b) identifying one or more of the isolated nucleic acid molecules that bind to one or more of the nucleic acid binding factors, wherein an isolated nucleic acid molecule that binds to an nucleic acid binding factor is characterized as a nucleic acid containing a cis acting nucleic acid element.

2. The method of claim 1, wherein said diverse population of isolated nucleic acid molecules comprises 10 or more different nucleic acid molecules.

3. The method of claim 1, wherein said diverse population of isolated nucleic acid molecules comprises greater than about 10⁵ different nucleic acid molecules.

4. The method of claim 1, wherein said diverse population of isolated nucleic acid molecules comprises nucleic acids attached to a solid support.

5. The method of claim 1, wherein said diverse population of nucleic acid binding factors comprises 10 or more different nucleic acid binding factors.

6. The method of claim 1, wherein said diverse population of nucleic acid binding factors comprises greater than about 10³ different nucleic acid binding factors.

7. The method of claim 1, wherein said preparation of nucleic acids bound to a diverse population of nucleic acid binding factors is selected from the group consisting of chromatin, a chromosome, a chromosome arm, a transcriptional domain, a gene family and a gene.

8. The method of claim 1, wherein said diverse population of isolated nucleic acid molecules comprises greater than about 200 different nucleic acid molecules.

9. The method of claim 1, wherein said diverse population of isolated nucleic acid molecules comprises greater than about 10³ different nucleic acid molecules.

10. The method of claim 1, wherein said diverse population of isolated nucleic acid molecules comprises greater than about 10⁸ different nucleic acid molecules.

11. The method of claim 1, wherein said diverse population of nucleic acid binding factors comprises greater than about 100 different nucleic acid binding factors.