Method for selecting nucleic acids on the basis of structure

• US 5,707,796 A
• Filed: 02/22/1994
• Issued: 01/13/1998
• Est. Priority Date: 06/11/1990
• Status: Expired due to Term

• Current Assignee: Gilead Sciences Inc.
• Original Assignee: NeXstar Pharmaceuticals, Inc. (Gilead Sciences Inc.)
• Inventors: Beutel, Bruce, Gold, Larry
• Primary Examiner(s): Zitomer, Stephanie W.
• Application Number:
  US08/198,670
• Time in Patent Office: 1,421 Days
• Field of Search: 435/6, 435/91.2, 435/962, 435/973, 935/77, 935/78, 536/25.4
• US Class Current: 435/6.11
• CPC Class Codes: A61K 47/547 Chelates, e.g. Gd-DOTA or Zinc-amino acid chelates; Chelate-forming compounds, e.g. DOTA or ethylenediamine being covalently linked or complexed to the pharmacologically- or therapeutically-active agent
• CPC Class Codes: A61K 47/549 Sugars, nucleosides, nucleotides or nucleic acids
• CPC Class Codes: B82Y 5/00 Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• 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: C07K 14/001 by chemical synthesis
• CPC Class Codes: C12N 15/1048 SELEX
• CPC Class Codes: C12N 15/115 Aptamers, i.e. nucleic acids binding a target molecule specifically and with high affinity without hybridising therewith ; Nucleic acids binding to non-nucleic acids, e.g. aptamers
• CPC Class Codes: C12Q 1/37 involving peptidase or proteinase
• CPC Class Codes: C12Q 1/6811 Selection methods for production or design of target specific oligonucleotides or binding molecules
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: G01N 2333/163 Regulatory proteins, e.g. tat, nef, rev, vif, vpu, vpr, vpt, vpx
• CPC Class Codes: G01N 2333/575 Hormones derived from pro-opiomelanocortin, pro-enkephalin or pro-dynorphin G01N2333/665, corticotropin G01N2333/695
• CPC Class Codes: G01N 2333/62 Insulins
• CPC Class Codes: G01N 2333/8125 Alpha-1-antitrypsin
• CPC Class Codes: G01N 2333/96433 Serine endopeptidases (3.4.21)
• CPC Class Codes: G01N 2333/96436 Granzymes
• CPC Class Codes: G01N 2333/96455 Kallikrein (3.4.21.34; 3.4.21.35)
• CPC Class Codes: G01N 2333/96486 : Metalloendopeptidases (3.4.24)
• CPC Class Codes: G01N 2333/966 : Elastase
• CPC Class Codes: G01N 2333/9726 : Tissue plasminogen activator
• CPC Class Codes: G01N 2333/974 : Thrombin
• CPC Class Codes: G01N 2333/976 : Trypsin; Chymotrypsin
• CPC Class Codes: G01N 33/531 : Production of immunochemical test materials
• CPC Class Codes: G01N 33/532 : Production of labelled immunochemicals
• CPC Class Codes: G01N 33/535 : with enzyme label or co-enzymes, co-factors, enzyme inhibitors or enzyme substrates
• CPC Class Codes: G01N 33/56988 : HIV or HTLV
• CPC Class Codes: G01N 33/68 : involving proteins, peptides or amino acids involving lipoproteins G01N33/92
• CPC Class Codes: G01N 33/76 : Human chorionic gonadotropin including luteinising hormone, follicle stimulating hormone, thyroid stimulating hormone or their receptors
• CPC Class Codes: Y10S 435/962 : Prevention or removal of interfering materials or reactants or other treatment to enhance results, e.g. determining or preventing nonspecific binding
• CPC Class Codes: Y10S 435/973 : Simultaneous determination of more than one analyte

Abstract

A method of selecting nucleic acids on the basis of physical structure is disclosed. A modification of the Systematic Evolution of Ligands by Exponential enrichment (SELEX) is used in conjunction with methods for differentiating between nucleic acid molecules on the basis of physical structure, such as chromatography, gel electrophoresis, solubility, and solvent partitioning. The disclosed method may be used in selecting single stranded DNA or RNA, or double stranded DNA or RNA. An example of the method selected nucleic acids of bent DNA. This method represents a new and powerful approach to select nucleic acid molecules with the physical structure required for specific biological activity, for example, in the regulation of gene expression.

Claims

1. A method for identifying nucleic acid molecules from a candidate mixture of nucleic acids on the basis of a specific structural characteristic, comprising:

a) subjecting said candidate mixture of nucleic acids to partitioning;

b) selecting nucleic acids having said specific structural characteristic as determined by their partitioning behavior;

c) amplifying the selected nucleic acids to yield an amplification mixture enriched for nucleic acids having the specific structural characteristic;

d) repeating steps b) and c), whereby nucleic acid molecules having said specific structural characteristic may be identified.

2. The method of claim 1 wherein said partitioning is by gel electrophoresis.

3. The method of claim 2 wherein said structural characteristic is bent DNA.

4. The method of claim 1 wherein said structural characteristic is compact conformation.

5. The method of claim 1 wherein said partitioning is by exposure to a solvent.

6. The method of claim 1 wherein said partitioning is between two solvent phases.

7. The method of claim 1 wherein said nucleic acid is single or double stranded DNA.

8. The method of claim 1 wherein said nucleic acid is single or double stranded RNA.

9. The method of claim 1 wherein said partitioning is by chromatography.