# US 5,707,796 A · Method for selecting nucleic acids on the basis of structure > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 5,707,796 A - Document ID: US5707796A - Status: Granted - Kind: A - Application number: 08/198,670 - Filed: 1994-02-22 - Granted: 1998-01-13 - Earliest claimed: 1990-06-11 - Assignees: NeXstar Pharmaceuticals, Inc. - Inventors: Larry Gold; Bruce Beutel - Web page: https://patentgrep.com/patent/US5707796A ## CPC - 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} - 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} - A61K 47/549: {Sugars, nucleosides, nucleotides or nucleic acids} - B82Y 5/00: Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery - C07H 19/06: Pyrimidine radicals - C07H 19/10: with the saccharide radical esterified by phosphoric or polyphosphoric acids - 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 - C07K 14/001: {by chemical synthesis} - C12N 15/1048: {SELEX} - C12Q 1/37: involving peptidase or proteinase - C12Q 1/6811: Selection methods for production or design of target specific oligonucleotides or binding molecules - G01N 33/531: Production of immunochemical test materials - G01N 33/532: Production of labelled immunochemicals - G01N 33/535: with enzyme label {or co-enzymes, co-factors, enzyme inhibitors or enzyme substrates} - G01N 33/56988: {HIV or HTLV} - G01N 33/68: involving proteins, peptides or amino acids {(involving lipoproteins G01N33/92)} - G01N 33/76: Human chorionic gonadotropin {including luteinising hormone, follicle stimulating hormone, thyroid stimulating hormone or their receptors} - C40B 40/00: Libraries per se, e.g. arrays, mixtures - G01N 2333/163: Regulatory proteins, e.g. tat, nef, rev, vif, vpu, vpr, vpt, vpx - G01N 2333/575: Hormones - G01N 2333/62: Insulins - G01N 2333/8125: Alpha-1-antitrypsin - G01N 2333/96433: Serine endopeptidases (3.4.21) - G01N 2333/96436: Granzymes - G01N 2333/96455: Kallikrein (3.4.21.34; 3.4.21.35) - G01N 2333/96486: Metalloendopeptidases (3.4.24) - G01N 2333/966: Elastase - G01N 2333/9726: Tissue plasminogen activator - G01N 2333/974: Thrombin - G01N 2333/976: Trypsin; Chymotrypsin - Y10S 435/962: Prevention or removal of interfering materials or reactants or other treatment to enhance results, e.g. determining or preventing nonspecific binding - Y10S 435/973: Simultaneous determination of more than one analyte - C12N: MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA (microbiological testing media C12Q1/00) - A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D) - B82Y: SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES - C07H: SUGARS; DERIVATIVES THEREOF; NUCLEOSIDES; NUCLEOTIDES; NUCLEIC ACIDS (derivatives of aldonic or saccharic acids C07C, C07D; aldonic acids, saccharic acids C07C59/105, C07C59/285; cyanohydrins C07C255/16; glycals C07D; compounds of unknown constitution C07G; polysaccharides, derivatives thereof C08B; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification C12N15/00; sugar industry C13) - C07K: PEPTIDES (peptides in foodstuffs A23; obtaining protein compositions for foodstuffs, working-up proteins for foodstuffs A23J; preparations for medicinal purposes A61K; peptides containing beta-lactam rings C07D; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, C07D; ergot alkaloids of the cyclic peptide type C07D519/02; macromolecular compounds having statistically distributed amino acid units in their molecules, i.e. when the preparation does not provide for a specific; but for a random sequence of the amino acid units, homopolyamides and block copolyamides derived from amino acids C08G69/00; macromolecular products derived from proteins C08H1/00; preparation of glue or gelatine C09H; single cell proteins, enzymes C12N; genetic engineering processes for obtaining peptides C12N15/00; compositions for measuring or testing processes involving enzymes C12Q; investigation or analysis of biological material G01N33/00) - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - C40B: COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES (in silico combinatorial libraries of nucleic acids, proteins or peptides G16B35/00; in silico combinatorial chemistry G16C20/60) - Y10S: TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS ## 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 ### Claim 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. ### Claim 2 (depends on 1) The method of claim 1 wherein said partitioning is by gel electrophoresis. ### Claim 3 (depends on 2) The method of claim 2 wherein said structural characteristic is bent DNA. ### Claim 4 (depends on 1) The method of claim 1 wherein said structural characteristic is compact conformation. ### Claim 5 (depends on 1) The method of claim 1 wherein said partitioning is by exposure to a solvent. ### Claim 6 (depends on 1) The method of claim 1 wherein said partitioning is between two solvent phases. ### Claim 7 (depends on 1) The method of claim 1 wherein said nucleic acid is single or double stranded DNA. ### Claim 8 (depends on 1) The method of claim 1 wherein said nucleic acid is single or double stranded RNA. ### Claim 9 (depends on 1) The method of claim 1 wherein said partitioning is by chromatography.