WO1999063077A3 - Compositions of nucleic acid which alter ligand-binding characteristics and related methods and products - Google Patents

Compositions of nucleic acid which alter ligand-binding characteristics and related methods and products Download PDF

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Publication number
WO1999063077A3
WO1999063077A3 PCT/US1999/012516 US9912516W WO9963077A3 WO 1999063077 A3 WO1999063077 A3 WO 1999063077A3 US 9912516 W US9912516 W US 9912516W WO 9963077 A3 WO9963077 A3 WO 9963077A3
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WO
WIPO (PCT)
Prior art keywords
binding affinity
given
sequence
dna
polynucleotide
Prior art date
Application number
PCT/US1999/012516
Other languages
French (fr)
Other versions
WO1999063077A2 (en
Inventor
Michael J Lane
Albert S Benight
Brian D Faldasz
Original Assignee
Tm Technologies Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Tm Technologies Inc filed Critical Tm Technologies Inc
Publication of WO1999063077A2 publication Critical patent/WO1999063077A2/en
Publication of WO1999063077A3 publication Critical patent/WO1999063077A3/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6811—Selection methods for production or design of target specific oligonucleotides or binding molecules

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Biomedical Technology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The invention details compositions of DNA sequence with the ability to confer a given relative binding affinity to any DNA ligand whose binding site is placed adjacent to the DNA sequence composition. Further, this invention features a method of creating and thereby systematically sampling polynucleotides of any given length sequence space for polynucleotide sequences given the nucleotides A, C, G, and T/U. This invention also features a method of grading the sequences created into a range of relative binding affinities from high binding affinity to low binding affinity, with respect to conferring a given relative binding affinity of any DNA ligand to its binding site placed adjacent to a polynucleotide sequence based on its nucleotide composition. In another aspect this invention features an algorithm for grouping homologous polynucleotide sequences into families related solely by their nucleotide composition. This invention also relates to methods for utilizing a member of a family to allow for the prediction of a region of any polynucleotide sequence or protein which is susceptible to mutation, for modulating the mutation rate of any polynucleotide sequence or protein, for altering the relative expression level of any gene, and the like.
PCT/US1999/012516 1998-06-04 1999-06-04 Compositions of nucleic acid which alter ligand-binding characteristics and related methods and products WO1999063077A2 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US8790598P 1998-06-04 1998-06-04
US60/087,905 1998-06-04
US32467299A 1999-06-03 1999-06-03
US09/324,672 1999-06-03

Publications (2)

Publication Number Publication Date
WO1999063077A2 WO1999063077A2 (en) 1999-12-09
WO1999063077A3 true WO1999063077A3 (en) 2000-06-29

Family

ID=26777506

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1999/012516 WO1999063077A2 (en) 1998-06-04 1999-06-04 Compositions of nucleic acid which alter ligand-binding characteristics and related methods and products

Country Status (1)

Country Link
WO (1) WO1999063077A2 (en)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6562955B2 (en) * 2000-03-17 2003-05-13 Tosoh Corporation Oligonucleotides for detection of Vibrio parahaemolyticus and detection method for Vibrio parahaemolyticus using the same oligonucleotides
WO2001092523A2 (en) * 2000-05-30 2001-12-06 Curagen Corporation Human polynucleotides and polypeptides encoded thereby
CN104975352A (en) * 2015-05-06 2015-10-14 重庆大学 Oligonucleotide fragment library used for regulation of gene expression level and application thereof

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1995000665A1 (en) * 1993-06-17 1995-01-05 The Research Foundation Of State University Of New York Thermodynamics, design, and use of nucleic acid sequences
WO1997008183A1 (en) * 1995-08-25 1997-03-06 Lane Michael J Nucleic acid capture moieties
US5726014A (en) * 1991-06-27 1998-03-10 Genelabs Technologies, Inc. Screening assay for the detection of DNA-binding molecules
WO1999032664A1 (en) * 1997-12-23 1999-07-01 Tm Technologies, Inc. Method of selecting flanking sequences which convey relative binding affinities to a ligand binding site
WO1999063117A1 (en) * 1998-06-04 1999-12-09 Tm Technologies, Inc. Method of creating flanking polynucleotide sequences which convey relative binding affinities to a ligand binding site

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5726014A (en) * 1991-06-27 1998-03-10 Genelabs Technologies, Inc. Screening assay for the detection of DNA-binding molecules
WO1995000665A1 (en) * 1993-06-17 1995-01-05 The Research Foundation Of State University Of New York Thermodynamics, design, and use of nucleic acid sequences
WO1997008183A1 (en) * 1995-08-25 1997-03-06 Lane Michael J Nucleic acid capture moieties
WO1999032664A1 (en) * 1997-12-23 1999-07-01 Tm Technologies, Inc. Method of selecting flanking sequences which convey relative binding affinities to a ligand binding site
WO1999063117A1 (en) * 1998-06-04 1999-12-09 Tm Technologies, Inc. Method of creating flanking polynucleotide sequences which convey relative binding affinities to a ligand binding site

Non-Patent Citations (9)

* Cited by examiner, † Cited by third party
Title
A.S. BENIGHT ET AL.: "Sequence contest and DNA reactivity: Application to sequence-specific cleavage of DNA.", ADVANCES IN BIOPHYSICAL CHEMISTRY, vol. 5, 1995, pages 1 - 55, XP002127590 *
BLACKWELL T K ET AL: "DIFFERENCES AND SIMILARITIES IN DNA-BINDING PREFERENCES OF MyoD AND E2A PROTEIN COMPLEXES REVEALED BY BINDING SITE SELECTION", SCIENCE,US,AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE,, vol. 250, no. 4984, pages 1104-1110, XP000371689, ISSN: 0036-8075 *
M.J. LANE ET AL.: "Non-contacted sequences flanking a ligand binding site can modulate the affinity of ligand binding: implications of such modulation in single strand to duplex reaction design.", BIOPHYSICAL JOURNAL, vol. 74, no. 2, part 2, 22 February 1998 (1998-02-22) - 26 February 1998 (1998-02-26), pages A5, XP002116814 *
OLIPHANT A R ET AL: "DEFINING THE SEQUENCE SPECIFICITY OF DNA-BINDING PROTEINS BY SELECTING BINDING SITES FROM RANDOM-SEQUENCE OLIGONUCLEOTIDES: ANALYSIS OF YEAST GCN4 PROTEIN", MOLECULAR AND CELLULAR BIOLOGY,US,AMERICAN SOCIETY FOR MICROBIOLOGY, WASHINGTON, vol. 9, no. 7, pages 2944-2949, XP000673592, ISSN: 0270-7306 *
P.L. NORBY ET AL.: "Determination of recognition-sequences for DNA-binding proteins by a polymerase chain reaction asisted binding site selection method (BSS) using nitrocellulose immobilized DNA binding protein.", NUCLEIC ACIDS RESEARCH, vol. 20, no. 23, 1992, pages 6317 - 6321, XP002116813 *
P.V. RICCELLI ET AL.: "Investigation of DNA context effects: Influences of flanking sequence stability on site specific binding of BamHI restriction enzyme to duplex DNA oligomers.", BIOPHYSICAL JOURNAL, vol. 72, no. 2, part 2, 1997, pages a95, XP000870137 *
PIERROU S ET AL: "SELECTION OF HIGH-AFFINITY BINDING SITES FOR SEQUENCE-SPECIFIC, DNA BINDING PROTEINS FROM RANDOM SEQUENCE OLIGONUCLEOTIDES", ANALYTICAL BIOCHEMISTRY,US,ACADEMIC PRESS, SAN DIEGO, CA, vol. 229, no. 1, pages 99-105, XP000524716, ISSN: 0003-2697 *
THIESEN H J ET AL: "TARGET DETECTION ASSAY (TDA): A VERSATILE PROCEDURE TO DETERMINE DNA BINDING SITES AS DEMONSTRATED ON SP1 PROTEIN", NUCLEIC ACIDS RESEARCH,GB,OXFORD UNIVERSITY PRESS, SURREY, vol. 18, no. 11, pages 3203-3209, XP000132496, ISSN: 0305-1048 *
Y. LIN ET AL.: "Peptide conjugation to an in vitro-selected DNA ligand improves enzyme inhibition.", PROC. NATL. ACAD. SCI. USA, vol. 92, November 1995 (1995-11-01), pages 11044 - 11048, XP002127589 *

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