WO2000004196A3 - Cis acting nucleic acid elements and methods of use - Google Patents

Cis acting nucleic acid elements and methods of use Download PDF

Info

Publication number
WO2000004196A3
WO2000004196A3 PCT/US1999/015860 US9915860W WO0004196A3 WO 2000004196 A3 WO2000004196 A3 WO 2000004196A3 US 9915860 W US9915860 W US 9915860W WO 0004196 A3 WO0004196 A3 WO 0004196A3
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
cis acting
compounds
binding
elements
Prior art date
Application number
PCT/US1999/015860
Other languages
French (fr)
Other versions
WO2000004196A2 (en
Inventor
Stuart A Kauffman
Marc Ballivet
Original Assignee
Cistem Molecular Corp
Stuart A Kauffman
Marc Ballivet
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 Cistem Molecular Corp, Stuart A Kauffman, Marc Ballivet filed Critical Cistem Molecular Corp
Priority to CA002337045A priority Critical patent/CA2337045A1/en
Priority to AU50999/99A priority patent/AU5099999A/en
Priority to JP2000560292A priority patent/JP2002520074A/en
Priority to EP99935539A priority patent/EP1098994A2/en
Publication of WO2000004196A2 publication Critical patent/WO2000004196A2/en
Publication of WO2000004196A3 publication Critical patent/WO2000004196A3/en

Links

Classifications

    • 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
    • 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
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • 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
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection

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 activites of nucleic acids involved in pathological conditions.
PCT/US1999/015860 1998-07-14 1999-07-13 Cis acting nucleic acid elements and methods of use WO2000004196A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
CA002337045A CA2337045A1 (en) 1998-07-14 1999-07-13 Cis acting nucleic acid elements and methods of use
AU50999/99A AU5099999A (en) 1998-07-14 1999-07-13 Cis acting nucleic acid elements and methods of use
JP2000560292A JP2002520074A (en) 1998-07-14 1999-07-13 Cis-acting nucleic acid elements and methods of use
EP99935539A EP1098994A2 (en) 1998-07-14 1999-07-13 Cis acting nucleic acid elements and methods of use

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US9269798P 1998-07-14 1998-07-14
US60/092,697 1998-07-14
US09/165,794 1998-10-02
US09/165,794 US6100035A (en) 1998-07-14 1998-10-02 Method of identifying cis acting nucleic acid elements

Publications (2)

Publication Number Publication Date
WO2000004196A2 WO2000004196A2 (en) 2000-01-27
WO2000004196A3 true WO2000004196A3 (en) 2000-04-20

Family

ID=26785953

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US1999/015860 WO2000004196A2 (en) 1998-07-14 1999-07-13 Cis acting nucleic acid elements and methods of use

Country Status (6)

Country Link
US (2) US6100035A (en)
EP (1) EP1098994A2 (en)
JP (1) JP2002520074A (en)
AU (1) AU5099999A (en)
CA (1) CA2337045A1 (en)
WO (1) WO2000004196A2 (en)

Families Citing this family (29)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7138511B1 (en) 1997-01-28 2006-11-21 The Regents Of The University Of California Nucleic acids, kits and methods for the diagnosis, prognosis and treatment of glaucoma and related disorders
US6475724B1 (en) * 1997-01-28 2002-11-05 The Regents Of The University Of California Nucleic acids, kits, and methods for the diagnosis, prognosis and treatment of glaucoma and related disorders
GB9703369D0 (en) * 1997-02-18 1997-04-09 Lindqvist Bjorn H Process
WO2002008286A2 (en) * 2000-07-21 2002-01-31 Syngenta Participations Ag Zinc finger domain recognition code and uses thereof
US6952678B2 (en) 2000-09-01 2005-10-04 Askme Corporation Method, apparatus, and manufacture for facilitating a self-organizing workforce
AU2002232510A1 (en) * 2000-11-13 2002-05-21 Cistem Molecular Corporation Methods for determining the biological effects of compounds on gene expression
CA2327561A1 (en) * 2000-12-27 2002-06-27 Pierre Rousseau Methods for the screening and/or for the identification of differentially active nucleic acid binding factors of nucleic acid binding elements using dna microarray technology (dpa):dna proteomic array
US20040058356A1 (en) * 2001-03-01 2004-03-25 Warren Mary E. Methods for global profiling gene regulatory element activity
EP1370686A2 (en) * 2001-03-01 2003-12-17 Cistem Molecular Corporation Methods for global profiling gene regulatory element activity
US20030113714A1 (en) * 2001-09-28 2003-06-19 Belcher Angela M. Biological control of nanoparticles
US20030148380A1 (en) * 2001-06-05 2003-08-07 Belcher Angela M. Molecular recognition of materials
US20050164515A9 (en) * 2001-06-05 2005-07-28 Belcher Angela M. Biological control of nanoparticle nucleation, shape and crystal phase
US7981842B2 (en) 2001-06-08 2011-07-19 Panomics, Inc. Method for detecting transcription factor-protein interactions
US20040214166A1 (en) * 2001-06-08 2004-10-28 Xianqiang Li Method for identifying a disease state based on a detected mixture of activated transcription factors
US6696256B1 (en) 2001-06-08 2004-02-24 Pandmics, Inc. Method, array and kit for detecting activated transcription factors by hybridization array
US6821737B2 (en) 2001-06-08 2004-11-23 Panomics, Inc. Method for screening for drug candidates for modulating transcription factor activity
US6924113B2 (en) 2001-06-08 2005-08-02 Panomics, Inc. Method and kit for isolating DNA probes that bind to activated transcription factors
US20030073104A1 (en) * 2001-10-02 2003-04-17 Belcher Angela M. Nanoscaling ordering of hybrid materials using genetically engineered mesoscale virus
US20030144823A1 (en) * 2001-11-01 2003-07-31 Fox Jeffrey J. Scale-free network inference methods
US20030119000A1 (en) * 2001-11-05 2003-06-26 Jon Polansky Methods to screen and treat individuals with glaucoma or the propensity to develop glaucoma
US20040048262A1 (en) * 2001-11-09 2004-03-11 Christopher Adams Methods for determining the bilogical effects of compounds on gene expression
US20030148287A1 (en) * 2002-01-24 2003-08-07 Xianqiang Li Libraries and kits for detecting transcription factor activity
US20030143547A1 (en) * 2002-01-24 2003-07-31 Xianqiang Li Method for identifying multiple activated transcription factors
US20050064508A1 (en) * 2003-09-22 2005-03-24 Semzyme Peptide mediated synthesis of metallic and magnetic materials
JP4576945B2 (en) * 2004-02-09 2010-11-10 ソニー株式会社 Detection surface for detecting interaction between substances, sensor chip, sensor device and detection method using the detection surface
US20090215029A1 (en) * 2007-01-16 2009-08-27 Cytocure, Inc. Methods of isolating and purifying nucleic acid-binding biomolecules and compositions including same
AU2008256851A1 (en) * 2007-05-23 2008-12-04 Oregon Health & Science University Microarray systems and methods for identifying DNA-binding proteins
EP2310524A4 (en) * 2008-07-10 2013-07-24 Versitech Ltd Methods for nucleic acid mapping and identification of fine-structural-variations in nucleic acids
US9546372B2 (en) 2012-06-12 2017-01-17 Synthetic Genomics, Inc. Regulatory elements and uses thereof

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0347915A2 (en) * 1988-06-23 1989-12-27 The Rockefeller University Method and agents for inhibiting low density lipoprotein synthesis
WO1995005389A1 (en) * 1993-08-18 1995-02-23 The Board Of Trustees Of The Leland Stanford Junior University Sequence-specific glycoconjugate transcriptional antagonists

Family Cites Families (27)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1989006694A1 (en) * 1988-01-15 1989-07-27 Trustees Of The University Of Pennsylvania Process for selection of proteinaceous substances which mimic growth-inducing molecules
US5861254A (en) * 1997-01-31 1999-01-19 Nexstar Pharmaceuticals, Inc. Flow cell SELEX
US5874218A (en) * 1990-06-11 1999-02-23 Nexstar Pharmaceuticals, Inc. Method for detecting a target compound in a substance using a nucleic acid ligand
US5789157A (en) * 1990-06-11 1998-08-04 Nexstar Pharmaceuticals, Inc. Systematic evolution of ligands by exponential enrichment: tissue selex
US5763566A (en) * 1990-06-11 1998-06-09 Nexstar Pharmaceuticals, Inc. Systematic evolution of ligands by exponential enrichment: tissue SELEX
US5567588A (en) * 1990-06-11 1996-10-22 University Research Corporation Systematic evolution of ligands by exponential enrichment: Solution SELEX
US5853984A (en) * 1990-06-11 1998-12-29 Nexstar Pharmaceuticals, Inc. Use of nucleic acid ligands in flow cytometry
US5683867A (en) * 1990-06-11 1997-11-04 Nexstar Pharmaceuticals, Inc. Systematic evolution of ligands by exponential enrichment: blended SELEX
US5712375A (en) * 1990-06-11 1998-01-27 Nexstar Pharmaceuticals, Inc. Systematic evolution of ligands by exponential enrichment: tissue selex
US5270163A (en) * 1990-06-11 1993-12-14 University Research Corporation Methods for identifying nucleic acid ligands
US5750342A (en) * 1990-06-11 1998-05-12 Nexstar Pharmaceuticals, Inc. Nucleic acid ligands of tissue target
US5637459A (en) * 1990-06-11 1997-06-10 Nexstar Pharmaceuticals, Inc. Systematic evolution of ligands by exponential enrichment: chimeric selex
US5705337A (en) * 1990-06-11 1998-01-06 Nexstar Pharmaceuticals, Inc. Systematic evolution of ligands by exponential enrichment: chemi-SELEX
US5496938A (en) * 1990-06-11 1996-03-05 Nexstar Pharmaceuticals, Inc. Nucleic acid ligands to HIV-RT and HIV-1 rev
US5688935A (en) * 1990-06-11 1997-11-18 Nexstar Pharmaceuticals, Inc. Nucleic acid ligands of tissue target
US5723289A (en) * 1990-06-11 1998-03-03 Nexstar Pharmaceuticals, Inc. Parallel selex
EP0533838B1 (en) * 1990-06-11 1997-12-03 NeXstar Pharmaceuticals, Inc. Nucleic acid ligands
US5864026A (en) * 1990-06-11 1999-01-26 Nexstar Pharmaceuticals, Inc. Systematic evolution of ligands by exponential enrichment: tissue selex
US5763177A (en) * 1990-06-11 1998-06-09 Nexstar Pharmaceuticals, Inc. Systematic evolution of ligands by exponential enrichment: photoselection of nucleic acid ligands and solution selex
US5578444A (en) * 1991-06-27 1996-11-26 Genelabs Technologies, Inc. Sequence-directed DNA-binding molecules compositions and methods
DE69225227T2 (en) * 1991-06-27 1998-10-29 Genelabs Tech Inc SCREENING TEST FOR DETECTING DNA-BINDING MOLECULES
US5726014A (en) * 1991-06-27 1998-03-10 Genelabs Technologies, Inc. Screening assay for the detection of DNA-binding molecules
US5582981A (en) * 1991-08-14 1996-12-10 Gilead Sciences, Inc. Method for identifying an oligonucleotide aptamer specific for a target
JPH08503853A (en) * 1992-11-30 1996-04-30 チューア，ナム−ハイ Expression motifs that confer tissue- and development-specific expression in plants
WO1994024314A1 (en) * 1993-04-19 1994-10-27 Kauffman Stuart A Random chemistry for the generation of new compounds
US5616475A (en) * 1995-02-03 1997-04-01 The Regents Of The University Of California Human T-cell leukemia virus transcription modulators and screening assays
US5861246A (en) * 1996-01-24 1999-01-19 Yale University Multiple selection process for binding sites of DNA-binding proteins

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0347915A2 (en) * 1988-06-23 1989-12-27 The Rockefeller University Method and agents for inhibiting low density lipoprotein synthesis
WO1995005389A1 (en) * 1993-08-18 1995-02-23 The Board Of Trustees Of The Leland Stanford Junior University Sequence-specific glycoconjugate transcriptional antagonists

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
GOLD L. ET AL.: "From oligonucleotide shapes to genomic SELEX: Novel biological regulatory loops", PROC. NAT. ACAD. SCI. USA, vol. 94, January 1997 (1997-01-01), us, pages 59 - 64, XP002126528 *
GROSSMAN J.S. ET AL: "The use of antibodies to the polypyrimidine tract binding protein (PTB) to analyze theprotein components that assemble on alternatively spliced pre-mRNAs that use distant branch points", RNA, vol. 4, no. 6, June 1998 (1998-06-01), US, pages 613 - 6125, XP002125747 *
VANT-HULL B. ET AL.: "The mathematics of SELEX against complex targets", JOURN. MOL. BIOL., vol. 278, 8 May 1998 (1998-05-08), GB, pages 579 - 597, XP002126527 *
YU W. ET AL.: "Specific binding of host cellular proteins to multiple sites within the 3' end of mouse hepatitis virus genomic RNA", JOURNAL OF VIROLOGY, vol. 69, no. 4, April 1995 (1995-04-01), US, pages 2016 - 2023, XP002125746 *

Also Published As

Publication number Publication date
WO2000004196A2 (en) 2000-01-27
EP1098994A2 (en) 2001-05-16
AU5099999A (en) 2000-02-07
JP2002520074A (en) 2002-07-09
US6413723B1 (en) 2002-07-02
US6100035A (en) 2000-08-08
CA2337045A1 (en) 2000-01-27

Similar Documents

Publication Publication Date Title
WO2000004196A3 (en) Cis acting nucleic acid elements and methods of use
DE69731939D1 (en) ISOLATION OF SINGLE-STRUCTURED NUCLEIC ACIDS
CA2223566A1 (en) Method for identifying or isolating a molecule and molecules identified thereby
GB9425138D0 (en) Isolation of nucleic acid
WO1997026270A3 (en) Synthesis of methoxy nucleosides and enzymatic nucleic acid molecules
EP1097994A3 (en) Human bad polypeptides, encoding nucleic acids and methods of use
ATE239090T1 (en) METHOD FOR GENERATING SINGLE STRANDED DNA MOLECULES
ZA981762B (en) Nucleic acid molecules encoding enzymes having fructosyl polymerase activity.
AU4567499A (en) Novel mtbx protein and nucleic acid molecules and uses therefor
WO2002063030A3 (en) Charge tags and separation of nucleic acid molecules
AU3699899A (en) Method for conducting the synthesis of nucleic acid molecules
WO2000012726A3 (en) Rationally designed heparinases derived from heparinase i and ii
CA2295306A1 (en) Dna polymerase-related factors
AU9550198A (en) Jmy, a co-activator for p300/cbp, nucleic acid encoding jmy and uses thereof
WO1997012039A3 (en) Sh2-containing inositol-phosphatase
ZA97835B (en) Purified sr-p70 protein
ATE305037T1 (en) PEPTIDES CAPABLE OF BINDING THE SH3 DOMAIN OF THE GAP PROTEIN, ITS CODING DNA, THEIR PREPARATION AND USE
WO2000040757A3 (en) Method of identifying nucleic acids
WO2001016317A3 (en) Polycyclic aromatic hydrocarbon induced molecules
WO2001016170A3 (en) Card proteins involved in cell death regulation
IL138216A0 (en) Novel fdrg protein and nucleic acid molecules and uses therefor
WO1997020928A1 (en) Novel semaphorin z and gene encoding the same
EP0620439A3 (en) Method of determining the binding of transcription factors to nucleic acids.
CA2243578A1 (en) High affinity nucleic acid ligands of complement system proteins
WO2002052037A3 (en) Method for screening and/or identifying factors that bind to nucleic acids

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A2

Designated state(s): AE AL AM AT AT AU AZ BA BB BG BR BY CA CH CN CU CZ CZ DE DE DK DK EE EE ES FI FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SK SL TJ TM TR TT UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A2

Designated state(s): GH GM KE LS MW SD SL SZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

121 Ep: the epo has been informed by wipo that ep was designated in this application
DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
AK Designated states

Kind code of ref document: A3

Designated state(s): AE AL AM AT AT AU AZ BA BB BG BR BY CA CH CN CU CZ CZ DE DE DK DK EE EE ES FI FI GB GD GE GH GM HR HU ID IL IN IS JP KE KG KP KR KZ LC LK LR LS LT LU LV MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK SK SL TJ TM TR TT UA UG US UZ VN YU ZA ZW

AL Designated countries for regional patents

Kind code of ref document: A3

Designated state(s): GH GM KE LS MW SD SL SZ UG ZW AM AZ BY KG KZ MD RU TJ TM AT BE CH CY DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN GW ML MR NE SN TD TG

WWE Wipo information: entry into national phase

Ref document number: 1999935539

Country of ref document: EP

ENP Entry into the national phase

Ref document number: 2337045

Country of ref document: CA

ENP Entry into the national phase

Ref country code: JP

Ref document number: 2000 560292

Kind code of ref document: A

Format of ref document f/p: F

WWE Wipo information: entry into national phase

Ref document number: 50999/99

Country of ref document: AU

WWP Wipo information: published in national office

Ref document number: 1999935539

Country of ref document: EP

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWW Wipo information: withdrawn in national office

Ref document number: 1999935539

Country of ref document: EP