CA2480646A1 - Detection of dna-binding proteins - Google Patents

Detection of dna-binding proteins Download PDF

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Publication number
CA2480646A1
CA2480646A1 CA002480646A CA2480646A CA2480646A1 CA 2480646 A1 CA2480646 A1 CA 2480646A1 CA 002480646 A CA002480646 A CA 002480646A CA 2480646 A CA2480646 A CA 2480646A CA 2480646 A1 CA2480646 A1 CA 2480646A1
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CA
Canada
Prior art keywords
duplex
detection
binding protein
restriction endonuclease
capture
Prior art date
Legal status (The legal status 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 status listed.)
Granted
Application number
CA002480646A
Other languages
French (fr)
Other versions
CA2480646C (en
Inventor
Peter A. Clausen
James G. Lazar
David P. Carlson
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Marligen Biosciences Inc
Original Assignee
Marligen Biosciences, Inc.
Peter A. Clausen
James G. Lazar
David P. Carlson
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 Marligen Biosciences, Inc., Peter A. Clausen, James G. Lazar, David P. Carlson filed Critical Marligen Biosciences, Inc.
Publication of CA2480646A1 publication Critical patent/CA2480646A1/en
Application granted granted Critical
Publication of CA2480646C publication Critical patent/CA2480646C/en
Anticipated expiration legal-status Critical
Expired - Fee Related legal-status Critical Current

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Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/34Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
    • C12Q1/44Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving esterase
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6875Nucleoproteins
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/435Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
    • G01N2333/46Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
    • G01N2333/47Assays involving proteins of known structure or function as defined in the subgroups
    • G01N2333/4701Details
    • G01N2333/4703Regulators; Modulating activity
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2333/00Assays involving biological materials from specific organisms or of a specific nature
    • G01N2333/90Enzymes; Proenzymes
    • G01N2333/914Hydrolases (3)
    • G01N2333/916Hydrolases (3) acting on ester bonds (3.1), e.g. phosphatases (3.1.3), phospholipases C or phospholipases D (3.1.4)
    • G01N2333/922Ribonucleases (RNAses); Deoxyribonucleases (DNAses)

Abstract

Compositions and methods are provided for detecting and measuring DNA-binding proteins. The compositions and methods permit the simultaneous or near-simultaneous detection of multiple DNA-binding proteins in a multiplex or array format, and can be used to generate profiles of DNA binding activity by proteins, specifically, transcription factors. Multiple protein-DNA binding events in a single sample may be detected and quantitated in a high-throughput format.

Claims (16)

1. A method for detecting sequence specific DNA binding proteins, comprising:
(a) contacting a detection duplex with a sample suspected of containing at least one sequence specific DNA binding protein for a time sufficient to permit sequence-specific binding between said duplex and said binding protein;
(b) contacting the mixture from step (a) with a cleavage reagent that is capable of cleaving said detection duplex, wherein cleavage of said detection duplex is inhibited by binding of said DNA binding protein to said duplex; and (c) detecting the inhibition of said cleavage by said DNA binding protein.
2. The method according to claim 1, wherein said cleavage reagent is a sequence specific cleavage reagent.
3. The method according to claim 1, wherein said sequence specific cleavage reagent is a restriction endonuclease and said detection duplex comprises a restriction endonuclease recognition site.
4. The method according to claim 3, wherein said restriction endonuclease is a Type II restriction endonuclease and said restriction endonuclease recognition site is a Type II restriction endonuclease recognition site.
5. The method according to claim 3, wherein said restriction endonuclease is a Type IIs restriction endonuclease and said restriction endonuclease recognition site is a Type IIs restriction endonuclease recognition site.
6. The method according to claim 1 wherein said nuclease is an exonuclease that lacks significant endonuclease activity.
7. The method according to claim 1, wherein said detection duplex comprises (i) a first oligonucleotide comprising a tag sequence and (ii) a second oligonucleotide that is complementary to said first oligonucleotide, and wherein said second oligonucleotide comprises a detectable label.
8. The method according to claim 7, wherein said detection duplex further comprises a capture tag.
9. The method according to claim 8, wherein said detection duplex is immobilized on a solid support via said capture tag prior to contacting with said sample.
10. The method according to claim 8, wherein said detection duplex is immobilized on a solid support via said capture tag.
11. The method according to claim 8, wherein a plurality of detection duplexes is used, and each detection duplex carries a capture tag that permits capture of the duplex at a predetermined position on a solid surface.
12. A method for detecting sequence specific DNA binding proteins, comprising:
(a) contacting a sample suspected of containing at least one sequence specific DNA binding protein with a detection duplex for a time sufficient to permit sequence-specific binding between said duplex and said binding protein;
and (b) detecting binding between said duplex and said binding protein.
13. The method according to claim 12, further comprising immobilizing said detection duplex on a solid support before or after steps (a) or (b).
14. The method according to claim 13, wherein said immobilization occurs via a capture tag on said duplex.
15. The method according to claim 14, wherein said detection is achieved by labeling said protein sample with a detectable label prior to contacting with said detection duplex.
16. The method according to claim 14, wherein detection is achieved via a detection reagent that specifically binds said binding protein.
18. The method according to claim 16, wherein said detection reagent is an antibody.
19. The method according to claim 13, wherein said detection duplex is labeled, and said immobilizing step is achieved via capture of the binding protein onto a surface.
20. A method for detecting sequence specific DNA binding proteins, comprising:
(a) contacting a capture surface with a sample suspected of containing at least one sequence specific DNA binding protein, for a time sufficient to permit capture of said sequence-specific binding protein on said capture surface;
(b) contacting said capture surface with a detection duplex, and (c) detecting binding between said duplex and said binding protein.
CA2480646A 2002-03-28 2003-03-28 Detection of dna-binding proteins Expired - Fee Related CA2480646C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US36770302P 2002-03-28 2002-03-28
US60/367,703 2002-03-28
PCT/US2003/009604 WO2003083476A1 (en) 2002-03-28 2003-03-28 Detection of dna-binding proteins

Publications (2)

Publication Number Publication Date
CA2480646A1 true CA2480646A1 (en) 2003-10-09
CA2480646C CA2480646C (en) 2010-08-03

Family

ID=28675388

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2480646A Expired - Fee Related CA2480646C (en) 2002-03-28 2003-03-28 Detection of dna-binding proteins

Country Status (9)

Country Link
US (2) US7122317B2 (en)
EP (1) EP1490682B1 (en)
JP (1) JP4425640B2 (en)
AT (1) ATE377753T1 (en)
AU (1) AU2003226116B2 (en)
CA (1) CA2480646C (en)
DE (1) DE60317315T2 (en)
DK (1) DK1490682T3 (en)
WO (1) WO2003083476A1 (en)

Families Citing this family (17)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
DE60317315T2 (en) * 2002-03-28 2008-08-21 Marligen Biosciences, Inc. DETECTION OF DNA BINDING PROTEINS
US20040229284A1 (en) * 2003-02-19 2004-11-18 The Regents Of The University Of California Multiplex analysis of proteins
US20060194215A1 (en) * 2005-02-28 2006-08-31 Kronick Mel N Methods, reagents and kits for reusing arrays
US20070015166A1 (en) * 2005-07-14 2007-01-18 Nilsen Thor W Lateral flow methods and devices for detection of nucleic acid binding proteins
JP2007222160A (en) * 2006-01-26 2007-09-06 National Institute Of Advanced Industrial & Technology Method for analyzing protein in living body-originated specimen
US7833716B2 (en) 2006-06-06 2010-11-16 Gen-Probe Incorporated Tagged oligonucleotides and their use in nucleic acid amplification methods
CA2687804A1 (en) * 2007-05-23 2008-12-04 Oregon Health & Science University Microarray systems and methods for identifying dna-binding proteins
DE102011109063B3 (en) * 2011-07-28 2012-12-20 NMI Naturwissenschaftliches und Medizinisches Institut an der Universität Tübingen Method for the detection of biomolecules
GB201311057D0 (en) 2013-06-21 2013-08-07 Univ Greenwich Antisense oligonucleotide compositions
WO2015031628A1 (en) * 2013-08-28 2015-03-05 Oregon Health & Science University Synthetic oligonucleotides for detection of nucleic acid binding proteins
CN103472236B (en) * 2013-09-11 2015-06-03 深圳先进技术研究院 Method for detecting DNA (deoxyribonucleic acid) binding protein
WO2016058171A1 (en) * 2014-10-17 2016-04-21 Shanghai Sidansai Biotechnology Co.,Ltd Method for directional cloning
US10081829B1 (en) 2017-06-13 2018-09-25 Genetics Research, Llc Detection of targeted sequence regions
US10527608B2 (en) 2017-06-13 2020-01-07 Genetics Research, Llc Methods for rare event detection
US10947599B2 (en) 2017-06-13 2021-03-16 Genetics Research, Llc Tumor mutation burden
WO2018231955A2 (en) 2017-06-13 2018-12-20 Genetics Research, Llc, D/B/A Zs Genetics, Inc. Isolation of target nucleic acids
US20180355380A1 (en) * 2017-06-13 2018-12-13 Genetics Research, Llc, D/B/A Zs Genetics, Inc. Methods and kits for quality control

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
ES2089057T3 (en) * 1990-07-18 1996-10-01 Abbott Lab AN ANALYTE SUBSTITUTE REAGENT FOR USE IN SPECIFIC FIXATION TEST METHODS, DEVICES AND KITS.
US5518885A (en) * 1994-04-19 1996-05-21 The United States Of America As Represented By The Department Of Health & Human Services ERBB2 promoter binding protein in neoplastic disease
US5834236A (en) * 1996-06-27 1998-11-10 The Salk Institute For Biological Studies AATT repeat transcription enhancer element
US5939261A (en) * 1997-06-24 1999-08-17 Sarnoff Corporation Method for capturing a nucleic acid
US6312896B1 (en) * 1998-09-17 2001-11-06 Igen Inaternational, Inc. Assays for measuring nucleic acid binding proteins and enzyme activities
US6297013B1 (en) * 1999-06-24 2001-10-02 Dnab Diagnostics Inc. Compositions and methods for determining the activity of DNA-binding proteins and of initiation of transcription
DE60317315T2 (en) * 2002-03-28 2008-08-21 Marligen Biosciences, Inc. DETECTION OF DNA BINDING PROTEINS

Also Published As

Publication number Publication date
JP4425640B2 (en) 2010-03-03
CA2480646C (en) 2010-08-03
ATE377753T1 (en) 2007-11-15
EP1490682A1 (en) 2004-12-29
US20090208927A1 (en) 2009-08-20
US20030215854A1 (en) 2003-11-20
DE60317315T2 (en) 2008-08-21
EP1490682A4 (en) 2006-05-24
WO2003083476A1 (en) 2003-10-09
DK1490682T3 (en) 2008-03-25
AU2003226116B2 (en) 2010-04-01
JP2005521411A (en) 2005-07-21
DE60317315D1 (en) 2007-12-20
AU2003226116A1 (en) 2003-10-13
US7122317B2 (en) 2006-10-17
EP1490682B1 (en) 2007-11-07
US7771940B2 (en) 2010-08-10

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