CA2480646A1 - Detection of dna-binding proteins - Google Patents
Detection of dna-binding proteins Download PDFInfo
- 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
- Authority
- 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
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
- C12Q1/34—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase
- C12Q1/44—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving hydrolase involving esterase
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
- G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6875—Nucleoproteins
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
- G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
- G01N2333/46—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans from vertebrates
- G01N2333/47—Assays involving proteins of known structure or function as defined in the subgroups
- G01N2333/4701—Details
- G01N2333/4703—Regulators; Modulating activity
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
- G01N2333/90—Enzymes; Proenzymes
- G01N2333/914—Hydrolases (3)
- G01N2333/916—Hydrolases (3) acting on ester bonds (3.1), e.g. phosphatases (3.1.3), phospholipases C or phospholipases D (3.1.4)
- G01N2333/922—Ribonucleases (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.
(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.
(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.
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.
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)
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)
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 |
-
2003
- 2003-03-28 DE DE60317315T patent/DE60317315T2/en not_active Expired - Lifetime
- 2003-03-28 DK DK03745653T patent/DK1490682T3/en active
- 2003-03-28 AT AT03745653T patent/ATE377753T1/en active
- 2003-03-28 EP EP03745653A patent/EP1490682B1/en not_active Expired - Lifetime
- 2003-03-28 CA CA2480646A patent/CA2480646C/en not_active Expired - Fee Related
- 2003-03-28 US US10/400,670 patent/US7122317B2/en not_active Expired - Fee Related
- 2003-03-28 AU AU2003226116A patent/AU2003226116B2/en not_active Ceased
- 2003-03-28 JP JP2003580858A patent/JP4425640B2/en not_active Expired - Fee Related
- 2003-03-28 WO PCT/US2003/009604 patent/WO2003083476A1/en active IP Right Grant
-
2006
- 2006-10-16 US US11/549,830 patent/US7771940B2/en not_active Expired - Fee Related
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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Legal Events
Date | Code | Title | Description |
---|---|---|---|
EEER | Examination request | ||
MKLA | Lapsed |
Effective date: 20130328 |