DNA-protein interactions : principles and protocols / edited by Tom Moss and Benoît Leblanc.

Contributor(s): Moss, Tom (Thomas) | Leblanc, Benoît
Material type: TextTextSeries: Methods in molecular biology (Clifton, N.J.): volume 543.; Springer protocols (Series): Publisher: New York : Humana, ©2009Edition: 3rd edDescription: 1 online resource (xvii, 680 pages) : illustrationsContent type: text Media type: computer Carrier type: online resourceISBN: 9781603270151; 1603270159Subject(s): DNA-protein interactions -- Laboratory manuals | DNA Footprinting | Genetic Techniques | Nuclease Protection Assays | Investigative Techniques | Amino Acids, Peptides, and Proteins | Chemicals and Drugs | Analytical, Diagnostic and Therapeutic Techniques and Equipment | DNA-Binding Proteins | Proteins | DNA-protein interactions | dna | dna binding proteins | nucleic acids | moleculaire biologie | molecular biology | biologische technieken | biological techniques | protocollen | protocols | Nucleic AcidsGenre/Form: Laboratory Manual. | Electronic books. | Laboratory manuals. Additional physical formats: Print version:: DNA-protein interactions.DDC classification: 572.8/64 LOC classification: QP624.75.P74Online resources: Click here to access online
Contents:
Filter-binding assays / P.G. Stockley -- Electrophoretic mobility shift assays for the analysis of DNA-protein interactions / M. Gaudreault [and others] -- DNase I footprinting / B. Leblanc and T. Moss -- Exonuclease III footprinting on immobilized DNA templates / P. Spitalny and M. Thomm -- Hydroxyl radical footprinting of protein-DNA complexes / I. Jagannathan and J.J. Hayes -- The use of diethyl pyrocarbonate and potassium permanganate as probes for strand separation and structural distortions in DNA / B.F. Kahl and M.R. Paule -- Uranyl photofootprinting / P.E. Nielsen -- Identification of protein/DNA contacts with dimethyl sulfate: Methylation protection and methylation interference / P.E. Shaw and A.F. Stewart -- Ethylation interference footprinting of DNA-protein complexes / I.W. Manfield and P.G. Stockley -- Site-directed cleavage of DNA by protein-Fe(II) EDTA conjugates within model chromatin complexes / D.R. Chafin and J.J. Hayes -- Identification of nucleic acid high-affinity binding sequences of proteins by SELEX / P. Bouvet -- Identification of sequence-specific DNA-binding proteins by southwestern blotting / S. Labbe, J.F. Harrisson and C. Seguin -- Footprinting DNA-protein Interactions in native polyacrylamide gels by chemical nucleolytic activity of 1,10-phenanthroline-copper / A.G. Papavassiliou -- Determination of a transcription factor-binding site by nuclease protection footprinting onto southwestern Blots / A.G. Papavassiliou -- Use of a reporter gene assay in yeast for genetic analysis of DNA-protein interactions / D.R. Setzer [and others] -- Chromatin immunoprecipitation in mammalian cells / A. Svotelis, N. Gevry and L. Gaudreau -- Sequential chromatin immunoprecipitation protocol: ChIP-reChIP / M. Furlan-Magaril, H. Rincon-Arano and F. Recillas-Targa -- Profiling genome-wide histone modifications and variants by ChIP-chip on tiling microarrays in S. cerevisiae / A.R. Bataille and F. Robert -- Nucleosome mapping / N. Gevry [and others] -- In cellulo DNA analysis (LMPCR footprinting) / R. Drouin [and others] -- Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: silatrane surface chemistry / Y.L. Lyubchenko, L.S. Shlyakhtenko and A.A. Gall -- Two-dimensional crystallisation of soluble protein complexes / P. Schultz, C. Crucifix and L. Lebeau -- Assays for transcription factor activity / D. Browning [and others] -- Ultraviolet crosslinking of DNA protein complexes via 8-azidoadenine / R. Meffert [and others] -- Static and kinetic site-specific protein-DNA photocrosslinking: Analysis of bacterial transcription initiation complexes / N. Naryshkin [and others] -- Use of site-specific protein-DNA photocrosslinking of purified complexes to analyze the topology of the RNA polymerase II transcription initiation complex / D. Forget, C. Domecq and B. Coulombe -- Site-directed DNA crosslinking of large multisubunit protein-DNA complexes / J. Persinger and B. Bartholomew -- Functional studies of DNA-protein interactions using FRET techniques / S. Blouin [and others] -- Single-molecule FRET analysis of protein-DNA complexes / M. Heilemann [and others] -- Analysis of DNA supercoiling induced by DNA-protein interactions / D.J. Clark and B. Leblanc -- The cruciform DNA mobility shift assay: A tool to study proteins that recognize bent DNA / V.Y. Stefanovsky and T. Moss -- Plasmid vectors for the analysis of protein-induced DNA bending / C. Zwieb and S. Adhya -- Analysis of distant communication on defined chromatin templates in vitro / Y.S. Polikanov and V.M. Studitsky -- A competition assay for DNA binding using the fluorescent probe ANS / I.A. Taylor and G.G. Kneale -- Fluorescence spectroscopy and anisotropy in the analysis of DNA-protein interactions / R. Favicchio [and others] -- Circular dichroism for the analysis of protein-DNA interactions / P.D. Cary and G.G. Kneale -- Defining the thermodynamics of protein/DNA complexes and their components using micro-calorimetry / C. Crane-Robinson, A.I. Dragan and C.M. Read -- Surface plasmon resonance assays of DNA-protein interactions / P.G. Stockley and B. Persson.
Summary: Gene expression can mean the difference between a functional and non-functional genome, between health and disease, and with the development of transgenic crops, the difference between survival and starvation. In DNA-Protein Interactions: Principles and Protocols, Third Edition, this vital subject is brought up to date with protocols exploring the most cutting-edge developments in the field, including in vivo and genome-wide interaction techniques. Addressing topics such as chromatin immunoprecipitation, topological studies, photocrosslinking, FRET and imaging techniques, the volume fully updates and expands upon the successful previous editions. Written in the convenient and informative Methods in Molecular Biology series format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and authoritative, DNA-Protein Interactions: Principles and Protocols, Third Edition serves as an ideal guide for all those exploring this dynamic, essential, and increasingly affordable area of research.
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Previous edition: published as DNA-protein interaction protocols. 2000.

Includes bibliographical references and index.

Filter-binding assays / P.G. Stockley -- Electrophoretic mobility shift assays for the analysis of DNA-protein interactions / M. Gaudreault [and others] -- DNase I footprinting / B. Leblanc and T. Moss -- Exonuclease III footprinting on immobilized DNA templates / P. Spitalny and M. Thomm -- Hydroxyl radical footprinting of protein-DNA complexes / I. Jagannathan and J.J. Hayes -- The use of diethyl pyrocarbonate and potassium permanganate as probes for strand separation and structural distortions in DNA / B.F. Kahl and M.R. Paule -- Uranyl photofootprinting / P.E. Nielsen -- Identification of protein/DNA contacts with dimethyl sulfate: Methylation protection and methylation interference / P.E. Shaw and A.F. Stewart -- Ethylation interference footprinting of DNA-protein complexes / I.W. Manfield and P.G. Stockley -- Site-directed cleavage of DNA by protein-Fe(II) EDTA conjugates within model chromatin complexes / D.R. Chafin and J.J. Hayes -- Identification of nucleic acid high-affinity binding sequences of proteins by SELEX / P. Bouvet -- Identification of sequence-specific DNA-binding proteins by southwestern blotting / S. Labbe, J.F. Harrisson and C. Seguin -- Footprinting DNA-protein Interactions in native polyacrylamide gels by chemical nucleolytic activity of 1,10-phenanthroline-copper / A.G. Papavassiliou -- Determination of a transcription factor-binding site by nuclease protection footprinting onto southwestern Blots / A.G. Papavassiliou -- Use of a reporter gene assay in yeast for genetic analysis of DNA-protein interactions / D.R. Setzer [and others] -- Chromatin immunoprecipitation in mammalian cells / A. Svotelis, N. Gevry and L. Gaudreau -- Sequential chromatin immunoprecipitation protocol: ChIP-reChIP / M. Furlan-Magaril, H. Rincon-Arano and F. Recillas-Targa -- Profiling genome-wide histone modifications and variants by ChIP-chip on tiling microarrays in S. cerevisiae / A.R. Bataille and F. Robert -- Nucleosome mapping / N. Gevry [and others] -- In cellulo DNA analysis (LMPCR footprinting) / R. Drouin [and others] -- Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: silatrane surface chemistry / Y.L. Lyubchenko, L.S. Shlyakhtenko and A.A. Gall -- Two-dimensional crystallisation of soluble protein complexes / P. Schultz, C. Crucifix and L. Lebeau -- Assays for transcription factor activity / D. Browning [and others] -- Ultraviolet crosslinking of DNA protein complexes via 8-azidoadenine / R. Meffert [and others] -- Static and kinetic site-specific protein-DNA photocrosslinking: Analysis of bacterial transcription initiation complexes / N. Naryshkin [and others] -- Use of site-specific protein-DNA photocrosslinking of purified complexes to analyze the topology of the RNA polymerase II transcription initiation complex / D. Forget, C. Domecq and B. Coulombe -- Site-directed DNA crosslinking of large multisubunit protein-DNA complexes / J. Persinger and B. Bartholomew -- Functional studies of DNA-protein interactions using FRET techniques / S. Blouin [and others] -- Single-molecule FRET analysis of protein-DNA complexes / M. Heilemann [and others] -- Analysis of DNA supercoiling induced by DNA-protein interactions / D.J. Clark and B. Leblanc -- The cruciform DNA mobility shift assay: A tool to study proteins that recognize bent DNA / V.Y. Stefanovsky and T. Moss -- Plasmid vectors for the analysis of protein-induced DNA bending / C. Zwieb and S. Adhya -- Analysis of distant communication on defined chromatin templates in vitro / Y.S. Polikanov and V.M. Studitsky -- A competition assay for DNA binding using the fluorescent probe ANS / I.A. Taylor and G.G. Kneale -- Fluorescence spectroscopy and anisotropy in the analysis of DNA-protein interactions / R. Favicchio [and others] -- Circular dichroism for the analysis of protein-DNA interactions / P.D. Cary and G.G. Kneale -- Defining the thermodynamics of protein/DNA complexes and their components using micro-calorimetry / C. Crane-Robinson, A.I. Dragan and C.M. Read -- Surface plasmon resonance assays of DNA-protein interactions / P.G. Stockley and B. Persson.

Print version record.

Gene expression can mean the difference between a functional and non-functional genome, between health and disease, and with the development of transgenic crops, the difference between survival and starvation. In DNA-Protein Interactions: Principles and Protocols, Third Edition, this vital subject is brought up to date with protocols exploring the most cutting-edge developments in the field, including in vivo and genome-wide interaction techniques. Addressing topics such as chromatin immunoprecipitation, topological studies, photocrosslinking, FRET and imaging techniques, the volume fully updates and expands upon the successful previous editions. Written in the convenient and informative Methods in Molecular Biology series format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and authoritative, DNA-Protein Interactions: Principles and Protocols, Third Edition serves as an ideal guide for all those exploring this dynamic, essential, and increasingly affordable area of research.

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