Title DNA-protein interactions : principles and protocols / edited by Tom Moss

Edition 2nd ed Published Totowa, N.J. : Humana Press, ©2001

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Description 1 online resource (xvii, 638 pages) : illustrations Series Methods in molecular biology ; v. 148 Methods in molecular biology (Clifton, N.J.) ; v. 148. Contents Filter-binding assays / Peter G. Stockley -- Electrophoretic mobility shift assays for the analysis of DNA-protein interactions / Marc-André, Alain Béliveau, and Sylvain L. Guérin -- DNase I footprinting / Benoît Leblanc and Tom Moss -- Footprinting with exonuclease III / Willi Metzger and Hermann Heumann -- Hydroxyl redical footprinting / Evgeny Zaychikov [and others] -- Use of diethyl pyrocaaarbonate and potassium permanganate as probes for strand separation and structural disstortions in DNA / Brenda F. Kahl and Marvin R. Paule -- Footprinting DNA-protein interactions in native polyacrylamide gels by chemical nucleolytic activity of 1,10-phenanthroline-copper / Athanasios G. Papavassilious -- Uranyl photofootpriting / Peter E. Nielsen -- Osmium tetroxide modification and the study of DNA-interactions / James A. McClellan -- Setermination of a transcription-factor-binding site by nuclease protection footprinting onto southwestern blots / Athanasios G. Papavassiliou -- Diffusible signlet oxygen as a probe of DNA deformation / Malcome Buckle and Andrew A. Travers -- Ultraviolet-laser footorinting / Johannes Geiselmann and Frederic Boccard -- In vivo DNA analysis / Régen Drouin [and others] -- Identification of protein-DNA contacts with dimethyl sulfate: methylation protection and methylation interference / Peter E. Shaw and A. Francis Stewart -- Ethylation interference / Iaain W. Mnfield and Peter G. Stockley -- Hydroxyl radical interference / Peter Schickor, evgeny Zaychikov, and Hermann Heumann -- Identification of sequence-specific DNA-binding proteins by southwestern blotting / Simon Labbeé [and others] -- Competition assay for DNA binding using the fluorescent probe ANS / Ian A. Taylor and G. Geoff Kneale -- Site-directed cleavage of DNA by linker histone-fe(II) EDTA conjugates / David R. Chafin and Jeffrey J. Hayes -- Nitration of tyrosine residues in protein-nucleic acid complexes / Simon E. Plyte -- Chemical modification of lysine by reductive methylation: a probe of residues involved in DNA binding / Ian A. Taylor and Michelle Webb -- Limited proteolysis of protein-nucleic acid complexes / Simon E. Plyte and G. Geoff Kneale -- Ultraviolet crosslinking of DNA-protein complexes via 8-azidoadenine / Rainer Meffert [and others] -- Site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes / Nikolai Naryshkin [and others] -- Site-directed DNA photoaffinity labeling of RNA polymerase III transcription complexes / Jim Persinger and Blaine Bartholomew -- Use of site-specific protein-DNA photocrosslinking to analyze the molecular organization of the RNA polymerase II initiation complex / François Robert and Benoît Coulombe -- UV laser-induced protein-DNA crosslinking / Stefan I. Dimitrov and Tom Moss -- Plasmid vectors for the analysis of protein-induced DNA bending / Christian Zwieb and Sankar Adhya -- Engineering nucleic acid-binding proteins by phage display / Mark Isalan and Yen Choo -- Genetic analysis of DNA-protein interactions using a reporter gene assay in yeast / David R. Setzer, Doborah B. Schulman, and Michael J. Bumbulis -- Assays for transcription factor activity / Virgil Rhodius [and others] -- Essay of restriction endonucleases using oligonucleotides / Berbard A. Connolly [and others] -- Analysis of DNA-protein interactions by intrinsic fluorescence / Mark L. Carpenter, Anthony W. Oliver, and G. Geoff Kneale -- Circular dichroism for the analysis of protein-DNA interactions / Nark L. Carpenter, Anthony W. Oliver, and G. Geoff Kneale -- Calorimetry of protein-DNA complexes and their components / Christopher M. Read and Ilian Jelesarov -- Surface plasmon resonance applied to DNA-protein complexes / Malcolm Buckle -- Reconstitution of protein-DNA complexes for crystallization / Rachel M. Conlin and Raymond S. Brown -- Two-dimensional crystallization of soluble protein complexes / Patrick Schultz, Nicolas Bischler, and Luc Lebeau -- Atomic force microscopy of DNA and protein-DNA complexes using functionalized mica substrates / Yuri L. Lyubchenko, Alexander A. Gall, and Luda S. Shlyakhtenko -- Electron microscopy of protein-nucleic acid complexes: uniform spreading of flexible complexes, staining with a uniform thin layer of uranyl acetate, and determining helix handedness / Carla W. Gray -- Scanning transmission electron microscopy of DNA-protein complexes / Joseph S. Wall and Martha N. Simon -- Determination of nucleic acid recognition sequences by SELEX / Philippe Bouvet -- High DNA-protein crosslinking yield with two-wavelength femtosecond laser irradiation / Christoph Russmann, Rene Beigang, and Miguel Beato Summary DNA-protein interactions are fundamental to understanding biological growth, development, differentiation, evolution, and disease, and are also increasingly important to the biotechnology industry. In DNA-Protein Interactions: Principles and Protocols, 2nd Edition, Dr. Tom Moss assembles the new standard collection of cutting-edge techniques to identify key protein-DNA interactions, define their components, and determine the nature of their interactions and their manner of function, both in the cell and in the test tube. Each detailed method has been optimized and tested by a hands-on expert to ensure experimental success, and provides helpful notes on pitfalls to avoid, as well as alternate strategies. The techniques span a wide range, from factor identification to atomic detail, and include multiple DNA footprinting analyses, including in vivo strategies, gel shift (EMSA) optimization, SELEX, surface plasmon resonance, site-specific DNA-protein crosslinking, and UV laser crosslinking. There are also vanguard methods for designing proteins to fit DNA, site-specific protein-directed DNA cleavage, and 2D semicrystalline arrays of nucleoproteins for structure determination. Comprehensive and broad ranging, DNA-Protein Interactions: Principles and Protocols, 2nd Edition, offers a stellar array of over 100 up-to-date and readily reproducible techniques that biochemists and molecular, cellular, and developmental biologists can use successfully today to illuminate DNA-protein interactions Analysis dna eiwitten proteins interacties interactions Biochemistry Biochemie Bibliography Includes bibliographical references and index Notes Print version record Subject DNA-protein interactions. DNA-Binding Proteins -- genetics DNA Footprinting -- methods DNA-Binding Proteins -- chemistry SCIENCE -- Life Sciences -- Genetics & Genomics. DNA-protein interactions Genre/Form Laboratory manuals Laboratory manuals. Manuels de laboratoire. Form Electronic book Author Moss, Tom LC no. 00054100 ISBN 9781592592081 1592592082 0585403228 9780585403229 0896036251 9780896036253 0896036715 9780896036710

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