DNA-protein interactions : principles and protocols

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 ...[et al.] -- 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 ...[et al.] -- 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 ...[et al.] -- 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 ...[et al.] -- Site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes / Nikolai Naryshkin ...[et al.] -- 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 ...[et al.] -- Essay of restriction endonucleases using oligonucleotides / Berbard A. Connolly ...[et al.] -- 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.