DNA-protein interactions : principles and protocols

DNase I footprinting / Benoit Leblanc, Tom Moss -- Footprinting with exonuclease III / Willi Metzger, Hermann Heumann -- Hydroxyl radical footprinting / Peter Schickor, Hermann Heumann -- Hydroxyl radical interference / Peter Schickor, Hermann Heumann -- 1,10-phenanthroline-copper ion nuclease footprinting of DNA-protein complexes in situ following mobility-shift electrophoresis assays / Athanasios G. Papavassilou -- Identification of protein-DNA contacts with dimethyl sulfate: methylation protection and methylation interference / Peter E. Shaw, A. Francis Stewart -- Diethyl pyrocarbonate as a probe of protein-DNA interactions / Michael J. McLean -- Osmium tetroxide modification and the study of DNA-protein interactions / James A. McClellan -- Diffusible singlet oxygen as a probe of DNA deformation / Malcolm Buckle, Andrew A. Travers -- Ethylation interference / Iain Manfield, Peter G. Stockley -- Uranyl photofootprinting of DNA-protein complexes / Peter E. Nielsen -- Nitration of tyrosine residues in protein-nucleic acid complexes / Simon E. Plyte -- Limited proteolysis of protein-nucleic acid complexes / Simon E. Plyte, G. Geoff Kneale -- Cloning and expression of DNA binding domains using PCR / Daniel G. Fox, G. Geoff Kneale -- Overexpression and purification of eukaryotic transcription factors as glutathione-S-transferase fusions in E. coli / Kevin G. Ford, Alan J. Whitmarsh, David P. Hornby -- Site-directed mutagenesis by the cassette method / Andrew F. Worrall -- Site-directed and site-saturation mutagenesis using oligonucleotide primers / Michael J. O'Donohue, G. Geoff Kneale -- UV laser-induced protein-DNA crosslinking / Stefan I. Dimitrov, Tom Moss -- Ultraviolet crosslinking of DNA-protein complexes via 8-azidoadenine / Rainer Meffert ... [et al.] -- Filter-binding assays / Peter G. Stockley -- Gel shift assay for the analysis of DNA-protein interactions / John D. Taylor, Alison J. Ackroyd, Stephen E. Halford -- Improved plasmid vectors for the analysis of protein-induced DNA bending / Christian Zwieb, Sankar Adhya -- Determination of sequence preferences of DNA binding proteins using pooled solid-phase sequencing of low degeneracy oligonucleotide mixtures / Joseph A. Gogos, Fotis C. Kafatos -- Analysis of DNA-protein interactions by intrinsic fluorescence / Mark L. Carpenter, G. Geoff Kneale -- A competition assay for DNA binding using the fluorescent probe ANS / Ian Taylor, G. Geoff Kneale -- Circular dichroism for the analysis of protein-DNA interactions / Mark L. Carpenter, G. Geoff Kneale -- Electron microscopy of protein-nucleic acid complexes : uniform spreading and determination of helix handedness / Carla W. Gray -- Reconstitution of protein-DNA complexes for crystallization / Rachel M. Conlin, Raymond S. Brown -- Assay of restriction endonucleases using oligonucleotides / Bernard A. Connolly -- Assays for restriction endonucleases using plasmid substrates / Stephen E. Halford ... [et al.] -- Assays for transcription factor activity / Stephen Busby, Annie Kolb, Stephen Minchin -- An assay for in vitro recombination between duplex DNA molecules / Berndt Muller, Stephen C. West