DNA-protein interactions : principles and protocols / edited by G. Geoff Kneale.

Includes bibliographical references and index.

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 [and others] -- 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 [and others] -- 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.

Print version record.

The clear and easy-to-follow protocols collected here illuminate the molecular basis of protein-nucleic acid interactions. Use them successfully to reveal the location of the DNA binding site, the strength and specificity of a binding, the identities of individual groups on the actual bases involved in binding, and the specific amino acid residues of the protein that interact with the DNA. Some of the techniques can even be used to identify previously unknown DNA binding proteins from crude cell extracts, thus empowering you to make groundbreaking advances in your work.

English.