DNA-Protein Interactions is a novel compilation of methods for studying the interactions of proteins with DNA. It is a rapidly advancing research area in which multidisciplinary approaches are especially valuable for solving problems and obtaining a detailed understanding of the molecular regulatory interactions involved. This book covers all the major tools that are required for the study of the large macromolecular enzymatic machines that manipulate DNA, with particular emphasis on biophysical techniques applied to the analysis of transcription and its relation to chromatin structure. Knowledge of basic techniques is assumed, although advances in fundamental fields are covered.
Expression Systems; Gel electrophoresis and bending in cisplatin-modified linear DNA; Use of DNA microcircles in protein-DNA binding studies; Use of topology to measure protein-induced DNA bend and unwinding angles; Bandshift, gel retardation, or electrophoretic mobility shift assays; Practical aspects of Fluorescence Resonance Energy Transfer (FRET) and its applications in nucleic acid biochemistry; Determination of DNA-ligand interactions by fluorescence correlation spectroscopy; DNA wrapping in E. Coli RNA polymerase open promotor complexes revealed by scanning force microscopy; Microcalorimetry of protein-DNA interactions; DNA-protein cross-linking by formaldehyde: a probe for RNAP-open promoter complex structure; Solid-phase DNAse I footprinting; Hydroxyl radical footprinting; Radiolytic cleavage of DNA: Mapping of the Protein Interaction Sites; UV - Laser photoreactivity of nucleoprotein complexes in vitro; In vivo UV-laser footprinting; Digitization and quantitative analysis of footprinting gels; Mapping histone positions in chromatin by protein-directed DNA cross-linking and cleavage; Kinetics of DNA-protein interactions; Kinetics of DNA interactions studied by surface plasmon resonance spectroscopy; Quantitative DNase I Kinetics Footprinting; Real time fluorescence anisotropy for studying protein-DNA interactions; Analysis of protein-DNA interactions in complex nucleoprotein assemblies; Site-specific protein-DNA photocrosslinking; Visualization of protein-DNA complexes by cryo em and on grids; Characterization of T7 RNA polymerase protein-DNA interactions during the initiation and elongation phases
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