About the Book
Dr. Tom Moss assembles the new standard collection of cutting-edge techniques to identify key protein DNA interactions and define their components, their manner of interaction, and their manner of function, both in the cell and in the test tube. 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. 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 understand DNA protein interactions.
Table of Contents:
Filter-Binding Assays, Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions, DNase I Footprinting, Footprinting with Exonuclease III, Hydroxyl Radical Footprinting, The Use of Diethyl Pyrocarbonate (DEPC) and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DNA, Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper, Uranyl Photofootprinting, Osmium Tetroxide Modification and the Study of DNA-Protein Interactions, Determination of a Transcription Factor-Binding Site by Nuclease Protection Footprinting Onto Southwestern Blots, Diffusible Singlet Oxygen as a Probe of DNA Deformation, UV-Laser Footprinting, Determination of Nucleic Acid Recognition Sequences by SELEX, Identification of Protein-DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference, Ethylation Interference, Hydroxyl Radical Interference, Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting, A Competition Assay for DNA Binding Using the Fluorescent Probe ANS, Site-Directed Cleavage of DNA Protein-Fe(II) EDTA Conjugates, Nitration of Tyrosine Residues in Protein-Nucleic Acid Complexes, Chemical Modification of Lysine by Reductive Methylation; a Probe of Residues Involved in DNA Binding, Limited Proteolysis of Protein-Nucleic Acid Complexes, Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine, Site-Specific Protein-DNA Photocrosslinking: Analysis of Bacterial Transcription Initiation Complexes, Site Directed DNA Photoaffinity Labeling of RNA Polymerase III Transcription Complexes, The Use of Site-Specific Protein-DNA Photo-Crosslinking to Analyze the Molecular Organization of the RNA Polymerase II Initiation Complex, UV Laser-Induced Protein-DNA Crosslinking, Plasmid Vectors for the Analysis of Protein-Induced DNA Bending, Engineering Nucleic Acid-Binding Proteins Genetic Analysis Of DNA-Protein Interactions Using A Reporter Gene Assay In Yeast, Assays for Transcription Factor Activity, Assay of Restriction Endonucleases Using Oligonucleotides, Analysis of DNA-Protein Interactions by Intrinsic Fluorescence, Circular Dichroism for the Analysis of Protein-DNA Interactions, Calorimetry of Protein-DNA Complexes and Their Components, Surface Plasmon Resonance Applied to DNA-Protein Complexes, Reconstitution of Protein-DNA Complexes for Crystallization, 2D Crystal Arrays in Protein Structure Studies, Atomic Force Microscopy of DNA and Protein-DNA Complexes Using Functionalized Mica Substrates, Electron Microscopy of Protein-Nucleic Acid Complexes: Uniform Spreading of Flexible Complexes, Staining With a Uniform Thin Layer of Uranyl Acetate and Determination of Helix Handedness, Scanning Transmission Electron Microscopy of DNA-Protein Complexes, High DNA-Protein Crosslinking Yield With Two-Wavelength Femtosecond (TWF) Laser Irradiation,
Review :
The book, written by an impressive list of worldwide contributors, will provide readers with nearly all the necessary tools for studying DNA-protein interactions, making it a perfect cell laboratory manual. - Quarterly Review of Biology
