Title	DNA-Protein Interactions [electronic resource] : Principles and Protocols, Third Edition
Author	edited by Benoît Leblanc, Tom Moss
Imprint	Totowa, NJ : Humana Press, 2009
Edition	3
Connect to	http://dx.doi.org/10.1007/978-1-60327-015-1
Descript	XVIII, 680 p. 131 illus. online resource

Gene expression can mean the difference between a functional and non-functional genome, between health and disease, and with the development of transgenic crops, the difference between survival and starvation. In DNA-Protein Interactions: Principles and Protocols, Third Edition, this vital subject is brought up to date with protocols exploring the most cutting-edge developments in the field, including in vivo and genome-wide interaction techniques. Addressing topics such as chromatin immunoprecipitation, topological studies, photocrosslinking, FRET and imaging techniques, the volume fully updates and expands upon the successful previous editions. Written in the convenient and informative Methods in Molecular Biology™ series format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Comprehensive and authoritative, DNA-Protein Interactions: Principles and Protocols, Third Edition serves as an ideal guide for all those exploring this dynamic, essential, and increasingly affordable area of research

Filter-Binding Assays -- Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions -- DNase I Footprinting -- Exonuclease III Footprinting on Immobilized DNA Templates -- Hydroxyl Radical Footprinting of Protein-DNA Complexes -- The Use of Diethyl Pyrocarbonate and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DNA -- Uranyl Photofootprinting -- Identification of Protein/DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference -- Ethylation Interference Footprinting of DNA-Protein Complexes -- Site-Directed Cleavage of DNA by Protein-Fe(II) EDTA Conjugates Within Model Chromatin Complexes -- Identification of Nucleic Acid High-Affinity Binding Sequences of Proteins by SELEX -- Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting -- Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper -- Determination of a Transcription Factor-Binding Site by Nuclease Protection Footprinting onto Southwestern Blots -- Use of a Reporter Gene Assay in Yeast for Genetic Analysis of DNA-Protein Interactions -- Chromatin Immunoprecipitation in Mammalian Cells -- Sequential Chromatin Immunoprecipitation Protocol: ChIP-reChIP -- Profiling Genome-Wide Histone Modifications and Variants by ChIP-chip on Tiling Microarrays in S. cerevisiae -- Nucleosome Mapping -- In Cellulo DNA Analysis (LMPCR Footprinting) -- Atomic Force Microscopy Imaging and Probing of DNA, Proteins, and Protein-DNA Complexes: Silatrane Surface Chemistry -- Two-Dimensional Crystallisation of Soluble Protein Complexes -- Assays for Transcription Factor Activity -- Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine -- Static and Kinetic Site-Specific Protein-DNA Photocrosslinking: Analysis of Bacterial Transcription Initiation Complexes -- Use of Site-Specific Protein-DNA Photocrosslinking of Purified Complexes to Analyze the Topology of the RNA Polymerase II Transcription Initiation Complex -- Site-Directed DNA Crosslinking of Large Multisubunit Protein-DNA Complexes -- Functional Studies of DNA-Protein Interactions Using FRET Techniques -- Single-Molecule FRET Analysis of Protein-DNA Complexes -- Analysis of DNA Supercoiling Induced by DNA-Protein Interactions -- The Cruciform DNA Mobility Shift Assay: A Tool to Study Proteins that Recognize Bent DNA -- Plasmid Vectors for the Analysis of Protein-Induced DNA Bending -- Analysis of Distant Communication on Defined Chromatin Templates In Vitro -- A Competition Assay for DNA Binding Using the Fluorescent Probe ANS -- Fluorescence Spectroscopy and Anisotropy in the Analysis of DNA-Protein Interactions -- Circular Dichroism for the Analysis of Protein-DNA Interactions -- Defining the Thermodynamics of Protein/DNA Complexes and Their Components Using Micro-calorimetry -- Surface Plasmon Resonance Assays of DNA-Protein Interactions