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.
Filter-Binding Assays Peter G. Stockley Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions Marc-Andre Laniel, Alain Beliveau, and Sylvain L. Guerin DNase I Footprinting, Benoit Leblanc and Tom Moss. Footprinting with Exonuclease III Willi Metzger and Hermann Heumann Hydroxyl Radical Footprinting Evgeny Zaychikov, Peter Schickor, Ludmilla Denissova, and Hermann Heumann The Use of Diethyl Pyrocarbonate and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DNA Brenda F. Kahl and Marvin R. Paule Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10 -Phenanthroline-Copper Athanasios G. Papavassilou Uranyl Photofootprinting Peter E. Nielsen Osmium Tetroxide Modification and the Study of DNA-Protein Interactions James A. McClellan Determination of a Transcription Factor-Binding Site by Nuclease Protection Footprinting onto Southwestern Blots Athanasios G. Papavassilou Diffusible Singlet Oxygen as a Probe of DNA Deformation Malcolm Buckle and Andrew A. Travers Ultraviolet-Laser Footprinting Johannes Geiselmann and Frederic Boccard In Vivo DNA Analysis Regen Drouin, Jean-Philippe Therrien, Martin Angers, and Stephane Ouellet Identification of Protein-DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference Peter E. Shaw and A. Francis Stewart Ethylation Interference Iain W. Manfield and Peter G. Stockley Hydroxyl Radical Interference Peter Schickor, Evgeny Zaychiko, and Hermann Heumann Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting Simon Labbe, Gale Stewart, Olivier LaRochelle, Guy G. Poirier, and Carl Seguin A Competition Assay for DNA Binding Using the Fluorescent Probe ANS Ian Taylor and G. Geoff Kneale Site-Directed Cleavage of DNA by Linker Histone Protein-Fe(II) EDTA Conjugates David R. Chafin and Jeffrey J. Hayes Nitration of Tyrosine Residues in Protein-Nucleic Acid Complexes Simon E. Plyte Chemical Modification of Lysine by Reductive Methylation: A Probe of Residues Involved in DNA Binding Ian A. Taylor and Michelle Webb Limited Proteolysis of Protein-Nucleic Acid Complexes Simon E. Plyte and G. Geoff Kneale Ultraviolet Crosslinking of DNA-Protein Complexes Via 8-Azidoadenine Rainer Meffert, Klaus Dose, Gabriele Rathgeber, and Hans-Jochen Schafer Site-Specific Protein-DNA Photocrosslinking: Analysis of Bacterial Transcription Initiation Complexes Nikolai Naryshkin, Younggyu Kim, Qianping Dong, and Richard H. Ebright Site-Directed DNA Photoaffinity Labeling of RNA Polymerase II Transcription Complexes Jim Persinger and Blaine Bartholomew Use of Site-Specific Protein-DNA Photocrosslinking to Analyze the Molecular Organization of the RNA Polymerase II Initiation Complex Francois Robert and Benoit Coulombe UV Laser-Induced Protein-DNA Crosslinking Stefan I. Dimitrov and Tom Moss Plasmid Vectors for the Analysis of Protein-Induced DNA Bending Christian Zwieb and Sankar Adhya Engineering Nucleic Acid-Binding Proteins by Phage Display Mark Isalan and Yen Choo Genetic Analysis of DNA-Protein Interactions Using a Reporter Gene Assay in Yeast David R. Setzer, Deborah B. Schulman, and Michael J. Bumbulis Assays for Transcription Factor Activity Virgil Rhodius, Nigel Savery, Annie Kolb, and Stephen Busby Assay of Restriction Endonucleases Using Oligonucleotides Bernard A. Connolly, Hsiao-Hui Liu, Damian Parry, Lisa E. Engler, Michael R. Kurpiewski, and Linda Jen-Jacobson Analysis of DNA-Protein Interactions by Intrinsic Fluorescence Mark L. Carpenter, Anthony W. Oliver and G. Geoff Kneale Circular Dichroism for the Analysis of Protein-DNA Interactions Mark L. Carpenter, Anthony W. Oliver, and G. Geoff Kneale Calorimetry of Protein-DNA Complexes and Their Components Christopher M. Read and Ilian Jelesarov Surface Plasmon Resonance Applied to DNA-Protein Complexes Malcolm Buckle Reconstitution of Protein-DNA Complexes for Crystallization Rachel M. Conlin and Raymond S. Brown Two-Dimensional Crystallization of Soluble Protein Complexes Patrick Schultz, Nicolas Bischler, and Luc Lebeau Atomic Force Microscopy of DNA and Protein-DNA Complexes Using Functionalized Mica Substrates Yuri L. Lyubchenko, Alexander A. Gall, and Luda S. Shlyakhtenko Electron Microscopy of Protein-Nucleic Acid Complexes: Uniform Spreading of Flexible Complexes, Staining with a Uniform Thin Layer of Uranyl Acetate and Determining Helix Handedness Carla W. Gray Scanning Transmission Electon Microscopy of DNA-Protein Complexes Joseph S. Wall and Martha N. Simon Determination of Nuleic Acid Recognition Sequences by SELEX Philippe Bouvet High DNA-Protein Crosslinking Yield with Two-Wavelength Femtosecond Laser Irradiation Christoph Russmann, Rene Beigang, and Miguel Beato Appendices: I. EMSA/Gel Shift Conditions. II. DNA-Modification/Cleavage Reagents Index.