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
Peter G. Stockley
Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions
Marc-André Laniel, Alain Béliveau, and Sylvain L. Guérin
DNase I Footprinting, Benoît 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
Régen Drouin, Jean-Philippe Therrien, Martin Angers, and Stéphane 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 Labbé, Gale Stewart, Olivier LaRochelle, Guy G. Poirier, and Carl Séguin
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 Schäfer
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
François Robert and Benoît 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.
Review :
"The topics are organized in a sensible linear manner, starting with elementary protein-DNA binding assays such as filter binding and EMSA, leading to footprinting techniques for the identification of individual contacts and DNA distortion, through more complex crosslinking and spectroscopic methods, to the final chapters on crystallization and some highly specialized biophysical techniques such as force microscopy....this book will find favor with both the novice and the expert; the former will learn techniques that will be useful for many years whilst the latter will be inspired by discovering new applications." - Molecular Biotechnology
