DNA'Protein Interactions: Principles and Protocols / Edition 2

by Tom Moss

Overview

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 Prools, 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.

Product Details

ISBN-13:	9781617371257
Publisher:	Springer-Verlag New York, LLC
Publication date:	09/22/2011
Series:	Methods in Molecular Biology , #148
Edition description:	2nd ed. 2001
Pages:	638
Product dimensions:	5.98(w) x 9.02(h) x 0.06(d)

Table of Contents

Filter-Binding Assays

Peter G. Skley

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. Skley

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 Phorosslinking: 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 Phorosslinking 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.

Editorial Reviews

"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

From the Publisher

Assembles a collection of some 100 techniques for identifying key protein-DNA interactions and defining their components, their manner of interaction, and their manner of function, both in the cell and in the test tube. Techniques span a wide range, from factor identification to atomic detail, and include multiple DNA footprinting analyses, gel shift (EMSA) optimization, SELEX, surface plasmon resonance, site-specific DNA-protein crosslinking, and UV laser crosslinking. For biochemists and molecular, cellular, and developmental biologists. Moss is affiliated with the Center for Cancer Research at the University of Laval, France. Annotation c. Book News, Inc., Portland, OR (booknews.com)

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