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Life Sciences - Cell Biology | DNA'Protein Interactions - Principles and Protocols

DNA'Protein Interactions

Principles and Protocols

Series: Methods in Molecular Biology, Vol. 148

Moss, Tom (Ed.)

2nd ed. 2001, XVII, 638 p.

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DNA-protein interactions are fundamental to understanding biological growth, development, differentiation, evolution, and disease, and are also increasingly important to the biotechnology industry. In DNA-Protein Interactions: Principles and Protocols, 2nd Edition, Dr. Tom Moss assembles the new standard collection of cutting-edge techniques to identify key protein-DNA interactions, define their components, and determine the nature of their interactions and their manner of function, both in the cell and in the test tube. Each detailed method has been optimized and tested by a hands-on expert to ensure experimental success, and provides helpful notes on pitfalls to avoid, as well as alternate strategies. 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. There are also vanguard methods for designing proteins to fit DNA, site-specific protein-directed DNA cleavage, and 2D semicrystalline arrays of nucleoproteins for structure determination.
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 illuminate DNA-protein interactions.

Content Level » Research

Related subjects » Cell Biology

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


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