DNA’Protein Interactions: Principles and Protocols 2nd Edition
By Tom Moss
DNA’Protein Interactions: Principles and Protocols 2nd Edition PDF. 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
Preface
Contributors
1 Filter-Binding Assays
Peter G. Stockley
2 Electrophoretic Mobility Shift Assays for the Analysis
of DNA–Protein Interactions
Marc-André Laniel, Alain Béliveau, and Sylvain L. Guérin
3 DNase I Footprinting
Benoît Leblanc and Tom Moss
4 Footprinting with Exonuclease III
Willi Metzger and Hermann Heumann.
5 Hydroxyl Radical Footprinting
Evgeny Zaychikov, Peter Schickor, Ludmilla Denissova,
and Hermann Heumann
6 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
7 Footprinting DNA–Protein Interactions in Native Polyacrylamide Gels
by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper
Athanasios G. Papavassiliou
8 Uranyl Photofootprinting
Peter E. Nielsen
9 Osmium Tetroxide Modification and the Study
of DNA–Protein Interactions
James A. McClellan
10 Determination of a Transcription-Factor-Binding Site by Nuclease
Protection Footprinting onto Southwestern Blots
Athanasios G. Papavassiliou
11 Diffusible Singlet Oxygen as a Probe of DNA Deformation
Malcolm Buckle and Andrew A. Travers
12 Ultraviolet-Laser Footprinting
Johannes Geiselmann and Frederic Boccard
13 In Vivo DNA Analysis
Régen Drouin, Jean-Philippe Therrien, Martin Angers,
and Stéphane Ouellet
14 Identification of Protein–DNA Contacts with Dimethyl Sulfate:
Methylation Protection and Methylation Interference
Peter E. Shaw and A. Francis Stewart
15 Ethylation Interference
Iain W. Manfield and Peter G. Stockley
16 Hydroxyl Radical Interference
Peter Schickor, Evgeny Zaychikov, and Hermann Heumann
17 Identification of Sequence-Specific DNA-Binding Proteins
by Southwestern Blotting
Simon Labbé, Gale Stewart, Olivier LaRochelle,
Guy G. Poirier, and Carl Séguin
18 A Competition Assay for DNA Binding Using the Fluorescent
Probe ANS
Ian A. Taylor and G. Geoff Kneale
19 Site-Directed Cleavage of DNA by Linker Histone Protein-Fe(II)
EDTA Conjugates
David R. Chafin and Jeffrey J. Hayes
20 Nitration of Tyrosine Residues in Protein–Nucleic Acid Complexes
Simon E. Plyte
21 Chemical Modification of Lysine by Reductive Methylation:
A Probe of Residues Involved in DNA Binding
Ian A. Taylor and Michelle Webb
22 Limited Proteolysis of Protein–Nucleic Acid Complexes
Simon E. Plyte and G. Geoff Kneale
23 Ultraviolet Crosslinking of DNA–Protein Complexes
via 8-Azidoadenine
Rainer Meffert, Klaus Dose, Gabriele Rathgeber,
and Hans-Jochen Schäfer
24 Site-Specific Protein–DNA Photocrosslinking: Analysis of Bacterial
Transcription Initiation Complexes
Nikolai Naryshkin, Younggyu Kim, Qianping Dong,
and Richard H. Ebright
25 Site-Directed DNA Photoaffinity Labeling of RNA Polymerase III
Transcription Complexes
Jim Persinger and Blaine Bartholomew
26 Use of Site-Specific Protein–DNA Photocrosslinking to Analyze
the Molecular Organization of the RNA Polymerase
II Initiation Complex
François Robert and Benoît Coulombe
27 UV Laser-Induced Protein–DNA Crosslinking
Stefan I. Dimitrov and Tom Moss
28 Plasmid Vectors for the Analysis of Protein-Induced
DNA Bending
Christian Zwieb and Sankar Adhya
29 Engineering Nucleic Acid-Binding Proteins by Phage Display
Mark Isalan and Yen Choo
30 Genetic Analysis of DNA–Protein Interactions Using a Reporter
Gene Assay in Yeast
David R. Setzer, Deborah B. Schulman,
and Michael J. Bumbulis
31 Assays for Transcription Factor Activity
Virgil Rhodius, Nigel Savery, Annie Kolb,
and Stephen Busby
32 Assay of Restriction Endonucleases Using Oligonucleotides
Bernard A. Connolly, Hsiao-Hui Liu, Damian Parry,
Lisa E. Engler, Michael R. Kurpiewski,
and Linda Jen-Jacobson
33 Analysis of DNA–Protein Interactions by Intrinsic Fluorescence
Mark L. Carpenter, Anthony W. Oliver, and G. Geoff Kneale
34 Circular Dichroism for the Analysis of Protein–DNA Interactions
Mark L. Carpenter, Anthony W. Oliver, and G. Geoff Kneale
35 Calorimetry of Protein–DNA Complexes and Their Components
Christopher M. Read and Ilian Jelesarov
36 Surface Plasmon Resonance Applied to DNA–Protein Complexes
Malcolm Buckle
37 Reconstitution of Protein–DNA Complexes for Crystallization
Rachel M. Conlin and Raymond S. Brown
38 Two-Dimensional Crystallization of Soluble Protein Complexes
Patrick Schultz, Nicolas Bischler, and Luc Lebeau
39 Atomic Force Microscopy of DNA and Protein–DNA Complexes
Using Functionalized Mica Substrates
Yuri L. Lyubchenko, Alexander A. Gall,
and Luda S. Shlyakhtenko
40 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
41 Scanning Transmission Electon Microscopy
of DNA–Protein Complexes
Joseph S. Wall and Martha N. Simon
42 Determination of Nuleic Acid Recognition Sequences by SELEX
Philippe Bouvet
43 High DNA–Protein Crosslinking Yield with Two-Wavelength
Femtosecond Laser Irradiation
Christoph Russmann, Rene Beigang, and Miguel Beato
Appendices:
Appendix I: EMSA/Gel Shift Conditions
Appendix II: DNA-Modification/Cleavage Reagents
Index
