DNA’Protein Interactions: Principles and Protocols 2nd Edition

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