DNA'Protein Interactions

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.