DNA-Protein Interactions Principles and Protocols

About this book

Gene expression can mean the difference between a functional and non-functional genome, between health and disease, and with the development of transgenic crops, the difference between survival and starvation.

In "DNA-Protein Interactions: Principles and Protocols, Third Edition", this vital subject is brought up to date with protocols exploring the most cutting-edge developments in the field, including in vivo and genome-wide interaction techniques. Addressing topics such as chromatin immunoprecipitation, topological studies, photocrosslinking, FRET and imaging techniques, the volume fully updates and expands upon the successful previous editions.Written in the convenient and informative "Methods in Molecular Biology" series format, chapters include introductions to their respective subjects, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Comprehensive and authoritative, "DNA-Protein Interactions: Principles and Protocols, Third Edition" serves as an ideal guide for all those exploring this dynamic, essential, and increasingly affordable area of research.

Contents

1. Filter-Binding Assays Peter G. Stockley 2. Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions Manon Gaudreault, Marie-Eve Gingras, Maryse Lessard, Steeve Leclerc, and Sylvain L. Guerin 3. DNase I Footprinting Benoit Leblanc and Tom Moss 4. Exonuclease III Footprinting on Immobilized DNA Templates Patrizia Spitalny and Michael Thomm 5. Hydroxyl Radical Footprinting of Protein-DNA Complexes Indu Jagannathan and Jeffrey J. Hayes 6. The Use of Diethyl Pyrocarbonate (DEPC) and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DNA Brenda F. Kahl and Marvin R. Paule 7. Uranyl Photofootprinting Peter E. Nielsen 8. Identification of Protein/DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference Peter E. Shaw and A. Francis Stewart 9. Ethylation Interference Footprinting of DNA-Protein Complexes Iain W. Manfield and Peter G. Stockley 10. Site-Directed Cleavage of DNA by Protein-Fe(II) EDTA Conjugates within Model Chromatin Complexes David R. Chafin and Jeffrey J. Hayes 11. Identification of Nucleic Acid High Affinity Binding Sequences of Proteins by SELEX Philippe Bouvet 12. Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting Simon Labbe, Jean-Francois Harrisson, and Carl Seguin 13. Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper Athanasios G. Papavassiliou 14. Determination of a Transcription Factor-Binding Site by Nuclease Protection Footprinting onto Southwestern Blots Athanasios G. Papavassiliou 15. Use of a Reporter Gene Assay in Yeast for Genetic Analysis of DNA-Protein Interactions David R. Setzer, Deborah B. Schulman, Cathy V. Gunther, and Michael J. Bumbulis 16. Chromatin Immunoprecipitation in Mammalian Cells Amy Svotelis, Nicolas Gevry, and Luc Gaudreau 17. Sequential Chromatin Immunoprecipitation Protocol: ChIP-reChIP Mayra Furlan-Magaril, Hector Rincon-Arano, and Felix Recillas-Targa 18. Profiling Genome-Wide Histone Modifications and Variants by ChIP-chip on Tiling Microarrays in S. cerevisiae Alain R. Bataille and Francois Robert 19. Nucleosome Mapping Nicolas Gevry, Amy Svotelis, Marc Larochelle, and Luc Gaudreau 20. In Cellulo DNA Analysis (LMPCR Footprinting) Regen Drouin, Nathalie Bastien, Jean-Francois Millau, Francois Vigneault, and Isabelle Paradis 21. Atomic Force Microscopy Imaging and Probing of DNA, Proteins and Protein-DNA Complexes: Silatrane Surface Chemistry Yuri L. Lyubchenko, Luda S. Shlyakhtenko, and Alexander A. Gall 22. Two-Dimensional Crystallisation of Soluble Protein Complexes Patrick Schultz, Corinne Crucifix, and Luc Lebeau 23. Assays for Transcription Factor Activity Douglas Browning, Nigel Savery, Annie Kolb, and Stephen Busby 24. Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine Rainer Meffert, Klaus Dose, Gabriele Rathgeber, and Hans-Jochen Schafer 25. Static and Kinetic Site-Specific Protein-DNA Photocrosslinking: Analysis of Bacterial Transcription Initiation Complexes Nikolai Naryshkin, Sergei Druzhinin, Andrei Revyakin, Younggyu Kim, Vladimir Mekler, and Richard H. Ebright 26. Use of Site-Specific Protein-DNA Photocrosslinking of Purified Complexes to Analyze the Topology of the RNA Polymerase II Transcription Initiation Complex Diane Forget, Celine Domecq, and Benoit Coulombe 27. Site-Directed DNA Cross-Linking of Large Multi-Subunit Protein-DNA Complexes Jim Persinger and Blaine Bartholomew 28. Functional Studies of DNA-Protein Interactions Using FRET Techniques Simon Blouin, Timothy D. Craggs, Daniel A. Lafontaine, and J. Carlos Penedo 29. Single-Molecule FRET Analysis of Protein-DNA Complexes Mike Heilemann, Ling Chin Hwang, Konstantinos Lymperopoulos, and Achillefs N. Kapanidis 30. Analysis of DNA Supercoiling Induced by DNA-Protein Interactions David J. Clark and Benoit Leblanc 31. The Cruciform DNA Mobility Shift Assay: A Tool to Study Proteins that Recognize Bent DNA Victor Y. Stefanovsky and Tom Moss 32. Plasmid Vectors for the Analysis of Protein Induced DNA-Bending Christian Zwieb and Sankar Adhya 33. Analysis of Distant Communication on Defined Chromatin Templates In Vitro Yury S. Polikanov and Vasily M. Studitsky 34. A Competition Assay for DNA Binding Using the Fluorescent Probe ANS Ian A. Taylor and G. Geoff Kneale 35. Fluorescence Spectroscopy and Anisotropy in the Analysis of DNA-Protein Interactions Rosy Favicchio, Anatoly I. Dragan, G. Geoff Kneale, and Christopher M. Read 36. Circular Dichroism for the Analysis of Protein-DNA Interactions P.D. Cary and G. Geoff Kneale 37. Defining the Thermodynamics of Protein/DNA Complexes and Their Components Using Micro-Calorimetry Colyn Crane-Robinson, Anatoly I. Dragan, and Christopher M. Read 38. Surface Plasmon Resonance Assays of DNA-Protein Interactions Peter G. Stockley and Bjorn Persson

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