DNA-Protein Interactions. Principles and Protocols, изд. 2

Автор(ы):Moss Tom
Год изд.:2001
Описание: DNA-protein interactions are fundamental to the existence of life forms, providing the key to the genetic plan as well as mechanisms for its maintenance and evolution. The study of these interactions is therefore fundamental to our understanding of growth, development, differentiation, evolution, and disease. The manipulation of DNA-protein interactions is also becoming increasingly important to the biotechnology industry, permitting among other things the reprogramming of gene expression. The success of the first edition of DNA-Protein Interactions; Principles and Protocols was the result of Dr. G. Geoff Kneale's efforts in bringing together a broad range of relevant techniques. In producing the second edition of this book, the author has tried to further increase this diversity while presenting the reader with alternative approaches to obtaining the same information.
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1 Filter-Binding Assays Peter G. Stockley [1]
2 Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions Marc-Andre Laniel, Alain Beliveau, and Sylvain L. Guerin [13]
3 DNase I Footprinting Benoft Leblanc and Tom Moss [31]
4 Footprinting with Exonuclease III Willi Metzger and Hermann Heumann [39]
5 Hydroxyl Radical Footprinting Evgeny Zaychikov, Peter Schickor, Ludmilla Denissova, and Hermann Heumann [49]
6 The Use of Diethyl Pyrocarbonate and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DMA Brenda F. Kahl and Marvin R. Paule [63]
7 Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper Athanasios G. Papavassiliou [77]
8 Uranyl Photofootprinting Peter E. Nielsen [111]
9 Osmium Tetroxide Modification and the Study of DNA-Protein Interactions James A. McClellan [121]
10 Determination of a Transcription-Factor-Binding Site by Nuclease Protection Footprinting onto Southwestern Blots Athanasios G. Papavassiliou [135]
11 Diffusible Singlet Oxygen as a Probe of DNA Deformation Malcolm Buckle and Andrew A. Travers [151]
12 Ultraviolet-Laser Footprinting Johannes Geiselmann and Frederic Boccard [161]
13 In Vivo DMA Analysis Regen Drouin, Jean-Philippe Therrien, Martin Angers, and Stephane Ouellet [175]
14 Identification of Protein-DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference Peter E. Shaw and A. Francis Stewart [221]
15 Ethylation Interference lain W. Manfield and Peter G. Stockley [229]
16 Hydroxyl Radical Interference Peter Schickor, Evgeny Zaychikov, and Hermann Heumann [245]
17 Identification of Sequence-Specific DMA-Binding Proteins by Southwestern Blotting Simon Labbe, Gale Stewart, Olivier LaRochelle, Guy G. Poirier, and Carl Seguin [255]
18 A Competition Assay for DMA Binding Using the Fluorescent Probe ANS Ian A. Taylor and G. Geoff Kneale [265]
19 Site-Directed Cleavage of DMA by Linker Histone Protein-Fe(II) EDTA Conjugates David R. Chafin and Jeffrey J. Hayes [275]
20 Nitration of Tyrosine Residues in Protein-Nucleic Acid Complexes Simon E. Plyte [291]
21 Chemical Modification of Lysine by Reductive Methylation: A Probe of Residues Involved in DNA Binding Ian A. Taylor and Michelle Webb [301]
22 Limited Proteolysis of Protein-Nucleic Acid Complexes Simon E. Plyte and G. Geoff Kneale [315]
23 Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine Rainer Meffert, Klaus Dose, Gabriele Rathgeber, and Hans-Jochen Schafer [323]
24 Site-Specific Protein-DNA Photocrosslinking: Analysis of Bacterial Transcription Initiation Complexes Nikolai Naryshkin, Younggyu Kim, Qianping Dong, and Richard H. Ebright [337]
25 Site-Directed DMA Photoaffinity Labeling of RNA Polymerase III Transcription Complexes Jim Persinger and Blaine Bartholomew [363]
26 Use of Site-Specific Protein-DNA Photocrosslinking to Analyze the Molecular Organization of the RNA Polymerase II Initiation Complex Francois Robert and Benoft Coulombe [383]
27 UV Laser-Induced Protein-DNA Crosslinking Stefan I. Dimitrov and Tom Moss [395]
28 Plasmid Vectors for the Analysis of Protein-Induced DNA Bending Christian Zwieb and Sankar Adhya [403]
29 Engineering Nucleic Acid-Binding Proteins by Phage Display Mark Isalan and Yen Choo [417]
30 Genetic Analysis of DNA-Protein Interactions Using a Reporter Gene Assay in Yeast David R. Setzer, Deborah B. Schulman, and Michael J. Bumbulis [431]
31 Assays for Transcription Factor Activity Virgil Rhodius, Nigel Savery, Annie Kolb, and Stephen Busby [451]
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 [465]
33 Analysis of DNA-Protein Interactions by Intrinsic Fluorescence Mark L. Carpenter, Anthony W. Oliver, and G. Geoff Kneale [491]
34 Circular Dichroism for the Analysis of Protein-DNA Interactions Mark L. Carpenter, Anthony W. Oliver, and G. Geoff Kneale [503]
35 Calorimetry of Protein-DNA Complexes and Their Components Christopher M. Read and llian Jelesarov [511]
36 Surface Plasmon Resonance Applied to DNA-Protein Complexes Malcolm Buckle [535]
37 Reconstitution of Protein-DNA Complexes for Crystallization Rachel M. Conlin and Raymond S. Brown [547]
38 Two-Dimensional Crystallization of Soluble Protein Complexes Patrick Schultz, Nicolas Bischler, and Luc Lebeau [557]
39 Atomic Force Microscopy of DMA and Protein-DNA Complexes Using Functionalized Mica Substrates Yuri L. Lyubchenko, Alexander A. Gall, and Luda S. Shlyakhtenko [569]
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 [579]
41 Scanning Transmission Electon Microscopy of DNA-Protein Complexes Joseph S. Wall and Martha N. Simon [589]
42 Determination of Nuleic Acid Recognition Sequences by SELEX Philippe Bouvet [603]
43 High DNA-Protein Crosslinking Yield with Two-Wavelength Femtosecond Laser Irradiation Christoph Russmann, Rene Beigang, and Miguel Beato [611]
Appendix I: EMSA/Gel Shift Conditions [617]
Appendix II: DNA-Modification/Cleavage Reagents [619]
Index [621]
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