DNA'Protein Interactions: Principles and Protocols / Edition 2

DNA'Protein Interactions: Principles and Protocols / Edition 2

by Tom Moss
     
 

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ISBN-10: 1617371254

ISBN-13: 9781617371257

Pub. Date: 02/28/2014

Publisher: Springer-Verlag New York, LLC

DNA-protein interactions are fundamental to understanding biological growth, development, differentiation, evolution, and disease, and are also increasingly important to the biotechnology industry. In DNA-Protein Interactions: Principles and Protocols, 2nd Edition, Dr. Tom Moss assembles the new standard collection of cutting-edge techniques to identify key

Overview

DNA-protein interactions are fundamental to understanding biological growth, development, differentiation, evolution, and disease, and are also increasingly important to the biotechnology industry. In DNA-Protein Interactions: Principles and Protocols, 2nd Edition, Dr. Tom Moss assembles the new standard collection of cutting-edge techniques to identify key protein-DNA interactions, define their components, and determine the nature of their interactions and their manner of function, both in the cell and in the test tube. Each detailed method has been optimized and tested by a hands-on expert to ensure experimental success, and provides helpful notes on pitfalls to avoid, as well as alternate strategies. 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. There are also vanguard methods for designing proteins to fit DNA, site-specific protein-directed DNA cleavage, and 2D semicrystalline arrays of nucleoproteins for structure determination.

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 illuminate DNA-protein interactions.

Product Details

ISBN-13:
9781617371257
Publisher:
Springer-Verlag New York, LLC
Publication date:
02/28/2014
Series:
Methods in Molecular Biology Series , #148
Edition description:
Softcover reprint of 2nd ed. 2001
Pages:
638
Product dimensions:
6.00(w) x 9.00(h) x 1.46(d)

Table of Contents

Prefacev
Contributorsxiii
1Filter-Binding Assays1
2Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions13
3DNase I Footprinting31
4Footprinting with Exonuclease III39
5Hydroxyl Radical Footprinting49
6The Use of Diethyl Pyrocarbonate and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DNA63
7Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1, 10-Phenanthroline-Copper77
8Uranyl Photofootprinting111
9Osmium Tetroxide Modification and the Study of DNA-Protein Interactions121
10Determination of a Transcription-Factor-Binding Site by Nuclease Protection Footprinting onto Southwestern Blots135
11Diffusible Singlet Oxygen as a Probe of DNA Deformation151
12Ultraviolet-Laser Footprinting161
13In Vivo DNA Analysis175
14Identification of Protein-DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference221
15Ethylation Interference229
16Hydroxyl Radical Interference245
17Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting255
18A Competition Assay for DNA Binding Using the Fluorescent Probe ANS265
19Site-Directed Cleavage of DNA by Linker Histone-Fe(ll) EDTA Conjugates275
20Nitration of Tyrosine Residues in Protein-Nucleic Acid Complexes291
21Chemical Modification of Lysine by Reductive Methylation: A Probe of Residues Involved in DNA Binding301
22Limited Proteolysis of Protein-Nucleic Acid Complexes315
23Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine323
24Site-Specific Protein-DNA Photocrosslinking: Analysis of Bacterial Transcription Initiation Complexes337
25Site-Directed DNA Photoaffinity Labeling of RNA Polymerase III Transcription Complexes363
26Use of Site-Specific Protein-DNA Photocrosslinking to Analyze the Molecular Organization of the RNA Polymerase II Initiation Complex383
27UV Laser-Induced Protein-DNA Crosslinking395
28Plasmid Vectors for the Analysis of Protein-Induced DNA Bending403
29Engineering Nucleic Acid-Binding Proteins by Phage Display417
30Genetic Analysis of DNA-Protein Interactions Using a Reporter Gene Assay in Yeast431
31Assays for Transcription Factor Activity451
32Assay of Restriction Endonucleases Using Oligonucleotides465
33Analysis of DNA-Protein Interactions by Intrinsic Fluorescence491
34Circular Dichroism for the Analysis of Protein-DNA Interactions503
35Calorimetry of Protein-DNA Complexes and Their Components511
36Surface Plasmon Resonance Applied to DNA-Protein Complexes535
37Reconstitution of Protein-DNA Complexes for Crystallization547
38Two-Dimensional Crystallization of Soluble Protein Complexes557
39Atomic Force Microscopy of DNA and Protein-DNA Complexes Using Functionalized Mica Substrates569
40Electron Microscopy of Protein-Nucleic Acid Complexes: Uniform Spreading of Flexible Complexes, Staining with a Uniform Thin Layer of Uranyl Acetate, and Determining Helix Handedness579
41Scanning Transmission Electron Microscopy of DNA-Protein Complexes589
42Determination of Nucleic Acid Recognition Sequences by SELEX603
43High DNA-Protein Crosslinking Yield with Two-Wavelength Femtosecond Laser Irradiation611
Appendices
Appendix IEMSA/Gel Shift Conditions617
Appendix IIDNA-Modification/Cleavage Reagents619
Index621

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