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DNA'Protein Interactions

Principles and Protocols

  • Book
  • © 1994

Overview

Editors:
  1. G. Geoff Kneale

    1. School of Biological Sciences; University of Portsmouth, Portsmouth, UK

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Part of the book series: Methods in Molecular Biology (MIMB, volume 30)

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Table of contents (32 protocols)

  1. Front Matter

    Pages i-xv
    Download chapter PDF

  2. DNase I Footprinting

    • Benoît Lehlanc, Tom Moss
    Pages 1-10

  3. Footprinting with Exonuclease III

    • Willi Metzger, Hermann Heumann
    Pages 11-20

  4. Hydroxyl Radical Footprinting

    • Peter Schickor, Hermann Heumann
    Pages 21-32

  5. Hydroxyl Radical Interference

    • Peter Schickor, Hermann Heumann
    Pages 33-41

  6. 1,10-Phenanthroline-Copper Ion Nuclease Footprinting of DNA-Protein Complexes in Situ Following Mobility-Shift Electrophoresis Assays

    • Athanasios G. Papavassiliou, Hermann Heumann
    Pages 43-78

  7. Identification of Protein-DNA Contacts with Dimethyl Sulfate

    • Peter E. Shaw, A. Francis Stewart
    Pages 79-87

  8. Diethyl Pyrocarbonate as a Probe of Protein-DNA Interactions

    • Michael J. McLean
    Pages 89-95

  9. Osmium Tetroxide Modification and the Study of DNA-Protein Interactions

    • James A. McClellan
    Pages 97-112

  10. Diffusible Singlet Oxygen as a Probe of DNA Deformation

    • Malcolm Buckle, Andrew A. Wavers
    Pages 113-123

  11. Ethylation Interference

    • Iain Manfield, Peter G. Stockley
    Pages 125-139

  12. Uranyl Photofootprinting of DNA-Protein Complexes

    • Peter E. Nielsen
    Pages 141-149

  13. Nitration of Tyrosine Residues in Protein-Nucleic Acid Complexes

    • Simon E. Plyte
    Pages 151-160

  14. Limited Proteolysis of Protein-Nucleic Acid Complexes

    • Simon E. Plyte, G. GeoffKheale
    Pages 161-168

  15. Cloning and Expression of DNA Binding Domains Using PCR

    • Daniel G. Fox, G. GeoffKineale
    Pages 169-184

  16. Overexpression and Purification of Eukaryotic Transcription Factors as Glutathione-S-Transferase Fusions in E. coli

    • Kavin G. Ford, Alan J. Whitmarsh, David P. Hornby
    Pages 185-197

  17. Site-Directed Mutagenesis by the Cassette Method

    • Andrew F Worrall
    Pages 199-210

  18. Site-Directed and Site-Saturation Mutagenesis Using Oligonucleotide Primers

    • Michael J. O’Donohue, G. GeoffKneale
    Pages 211-225

  19. UV Laser-Induced Protein-DNA Crosslinking

    • Stefan I. Dimitrov, Tom Moss
    Pages 227-236

  20. Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine

    • Raker Meffert, Klaus Dose, Gabriele Rathgeber, Hans-Jochen SchÄfer
    Pages 237-250
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About this book

The study of protein-nucleic acid interactions is currently one of the most rapidly growing areas of molecular biology. DNA binding proteins are at the very heart of the regulation and control of gene expression, replication, and recombination: Enzymes that recognize and either modify or cleave specific DNA sequences are equally important to the cell. Some of the techniques reported in this volume can be used to identify previously unknown DNA binding proteins from crude cell extracts. Virtually all are capable of giving direct information on the molecular basis of the interaction—the location of the DNA binding site; the strength and specificity of binding; the identities of individual groups on specific bases involved in binding; the specific amino acid residues of the protein that interact with the DNA; or the effects of protein binding on gross conformation and local structure of DNA. The recognition of DNA sequences by proteins is a complex phenomenon, involving specific hydrogen bonding contacts to the DNA bases ("direct readout") and/or interactions with the sugar-phos­ phate backbone ("indirect readout"). The latter interactions can also be highly specific because of sequence-dependent conformational changes in the DNA. In addition, intercalation of planar aromatic amino acid side-chains between the DNA bases can occur, most notably with single-stranded DNA binding proteins. Furthermore, when bound, many DNA binding proteins induce drastic structural changes in the DNA as an integral part of their function.

Reviews

...useful for investigators with a wide range of expertise. - Biological Abstracts

Editors and Affiliations

  • School of Biological Sciences; University of Portsmouth, Portsmouth, UK

    G. Geoff Kneale

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