Library Science

The clear and easy-to-follow protocols collected here illuminate the molecular basis of protein???nucleic acid interactions. Use them successfully to reveal the location of the DNA binding site, the strength and specificity of a binding, the identities of individual groups on the actual bases involved in binding, and the specific amino acid residues of the protein that interact with the DNA. Some of the techniques can even be used to identify previously unknown DNA binding proteins from crude cell extracts, thus empowering you to make groundbreaking advances in your work.

Authors: Kneale, G. Geoff

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Table of Contents

1. DNase I Footprinting (pp. 1-10)
   Leblanc, Benoit; Moss, Tom
2. Footprinting with Exonuclease III (pp. 11-20)
   Metzger, Willi; Heumann, Hermann
3. Hydroxyl Radical Footprinting (pp. 21-32)
   Schickor, Peter; Heumann, Hermann
4. Hydroxyl Radical Interference (pp. 33-42)
   Schickor, Peter; Heumann, Hermann
5. 1,10-Phenanthroline-Copper Ion Nuclease Footprinting of DNA???Protein Complexes in Situ Following Mobility-Shift Electrophoresis Assays (pp. 43-78)
   Papavassiliou, Athanasios G.
6. Identification of Protein???DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference (pp. 79-88)
   Shaw, Peter E.; Stewart, A. Francis
7. Diethyl Pyrocarbonate as a Probe of Protein???DNA Interactions (pp. 89-96)
   McLean, Michael J.
8. Osmium Tetroxide Modification and the Study of DNA???Protein Interactions (pp. 97-112)
   McClellan, James A.
9. Diffusible Singlet Oxygen as a Probe of DNA Deformation (pp. 113-124)
   Buckle, Malcolm; Travers, Andrew A.
10. Ethylation Interference (pp. 125-140)
    Manfield, Iain; Stockley, Peter G.
11. Uranyl Photofootprinting of DNA???Protein Complexes (pp. 141-150)
    Nielsen, Peter E.
12. Nitration of Tyrosine Residues in Protein???Nucleic Acid Complexes (pp. 151-160)
    Plyte, Simon E.
13. Limited Proteolysis of Protein???Nucleic Acid Complexes (pp. 161-168)
    Plyte, Simon E.; Kneale, G. Geoff
14. Cloning and Expression of DNA Binding Domains Using PCR (pp. 169-184)
    Fox, Daniel G.; Kneale, G. Geoff
15. Overexpression and Purification of Eukaryotic Transcription Factors as Glutathione-S-Transferase Fusions in E. coli (pp. 185-198)
    Ford, Kevin G.; Whitmarsh, Alan J.; Hornby, David P.
16. Site-Directed Mutagenesis by the Cassette Method (pp. 199-210)
    Worall, Andrew F.
17. Site-Directed and Site-Saturation Mutagenesis Using Oligonucleotide Primers (pp. 211-226)
    O???Donohue, Michael J.; Kneale, G. Geoff
18. UV Laser-Induced Protein???DNA Crosslinking (pp. 227-236)
    Dimitrov, Stefan I.; Moss, Tom
19. Ultraviolet Crosslinking of DNA???Protein Complexes via 8-Azidoadenine (pp. 237-250)
    Meffert, Rainer; Dose, Klaus; Rathgeber, Gabriele; Schafer, Hans-Jochen
20. Filter-Binding Assays (pp. 251-262)
    Stockley, Peter G.
21. The Gel Shift Assay for the Analysis of DNA???Protein Interactions (pp. 263-280)
    Taylor, John D.; Ackroyd, Alison J.; Halford, Stephen E.
22. Improved Plasmid Vectors for the Analysis of Protein-Induced DNA Bending (pp. 281-294)
    Zwieb, Christian; Adhya, Sankar
23. Determination of Sequence Preferences of DNA Binding Proteins Using Pooled Solid-Phase Sequencing of Low Degeneracy Oligonucleotide Mixtures (pp. 295-312)
    Gogos, Joseph A.; Kafatos, Fotis C.
24. Analysis of DNA???Protein Interactions by Intrinsic Fluorescence (pp. 313-326)
    Carpenter, Mark L.; Kneale, G. Geoff
25. A Competition Assay for DNA Binding Using the Fluorescent Probe ANS (pp. 327-338)
    Taylor, Ian; Kneale, G. Geoff
26. Circular Dichroism for the Analysis of Protein???DNA Interactions (pp. 339-346)
    Carpenter, Mark L.; Kneale, G. Geoff
27. Electron Microscopy of Protein???Nucleic Acid Complexes: Uniform Spreading and Determination of Helix Handedness (pp. 347-356)
    Gray, Carla W.
28. Reconstitution of Protein???DNA Complexes for Crystallization (pp. 357-370)
    Colin, Rachel M.; Brown, Raymond S.
29. Assay of Restriction Endonucleases Using Oligonucleotides (pp. 371-384)
    Connolly, Bernard A.
30. Assays for Restriction Endonucleases Using Plasmid Substrates (pp. 385-396)
    Halford, Stephen E.; Taylor, John D.; Vermote, Christian L. M.; Vipond, I. Barry
31. Assays for Transcription Factor Activity (pp. 397-412)
    Busby, Stephen; Kolb, Annie; Minchin, Stephen
32. An Assay for In Vitro Recombination Between Duplex DNA Molecules (pp. 413-424)
    Muller, Berndt; West, Stephen C.

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