DNA-Protein Interactions: Principles and Protocols, 2nd ed. 

0-89603-671-5

978-0-89603-671-0

T. Moss, ed., Humana Press, 2001, 628 pp., soft cover

1 Filter-Binding Assays,
2 Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions
3 DNase I Footprinting
4 Footprinting with Exonuclease III,
5.Hydroxyl Radical Footprinting,
6 The Use of Diethyl Pyrocarbonate (DEPC) and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DNA,
7 Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper,
8 Uranyl Photofootprinting,
9 Osmium Tetroxide Modification and the Study of DNA-Protein Interactions,
10 Determination of a Transcription Factor-Binding Site by Nuclease Protection Footprinting Onto Southwestern Blots,
11 Diffusible Singlet Oxygen as a Probe of DNA Deformation,
12 UV-laser footprinting
13 Determination of nucleic acid recognition sequences by SELEX.
14 Identification of Protein-DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference,
15 Ethylation Interference,
16 Hydroxyl Radical Interference,
17 Identification of sequence-specific DNA-binding proteins by Southwestern blotting,
18 A Competition Assay for DNA Binding Using the Fluorescent Probe ANS,
19 Site-directed cleavage of DNA by linker histone protein-Fe(II) EDTA conjugates.
20 Nitration of Tyrosine Residues in Protein-Nucleic Acid Complexes.
21 Chemical modification of lysine by reductive methylation; a probe of residues involved in DNA binding.
22 Limited Proteolysis of Protein-Nucleic Acid Complexes,
23 Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine,
24 Site-specific protein-DNA photocrosslinking: analysis of bacterial transcription initiation complexes
25 Site Directed DNA Photoaffinity Labeling of RNA Polymerase III Transcription Complexes
26 The use of site-specific protein-DNA photo-crosslinking to analyze the molecular organization of the RNA polymerase II initiation complex
27 UV Laser-Induced Protein-DNA Crosslinking
28 Plasmid Vectors for the Analysis of Protein-Induced DNA Bending,
29 Engineering nucleic acid-binding proteins by phage display.
30 Genetic Analysis Of DNA-Protein Interactions Using A Reporter Gene Assay In Yeast,
31 Assays for Transcription Factor Activity,
32. Assay of Restriction Endonucleases Using Oligonucleotides
33 Analysis of DNA-Protein Interactions by Intrinsic Fluorescence,
34 Circular Dichroism for the Analysis of Protein-DNA Interactions,
35 Calorimetry of protein-DNA complexes and their components,
36 Surface plasmon resonance applied to DNA-protein complexes,
37 Reconstitution of Protein-DNA Complexes for Crystallization,
38. 2D crystal arrays in protein structure studies.
39 Atomic force microscopy of DNA and protein-DNA Complexes using functionalized mica substrates,
40 Electron microscopy of protein-nucleic acid complexes: Uniform spreading of flexible complexes, staining with a uniform thin layer of uranyl acetate and determination of helix handedness,
41 High DNA-protein crosslinking yield with two-wavelength femtosecond (TWF) laser irradiation