DNA Protein Interactions

DNAse I Footprinting. Footprinting with Exonuclease III Hydroxyl Radical Footprinting. Hydroxyl Radical Interference. 1,10-Phenanthroline-Copper Ion Nuclease Footprinting of DNA-Protein Complexes In Situ Following Mobility- Shift Electrophoresis Assays. Identification of Protein-DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference. Diethyl Pyrocarbonate as a Probe of Protein-DNA Interactions. Osmium Tetroxide Modification in the Study of DNA Protein Interactions. Diffusible Singlet Oxygen as a Probe of DNA Deformation. Ethylation Interference. Uranyl Photofootprinting of DNA-Protein Complexes. Nitration of Tyrosine Residues in Protein-Nucleic Acid Complexes. Limited Proteolysis of Protein-Nucleic Acid Complexes. Cloning and Expression of DNA Binding Domains Using PCR. Overexpression and Purification of Eukaryotic Transcription Factors as Glutathione-S-Transferase Fusions in E. coli. Site-Directed Mutagenesis by the Cassette Method. Site-Directed and Site-Saturation Mutagenesis Using Oligonucleotide Primers. UV Laser-Induced Protein-DNA Crosslinking. UV Crosslinking of DNA-Protein Complexes via 8-Azidoadenine. Filter Binding Assays. The Gel Shift Assay for the Analysis of DNA-Protein Interactions. Improved Plasmid Vectors for the Analysis of Protein-Induced DNA Bending. Determination of Sequence Preferences of DNA Binding Proteins Using Pooled Solid-Phase Sequencing of Low-Degeneracy Oligonucleotide Mixtures. Analysis of DNA-Protein Interactions by Intrinsic Fluorescence. A Competition Assay for DNA Binding Using the Fluorescent Probe, ANS. Circular Dichroism for the Analysis of DNA-Protein Interactions. Electron Microscopy of Protein-Nucleic Acid Complexes: Uniform Spreading and Determination of Helix Handedness. Reconstitution of Protein-Nucleic Acid Complexes for Crystallization. Assay for Restriction Endonucleases Using Oligonucleotides. Assay of Restriction Endonucleases Plasmid Substrates. Assays for Transcription Factor Activity. An Assay for In Vitro Recombination Between Duplex DNA Molecules. Index.