DNA-Protein Interactions

Filter-Binding Assays.- Electrophoretic Mobility Shift Assays for the Analysis of DNA-Protein Interactions.- DNase I Footprinting.- Exonuclease III Footprinting on Immobilized DNA Templates.- Hydroxyl Radical Footprinting of Protein-DNA Complexes.- The Use of Diethyl Pyrocarbonate and Potassium Permanganate as Probes for Strand Separation and Structural Distortions in DNA.- Uranyl Photofootprinting.- Identification of Protein/DNA Contacts with Dimethyl Sulfate: Methylation Protection and Methylation Interference.- Ethylation Interference Footprinting of DNA-Protein Complexes.- Site-Directed Cleavage of DNA by Protein-Fe(II) EDTA Conjugates Within Model Chromatin Complexes.- Identification of Nucleic Acid High-Affinity Binding Sequences of Proteins by SELEX.- Identification of Sequence-Specific DNA-Binding Proteins by Southwestern Blotting.- Footprinting DNA-Protein Interactions in Native Polyacrylamide Gels by Chemical Nucleolytic Activity of 1,10-Phenanthroline-Copper.- Determination of a Transcription Factor-Binding Site by Nuclease Protection Footprinting onto Southwestern Blots.- Use of a Reporter Gene Assay in Yeast for Genetic Analysis of DNA-Protein Interactions.- Chromatin Immunoprecipitation in Mammalian Cells.- Sequential Chromatin Immunoprecipitation Protocol: ChIP-reChIP.- Profiling Genome-Wide Histone Modifications and Variants by ChIP-chip on Tiling Microarrays in S. cerevisiae.- Nucleosome Mapping.- In Cellulo DNA Analysis (LMPCR Footprinting).- Atomic Force Microscopy Imaging and Probing of DNA, Proteins, and Protein-DNA Complexes: Silatrane Surface Chemistry.- Two-Dimensional Crystallisation of Soluble Protein Complexes.- Assays for Transcription Factor Activity.- Ultraviolet Crosslinking of DNA-Protein Complexes via 8-Azidoadenine.- Static and KineticSite-Specific Protein-DNA Photocrosslinking: Analysis of Bacterial Transcription Initiation Complexes.- Use of Site-Specific Protein-DNA Photocrosslinking of Purified Complexes to Analyze the Topology of the RNA Polymerase II Transcription Initiation Complex.- Site-Directed DNA Crosslinking of Large Multisubunit Protein-DNA Complexes.- Functional Studies of DNA-Protein Interactions Using FRET Techniques.- Single-Molecule FRET Analysis of Protein-DNA Complexes.- Analysis of DNA Supercoiling Induced by DNA-Protein Interactions.- The Cruciform DNA Mobility Shift Assay: A Tool to Study Proteins that Recognize Bent DNA.- Plasmid Vectors for the Analysis of Protein-Induced DNA Bending.- Analysis of Distant Communication on Defined Chromatin Templates In Vitro.- A Competition Assay for DNA Binding Using the Fluorescent Probe ANS.- Fluorescence Spectroscopy and Anisotropy in the Analysis of DNA-Protein Interactions.- Circular Dichroism for the Analysis of Protein-DNA Interactions.- Defining the Thermodynamics of Protein/DNA Complexes and Their Components Using Micro-calorimetry.- Surface Plasmon Resonance Assays of DNA-Protein Interactions.