Electrophoretic Mobility Shift Assay Using Radiolabeled DNA Probes -- In Vitro DNase I Footprinting -- Determining the Architecture of a Protein/DNA Complex by Combining FeBABE Cleavage Analyses, 3-D Printed Structures, and the ICM Molsoft Program -- In Cellulo DNA Analysis: LMPCR Footprinting -- Southwestern Blotting Assay -- Single-Molecule Approaches for the Characterization of Riboswitch Folding Mechanisms -- Probing of Nascent Riboswitch Transcripts -- Functional Studies of DNA-Protein Interactions Using FRET Techniques -- Precise Identification of Genome-Wide Transcription Start Sites in Bacteria by 5' Rapid Amplification of cDNA Ends (5'-RACE) -- Analysis of DNA Supercoiling Induced by DNA-Protein Interactions -- Precise Identification of DNA-Binding Proteins Genomic Location by Exonuclease Coupled Chromatin Immunoprecipitation (ChIP-exo) -- The Cruciform DNA Mobility Shift Assay: A Tool to Study Proteins that Recognize Bent DNA -- Individual and Sequential Chromatin Immunoprecipitation Protocols -- Chromatin Endogenous Cleavage (ChEC) as a Method to Quantify Protein Interaction with Genomic DNA in Saccharomyces cerevisiae -- Selection and Validation of Spacer Sequences for CRISPR-Cas9 Genome Editing and Transcription Regulation in Bacteria -- Detection of Short-Range DNA Interactions in Mammalian Cells Using High-Resolution Circular Chromosome Conformation Capture Coupled to Deep Sequencing -- Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq) -- Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler -- Circular Dichroism for the Analysis of Protein-DNA Interactions -- Quantitative Investigation of Protein-Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance -- Identification of Nucleic Acid High Affinity Binding Sequences of Proteins by SELEX.

This fourth edition reflects the most recent technical advances in DNA-protein interaction research. With fully updated chapters that describe techniques proven by their continuous value, the volume also many new chapters have been added that mostly deal with larger-scale experiments, reflecting recent advances in "big biology", combining to offer a very useful compendium of protocols allowing readers to delve into the intricacies of protein-DNA interaction at levels ranging from the very small (as in the case of single-molecule FRET) to the very complex (as with circular chromatin conformation capture, or 4C). Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and up-to-date, DNA-Protein Interactions: Principles and Protocols, Fourth Edition will aid researchers in continuing the incredible progress made in this vital area of study.