DNA-Protein Interactions Principles and Protocols

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.