Bookedited by Benoit P. Leblanc and Sebastien Rodrigue.
Contents:
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.