Title DNA-protein interactions : principles and protocols / edited by Benoit P. Leblanc and Sebastien Rodrigue

Edition Fourth edition Published New York : Humana Press : Springer, [2015] ©2015

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Description 1 online resource (xvi, 347 pages) : illustrations (some color) Series Methods in molecular biology, 1064-3745 ; volume 1334 Springer protocols Methods in molecular biology (Clifton, N.J.) ; v. 1334. 1064-3745 Springer protocols (Series) 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 Summary This title presents the most recent technical advances in DNA-protein interaction research. With fully updated chapters that describe techniques proven by their continuous value, it also includes new chapters dealing with larger-scale experiments, to reflect recent advances in 'big biology'. As a whole, it offers a very useful compendium of protocols, allowing readers to delve into the intricacies of protein-DNA interaction at levels ranging from the very small to the very complex Bibliography Includes bibliographical references and index Subject DNA-protein interactions -- Laboratory manuals DNA-Binding Proteins -- genetics DNA Footprinting -- methods DNA-Binding Proteins -- chemistry Proteins. Medical genetics. Science -- Life Sciences -- Biochemistry. Medical -- Genetics. DNA-protein interactions Genre/Form Laboratory manuals Laboratory manuals. Manuels de laboratoire. Form Electronic book Author Rodrigue, Sébastien, editor Leblanc, Benoît, editor. ISBN 9781493928774 1493928775 1493928767 9781493928767

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