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DNA-Protein Interactions

Principles and Protocols

  • Book
  • © 2015

Overview

Editors:
  1. Benoît P. Leblanc

    1. Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada

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  2. Sébastien Rodrigue

    1. Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Includes fully updated, cutting-edge methods and protocols for studying protein-DNA interactions
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1334)

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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Electrophoretic Mobility Shift Assay Using Radiolabeled DNA Probes

    • Dominic Poulin-Laprade, Vincent Burrus
    Pages 1-15

  3. In Vitro DNase I Footprinting

    • Benoît P. Leblanc, Tom Moss
    Pages 17-27

  4. Determining the Architecture of a Protein–DNA Complex by Combining FeBABE Cleavage Analyses, 3-D Printed Structures, and the ICM Molsoft Program

    • Tamara James, Meng-Lun Hsieh, Leslie Knipling, Deborah Hinton
    Pages 29-40

  5. In Cellulo DNA Analysis: LMPCR Footprinting

    • Régen Drouin, Nathalie Bastien, Jean-François Millau, François Vigneault, Isabelle Paradis
    Pages 41-84

  6. Southwestern Blotting Assay

    • Yinshan Jia, Linda Nagore, Harry Jarrett
    Pages 85-99

  7. Single-Molecule Approaches for the Characterization of Riboswitch Folding Mechanisms

    • Julien Boudreault, D. Cibran Perez-Gonzalez, J. Carlos Penedo, Daniel A. Lafontaine
    Pages 101-107

  8. Probing of Nascent Riboswitch Transcripts

    • Adrien Chauvier, Daniel A. Lafontaine
    Pages 109-114

  9. Functional Studies of DNA-Protein Interactions Using FRET Techniques

    • Simon Blouin, Timothy D. Craggs, Daniel A. Lafontaine, J. Carlos Penedo
    Pages 115-141

  10. Precise Identification of Genome-Wide Transcription Start Sites in Bacteria by 5′-Rapid Amplification of cDNA Ends (5′-RACE)

    • Dominick Matteau, Sébastien Rodrigue
    Pages 143-159

  11. Analysis of DNA Supercoiling Induced by DNA–Protein Interactions

    • David J. Clark, Benoît P. Leblanc
    Pages 161-172

  12. Precise Identification of DNA-Binding Proteins Genomic Location by Exonuclease Coupled Chromatin Immunoprecipitation (ChIP-exo)

    • Dominick Matteau, Sébastien Rodrigue
    Pages 173-193

  13. The Cruciform DNA Mobility Shift Assay: A Tool to Study Proteins That Recognize Bent DNA

    • Victor Y. Stefanovsky, Tom Moss
    Pages 195-203

  14. Individual and Sequential Chromatin Immunoprecipitation Protocols

    • Mayra Furlan-Magaril, Félix Recillas-Targa
    Pages 205-218

  15. Chromatin Endogenous Cleavage (ChEC) as a Method to Quantify Protein Interaction with Genomic DNA in Saccharomyces cerevisiae

    • Virginia Babl, Ulrike Stöckl, Herbert Tschochner, Philipp Milkereit, Joachim Griesenbeck
    Pages 219-232

  16. Selection and Validation of Spacer Sequences for CRISPR-Cas9 Genome Editing and Transcription Regulation in Bacteria

    • Frédéric Grenier, Jean-François Lucier, Sébastien Rodrigue
    Pages 233-244

  17. Detection of Short-Range DNA Interactions in Mammalian Cells Using High-Resolution Circular Chromosome Conformation Capture Coupled to Deep Sequencing

    • Jean-François Millau, Luc Gaudreau
    Pages 245-259

  18. Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq)

    • Stéphanie Bianco, Sébastien Rodrigue, Bruce D. Murphy, Nicolas Gévry
    Pages 261-272

  19. Aggregate and Heatmap Representations of Genome-Wide Localization Data Using VAP, a Versatile Aggregate Profiler

    • Mylène Brunelle, Charles Coulombe, Christian Poitras, Marc-Antoine Robert, Alexei Nordell Markovits, François Robert et al.
    Pages 273-298

  20. Circular Dichroism for the Analysis of Protein–DNA Interactions

    • Garry Scarlett, Giuliano Siligardi, Geoffrey G. Kneale
    Pages 299-312
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Keywords

About this book

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.

Editors and Affiliations

  • Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Canada

    Benoît P. Leblanc, Sébastien Rodrigue

Bibliographic Information

  • Book Title: DNA-Protein Interactions

  • Book Subtitle: Principles and Protocols

  • Editors: Benoît P. Leblanc, Sébastien Rodrigue

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-2877-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-2876-7Published: 26 September 2015

  • Softcover ISBN: 978-1-4939-4945-8Published: 22 October 2016

  • eBook ISBN: 978-1-4939-2877-4Published: 24 September 2015

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 4

  • Number of Pages: XI, 347

  • Number of Illustrations: 49 b/w illustrations, 24 illustrations in colour

  • Topics: Human Genetics, Proteomics

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