DNA-Protein Interactions (4^th Ed., Softcover reprint of the original 4th ed. 2015)
Principles and Protocols
Methods in Molecular Biology Series, Vol. 1334

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.

1. Electrophoretic Mobility Shift Assay Using Radiolabeled DNA Probes

            Dominic Poulin-Laprade and Vincent Burrus

2. In Vitro DNase I Footprinting

            Benoît P. Leblanc and Tom Moss

3. 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, and Deborah Hinton

4. In Cellulo DNA Analysis: LMPCR Footprinting

            Régen Drouin,  Nathalie Bastien, Jean-François Millau,  François Vigneault, and Isabelle Paradis

5. Southwestern Blotting Assay

            Yinshan Jia, Linda Nagore, and Harry Jarrett

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

            Julien Boudreault, D. Cibran Perez-Gonzalez, J. Carlos Penedo, and Daniel A. Lafontaine

7. Probing of Nascent Riboswitch Transcripts

            Adrien Chauvier and Daniel A. Lafontaine

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

            Simon Blouin, Timothy D. Craggs, Daniel A. Lafontaine, and J. Carlos Penedo

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

            Dominick Matteau and Sébastien Rodrigue

10. Analysis of DNA Supercoiling Induced by DNA-Protein Interactions

            David J. Clark and Benoît P. Leblanc

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

            Dominick Matteau and Sébastien Rodrigue

12. The Cruciform DNA Mobility Shift Assay: A Tool to Study Proteins that Recognize Bent DNA

            Victor Y. Stefanovsky and Tom Moss

13. Individual and Sequential Chromatin Immunoprecipitation Protocols

            Mayra Furlan-Magaril and Félix Recillas-Targa

14. 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, and Joachim Griesenbeck

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

            Frédéric Grenier, Jean-François Lucier, and Sébastien Rodrigue

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

            Jean-François Millau and Luc Gaudreau

17. 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, and Nicolas Gévry

18. 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, and Pierre-Étienne Jacques

19. Circular Dichroism for the Analysis of Protein-DNA Interactions

            Garry Scarlett, Giuliano Siligardi, and Geoffrey G. Kneale

20. Quantitative Investigation of Protein-Nucleic Acid Interactions by Biosensor Surface Plasmon Resonance

            Shuo Wang, Gregory M.K. Poon, and W. David Wilson

21. Identification of Nucleic Acid High Affinity Binding Sequences of Proteins by SELEX

            Philippe Bouvet

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