Main description:

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.

Contents:

1. Electrophoretic Mobility Shift Assay Using Radiolabeled DNA Probes

Dominic Poulin-Laprade and Vincent Burrus

2. In Vitro DNase I Footprinting

Benoit 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

Regen Drouin, Nathalie Bastien, Jean-Francois Millau, Francois 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 Sebastien Rodrigue

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

David J. Clark and Benoit P. Leblanc

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

Dominick Matteau and Sebastien 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 Felix Recillas-Targa

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

Virginia Babl, Ulrike Stoeckl, Herbert Tschochner, Philipp Milkereit, and Joachim Griesenbeck

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

Frederic Grenier, Jean-Francois Lucier, and Sebastien Rodrigue

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

Jean-Francois Millau and Luc Gaudreau

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

Stephanie Bianco, Sebastien Rodrigue, Bruce D. Murphy, and Nicolas Gevry

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

Mylene Brunelle, Charles Coulombe, Christian Poitras, Marc-Antoine Robert, Alexei Nordell Markovits, Francois Robert, and Pierre-Etienne 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