The Bacterial Nucleoid, Softcover reprint of the original 1st ed. 2017
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1624

This volume presents state-of-the-art protocols for key experiments that have revolutionized our understanding of the bacterial nucleoid. This book is divided into five parts: Part I introduces molecular genetic methods to study bacterial nucleoids; Part II highlights the study of bacterial nucleoid with whole genome analysis method; Part III discusses molecular biology methods to study nucleoid structuring factors; Part IV looks at imaging bacterial nucleoid; and Part V explores biophysics of the bacterial nucleoid. Written in the highly successful Methods in Molecular Biology series format, 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.

Thorough and cutting-edge, The Bacterial Nucleoid: Methods and Protocols is a valuable resource that provides a wealth of new information about this chromosome.

Preface…
Table of Contents…
Contributing Authors…

Part I Molecular Genetic Methods to Study Bacterial Nucleoid

1. Homologous Recombineering to Generate Chromosomal Deletions in Escherichia coli
Jack A. Bryant and David J. Lee
2. Measuring In Vivo Supercoil Dynamics and Transcription Elongation Rates in Bacterial Chromosomes
N. Patrick Higgins

3. Revealing Sister Chromatid Interactions with the loxP/Cre Recombination Assay
Elise Vickridge, Charlène Planchenault, and Olivier Espéli

4. Transposon Insertion Site Sequencing for Synthetic Lethal Screening
Yoshiharu Yamaichi and Tobias Dörr

Part II Study of bacterial nucleoid with whole genome analysis method

5. WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites
Mickaël Poidevin, Elisa Galli, Yoshiharu Yamaichi, and François-Xavier Barre < 6. High Resolution Chromatin Immunoprecipitation: ChIP-Sequencing
Roxanne E. Diaz, Aurore Sanchez, Véronique Anton Le Berre, and Jean-Yves Bouet

7. Generation and Analysis of Chromosomal Contact Maps of Bacteria
Martial Marbouty and Romain Koszul

8. Nucleoid Associated Proteins: Genome Level Occupancy and Expression Analysis
Parul Singh and Aswin Sai Narain Seshasayee

Part III Molecular Biology Methods to Study Nucleoid Structuring Factors

9. Isolation and Analysis of RNA Polymerase Supramolecular Complex with Associated Proteins
Sanja Mehandziska, Mircea A. Petrescu, and Georgi Muskhelishvili

10. A chromosome Co-Entrapment Assay to Study Topological Protein-DNA Interactions
Larissa Wilhelm and Stephan Gruber

11.Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins
Ramon A. van der Valk, Niels Laurens, and Remus T. Dame

12. Biochemical Analysis of Bacterial Condensins
Zoya M. Petrushenko and Valentin V. Rybenkov

13. Exploring Condensins with Magnetic Tweezers
Rupa Sarkar and Valentin V. Rybenkov

14.Applications of Magnetic Tweezers to Studies of NAPs
Ricksen S. Winardhi and Jie Yan

15. A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data
Damien Larivière, Rodrigo Galindo-Murillo, Eric Fourmentin, Samuel Hornus, Bruno Lévy, Julie Papillon, Jean-François Ménétret, and Valérie Lamour

Part IV Imaging Bacterial Nucleoid

16.Multi-Locus Imaging of the E. coli Chromosome by Fluorescent In Situ Hybridization
Bryan J. Visser, Mohan C. Joshi, and David Bates

17. Imaging the Cell Cycle of Pathogen E. coli During Growth in Macrophage
Gaëlle Demarre, Victoria Prudent, and Olivier Espéli

18. Measuring ivo Protein Dynamics throughout the Cell Cycle using Microfluidics
Roy de Leeuw, Peter Brazda, M. Charl Moolman, J.W.J. Kerssemakers, Belen Solano, and Nynke H. Dekker

19.Imaging of Bacterial Chromosome Organization by 3D Super-Resolution Microscopy
Antoine Le Gall, Diego I. Cattoni, and Marcelo Nollmann

20. Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins, the Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells
Christoph Spahn, Mathilda Glaesmann, Yunfeng Gao, Yong Hwee Foo, Marko Lampe, Linda J. Kenney, and Mike Heilemann

21. Procedures for Model-Guided Data Analysis of Chromosomal Loci Dynamics at Short Time Scales
Marco Gherardi and Marco Cosentino Lagomarsino

Part V Biophysics of the Bacterial Nucleoid

22.  Isolation and Characterization of Bacterial Nucleoids in Microuidic Devices
James Pelletier and Suckjoon Jun
23. Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix
Thibaut Lepage and Ivan Junier

24. Molecular Dynamics Simulation of Supercoiled, Knotted and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase
Dusan Racko, Fabrizio Benedetti, Julien Dorier, Yannis Burnier, and Andrzej Stasiak

Includes cutting-edge methods and protocols

Includes step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts

Includes supplementary material: sn.pub/extras