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The Bacterial Nucleoid

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Cover of 'The Bacterial Nucleoid'

Table of Contents

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    Book Overview
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    Chapter 1 Homologous Recombineering to Generate Chromosomal Deletions in Escherichia coli
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    Chapter 2 Measuring In Vivo Supercoil Dynamics and Transcription Elongation Rates in Bacterial Chromosomes
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    Chapter 3 Revealing Sister Chromatid Interactions with the loxP/ Cre Recombination Assay
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    Chapter 4 Transposon Insertion Site Sequencing for Synthetic Lethal Screening
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    Chapter 5 WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites
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    Chapter 6 High-Resolution Chromatin Immunoprecipitation: ChIP-Sequencing
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    Chapter 7 Generation and Analysis of Chromosomal Contact Maps of Bacteria
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    Chapter 8 Nucleoid-Associated Proteins: Genome Level Occupancy and Expression Analysis
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    Chapter 9 Isolation and Analysis of RNA Polymerase Supramolecular Complex with Associated Proteins
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    Chapter 10 A Chromosome Co-Entrapment Assay to Study Topological Protein–DNA Interactions
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    Chapter 11 Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins
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    Chapter 12 Biochemical Analysis of Bacterial Condensins
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    Chapter 13 Exploring Condensins with Magnetic Tweezers
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    Chapter 14 Applications of Magnetic Tweezers to Studies of NAPs
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    Chapter 15 A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data
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    Chapter 16 Multilocus Imaging of the E. coli Chromosome by Fluorescent In Situ Hybridization
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    Chapter 17 Imaging the Cell Cycle of Pathogen E. coli During Growth in Macrophage
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    Chapter 18 Measuring In Vivo Protein Dynamics Throughout the Cell Cycle Using Microfluidics
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    Chapter 19 Imaging of Bacterial Chromosome Organization by 3D Super-Resolution Microscopy
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    Chapter 20 Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins: The Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells
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    Chapter 21 Procedures for Model-Guided Data Analysis of Chromosomal Loci Dynamics at Short Time Scales
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    Chapter 22 Isolation and Characterization of Bacterial Nucleoids in Microfluidic Devices
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    Chapter 23 Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix
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    Chapter 24 Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase
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    Chapter 25 Erratum to: Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins, the Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells
Attention for Chapter 15: A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data
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Chapter title
A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data
Chapter number 15
Book title
The Bacterial Nucleoid
Published in
Methods in molecular biology, January 2017
DOI 10.1007/978-1-4939-7098-8_15
Pubmed ID
Book ISBNs
978-1-4939-7097-1, 978-1-4939-7098-8
Authors

Damien Larivière, Rodrigo Galindo-Murillo, Eric Fourmentin, Samuel Hornus, Bruno Lévy, Julie Papillon, Jean-François Ménétret, Valérie Lamour, Larivière, Damien, Galindo-Murillo, Rodrigo, Fourmentin, Eric, Hornus, Samuel, Lévy, Bruno, Papillon, Julie, Ménétret, Jean-François, Lamour, Valérie

Abstract

The structural modeling of a macromolecular machine is like a "Lego" approach that is challenged when blocks, like proteins imported from the Protein Data Bank, are to be assembled with an element adopting a serpentine shape, such as DNA templates. DNA must then be built ex nihilo, but modeling approaches are either not user-friendly or very long and fastidious. In this method chapter we show how to use GraphiteLifeExplorer, a software with a simple graphical user interface that enables the sketching of free forms of DNA, of any length, at the atomic scale, as fast as drawing a line on a sheet of paper. We took as an example the nucleoprotein complex of DNA gyrase, a bacterial topoisomerase whose structure has been determined using cryo-electron microscopy (Cryo-EM). Using GraphiteLifeExplorer, we could model in one go a 155 bp long and twisted DNA duplex that wraps around DNA gyrase in the cryo-EM map, improving the quality and interpretation of the final model compared to the initially published data.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 3 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 3 100%

Demographic breakdown

Readers by professional status Count As %
Professor 1 33%
Student > Ph. D. Student 1 33%
Student > Bachelor 1 33%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 1 33%
Agricultural and Biological Sciences 1 33%
Chemistry 1 33%