Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase.

Details

Serval ID
serval:BIB_E48F1B04C7E2
Type
Article: article from journal or magazin.
Publication sub-type
Review (review): journal as complete as possible of one specific subject, written based on exhaustive analyses from published work.
Collection
Publications
Institution
Title
Molecular Dynamics Simulation of Supercoiled, Knotted, and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase.
Journal
Methods in Molecular Biology
Author(s)
Racko D., Benedetti F., Dorier J., Burnier Y., Stasiak A.
ISSN
1940-6029 (Electronic)
ISSN-L
1064-3745
Publication state
Published
Issued date
2017
Peer-reviewed
Oui
Volume
1624
Pages
339-372
Language
english
Abstract
A detailed protocol of molecular dynamics simulations of supercoiled DNA molecules that can be in addition knotted or catenated is described. We also describe how to model ongoing action of DNA gyrase that introduces negative supercoing into DNA molecules. The protocols provide detailed instructions about model parameters, equations of used potentials, simulation, and visualization. Implementation of the model into a frequently used molecular dynamics simulation environment, ESPResSo, is shown step by step.

Keywords
Algorithms, Computational Biology/methods, DNA/chemistry, DNA Gyrase/metabolism, DNA, Catenated/chemistry, DNA, Superhelical/chemistry, Molecular Dynamics Simulation, Nucleic Acid Conformation, DNA gyrase, DNA knots and catenanes, DNA topoisomerases, Molecular dynamics, Supercoiled DNA
Pubmed
Web of science
Create date
12/09/2017 13:28
Last modification date
20/08/2019 16:08
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