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

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

  • Racko D Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland. dusan.racko@unil.ch.
  • Benedetti F Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
  • Dorier J Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
  • Burnier Y Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
  • Stasiak A Center for Integrative Genomics, University of Lausanne, 1015, Lausanne, Switzerland.
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  • 2017-08-27
Published in:
  • Methods in molecular biology (Clifton, N.J.). - 2017
DNA gyrase
DNA knots and catenanes
DNA topoisomerases
Molecular dynamics
Supercoiled DNA
Algorithms
Computational Biology
DNA
DNA Gyrase
DNA, Catenated
DNA, Superhelical
Molecular Dynamics Simulation
Nucleic Acid Conformation
English 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.
Language
  • English
Open access status
closed
Identifiers
Persistent URL
https://sonar.ch/global/documents/281303
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