Methods Mol Biol.: auth.: group Stasiak

Methods Mol Biol. 2017;1624:339-372. doi: 10.1007/978-1-4939-7098-8_24.

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

Racko D1,2,3Benedetti F4,5Dorier J4,5Burnier Y4,6Stasiak A4,7.


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.


DNA gyrase; DNA knots and catenanes; DNA topoisomerases; Molecular dynamics; Supercoiled DNA

PMID: 28842894