Molecular dynamics simulation of supercoiled DNA rings

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Arman Fathizadeh - , Institute for Research for Fundamental Sciences, Sharif University of Technology (Author)
  • Helmut Schiessel - , Leiden University (Author)
  • Mohammad Reza Ejtehadi - , Sharif University of Technology (Author)

Abstract

DNA supercoiling is a widespread phenomenon in biology. Here we introduce a coarse-grained DNA model and study supercoiled DNA rings via a rigid body molecular dynamics simulation. Our model allows us to investigate these structures in more detail than previously. The simulations are performed on rings of one to six kilobase pairs length and are compared to available experimental data and former simulation studies. The current study provides new additional information about some of the geometrical parameters of the supercoiled DNA rings. It also shows how enforcing a supercoiled DNA ring to two-dimensional space changes its geometrical parameters. Finally, our molecular dynamics method allows us to observe some dynamical effects like the creation and movement of supercoiled branches.

Details

Original languageEnglish
Pages (from-to)164-172
Number of pages9
JournalMacromolecules
Volume48
Issue number1
Publication statusPublished - 13 Jan 2015
Peer-reviewedYes
Externally publishedYes