Dynamical simulations of DNA supercoiling and compression. (21st March 2013)

• Record Type: Journal Article
• Authors: Swigon, David; Lim, Sookkyung; Kim, Yongsam
• Is Part Of: Biochemical Society transactions. Volume 41:Number 2(2013)
• Page Start: 554
• Page End: 558
• Publication Date: 2013-03-21
• Subjects: computational model -- DNA dynamics -- immersed boundary method -- polymer -- simulation -- supercoiling; Biochemistry -- Congresses; 572
• DOI: 10.1042/BST20120316
• Languages: English
• ISSNs: 0300-5127

Abstract

Abstract : In the present article, we summarize our recent studies of DNA dynamics using the generalized immersed boundary method. Our analysis of the effects of electrostatic repulsion on the dynamics of DNA supercoiling revealed that, after perturbation, a pre-twisted DNA collapses into a compact supercoiled configuration that is sensitive to the initial excess link and ionic strength of the solvent. A stochastic extension of the generalized immersed boundary method shows that DNA in solution subjected to a constant electric field is compressed into a configuration with smaller radius of gyration and smaller ellipticity ratio than those expected for such a molecule in a thermodynamic equilibrium.