Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots.
Details
Serval ID
serval:BIB_961F77F9175E
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots.
Journal
Biophysical Journal
ISSN
0006-3495[print], 0006-3495[linking]
Publication state
Published
Issued date
2004
Peer-reviewed
Oui
Volume
87
Number
5
Pages
2968-2975
Language
english
Notes
Publication types: Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Publication Status: ppublish
Abstract
The configuration space available to randomly cyclized polymers is divided into subspaces accessible to individual knot types. A phantom chain utilized in numerical simulations of polymers can explore all subspaces, whereas a real closed chain forming a figure-of-eight knot, for example, is confined to a subspace corresponding to this knot type only. One can conceptually compare the assembly of configuration spaces of various knot types to a complex foam where individual cells delimit the configuration space available to a given knot type. Neighboring cells in the foam harbor knots that can be converted into each other by just one intersegmental passage. Such a segment-segment passage occurring at the level of knotted configurations corresponds to a passage through the interface between neighboring cells in the foamy knot space. Using a DNA topoisomerase-inspired simulation approach we characterize here the effective interface area between neighboring knot spaces as well as the surface-to-volume ratio of individual knot spaces. These results provide a reference system required for better understanding mechanisms of action of various DNA topoisomerases.
Keywords
Bacteriophage T4/genetics, Computer Simulation, DNA, Viral/chemistry, Models, Chemical, Models, Molecular, Models, Statistical, Nucleic Acid Conformation
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2008 10:36
Last modification date
20/08/2019 14:58