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
Author(s)
Flammini A., Maritan A., Stasiak A.
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
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 11:36
Last modification date
20/08/2019 15:58
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