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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. [PUBLICATION ABSTRACT]

Details

Title
Simulations of Action of DNA Topoisomerases to Investigate Boundaries and Shapes of Spaces of Knots
Publication title
Volume
87
Issue
5
Pages
2968-75
Number of pages
8
Publication year
2004
Publication date
Nov 2004
Publisher
Biophysical Society
Place of publication
New York
Country of publication
United States
Publication subject
ISSN
00063495
e-ISSN
15420086
Source type
Scholarly Journal
Language of publication
English
Document type
Evaluation Studies
Document feature
Tables; Diagrams; Graphs; Illustrations; References
Accession number
15326026
ProQuest document ID
89157336
Document URL
https://www.proquest.com/scholarly-journals/simulations-action-dna-topoisomerases-investigate/docview/89157336/se-2?accountid=208611
Copyright
Copyright Biophysical Society Nov 2004
Last updated
2024-10-04
Database
ProQuest One Academic