Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots.

Détails

ID Serval
serval:BIB_961F77F9175E
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots.
Périodique
Biophysical Journal
Auteur(s)
Flammini A., Maritan A., Stasiak A.
ISSN
0006-3495[print], 0006-3495[linking]
Statut éditorial
Publié
Date de publication
2004
Peer-reviewed
Oui
Volume
87
Numéro
5
Pages
2968-2975
Langue
anglais
Notes
Publication types: Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Résumé
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.
Mots-clé
Bacteriophage T4/genetics, Computer Simulation, DNA, Viral/chemistry, Models, Chemical, Models, Molecular, Models, Statistical, Nucleic Acid Conformation
Pubmed
Web of science
Open Access
Oui
Création de la notice
24/01/2008 10:36
Dernière modification de la notice
20/08/2019 14:58
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