Simulations of electrophoretic collisions of DNA knots with gel obstacles

Details

Serval ID
serval:BIB_9F09EC636701
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Simulations of electrophoretic collisions of DNA knots with gel obstacles
Journal
Journal of Physics: Condensed Matter
Author(s)
Weber C., De Los Rios P., Dietler G., Stasiak A.
ISSN
0953-8984
Publication state
Published
Issued date
2006
Peer-reviewed
Oui
Volume
18
Number
14
Pages
S161-S171
Language
english
Notes
Proceedings Paper
Abstract
Gel electrophoresis can be used to separate nicked circular DNA molecules of equal length but forming different knot types. At low electric fields, complex knots drift faster than simpler knots. However, at high electric field the opposite is the case and simpler knots migrate faster than more complex knots. Using Monte Carlo simulations we investigate the reasons of this reversal of relative order of electrophoretic mobility of DNA molecules forming different knot types. We observe that at high electric fields the simulated knotted molecules tend to hang over the gel fibres and require passing over a substantial energy barrier to slip over the impeding gel fibre. At low electric field the interactions of drifting molecules with the gel fibres are weak and there are no significant energy barriers that oppose the detachment of knotted molecules from transverse gel fibres.
Keywords
MOLECULES, MECHANISM, MOBILITY, RECOMBINATION, DIMENSIONS, INVERSION, CATENANES, POLYMERS, MODEL
Web of science
Create date
10/03/2010 9:02
Last modification date
20/08/2019 15:05
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