Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields.

Details

Serval ID
serval:BIB_A0FA22C23609
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Numerical simulation of gel electrophoresis of DNA knots in weak and strong electric fields.
Journal
Biophysical Journal
Author(s)
Weber C., Stasiak A., De Los Rios P., Dietler G.
ISSN
0006-3495[print], 0006-3495[linking]
Publication state
Published
Issued date
05/2006
Peer-reviewed
Oui
Volume
90
Number
9
Pages
3100-3105
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Abstract
Gel electrophoresis allows one to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots, being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of a closed, knotted, charged DNA chain drifting in an external electric field in a topologically restricted medium. Using a Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the knot type and on the electric field intensity is investigated. The results are in qualitative and quantitative agreement with electrophoretic experiments done under conditions of low and high electric fields.
Keywords
Algorithms, Computer Simulation, DNA/chemistry, Electric Conductivity, Electrophoresis, Electrophoresis, Agar Gel, Electrophoresis, Gel, Two-Dimensional, Models, Genetic, Monte Carlo Method, Nucleic Acid Conformation
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2008 10:36
Last modification date
20/08/2019 15:07
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