dorsal/arxiv
View SchemaGel Electrophoresis of DNA Knots in Weak and Strong Electric Fields
| Authors | C. Weber, A. Stasiak, M. Fleurant, P. De Los Rios, G. Dietler |
|---|---|
| Categories | |
| ArXiv ID | physics/0503097 |
| URL | https://arxiv.org/abs/physics/0503097 |
| DOI | 10.1529/biophysj.105.070128 |
Abstract
Gel electrophoresis allows 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 simple Monte Carlo algorithm, the dependence of the electrophoretic migration of the DNA molecules on the type of knot and on the electric field intensity was investigated. The results are in qualitative agreement with electrophoretic experiments done under conditions of low and high electric fields: especially the inversion of the behavior from low to high electric field could be reproduced. The knot topology imposes on the problem the constrain of self-avoidance, which is the final cause of the observed behavior in strong electric field.
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"abstract": "Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal\nlength according to the knot type. At low electric fields, complex knots being\nmore compact, drift faster than simpler knots. Recent experiments have shown\nthat the drift velocity dependence on the knot type is inverted when changing\nfrom low to high electric fields. We present a computer simulation on a lattice\nof a closed, knotted, charged DNA chain drifting in an external electric field\nin a topologically restricted medium. Using a simple Monte Carlo algorithm, the\ndependence of the electrophoretic migration of the DNA molecules on the type of\nknot and on the electric field intensity was investigated. The results are in\nqualitative agreement with electrophoretic experiments done under conditions of\nlow and high electric fields: especially the inversion of the behavior from low\nto high electric field could be reproduced. The knot topology imposes on the\nproblem the constrain of self-avoidance, which is the final cause of the\nobserved behavior in strong electric field.",
"arxiv_id": "physics/0503097",
"authors": [
"C. Weber",
"A. Stasiak",
"M. Fleurant",
"P. De Los Rios",
"G. Dietler"
],
"categories": [
"physics.bio-ph"
],
"doi": "10.1529/biophysj.105.070128",
"title": "Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields",
"url": "https://arxiv.org/abs/physics/0503097"
},
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