期刊
BIOPHYSICAL CHEMISTRY
卷 148, 期 1-3, 页码 104-111出版社
ELSEVIER SCIENCE BV
DOI: 10.1016/j.bpc.2010.02.016
关键词
DNA electrophoresis; Supercoiling; Topoisomers; Writhe; Twist
资金
- DMS-NIGMS Joint Program in Mathematical Biology
- NIH [GM67242, 5SC3GM083779-02]
- NSF [DMS-800929]
- Direct For Mathematical & Physical Scien
- Division Of Mathematical Sciences [0800929] Funding Source: National Science Foundation
Agarose-gel electrophoresis has been used for more than thirty years to characterize the linking-number (Lk) distribution of closed-circular DNA molecules. Although the physical basis of this technique remains poorly understood, the gel-electrophoretic behavior of covalently closed DNAs has been used to determine the local unwinding of DNA by proteins and small-molecule ligands, characterize supercoiling-dependent conformational transitions in duplex DNA, and to measure helical-repeat changes due to shifts in temperature and ionic strength. Those results have been analyzed by assuming that the absolute mobility of a particular topoisomer is mainly a function of the integral number of superhelical turns, and thus a slowly varying function of plasmid molecular weight. In examining the mobilities of Lk topoisomers for a series of plasmids that differ incrementally in size over more than one helical turn, we found that the size-dependent agarose-gel mobility of individual topoisomers with identical values of Lk ( but different values of the excess linking number, Delta Lk) vary dramatically over a duplex turn. Our results suggest that a simple semi-empirical relationship holds between the electrophoretic mobility of linking-number topoisomers and their average writhe in solution. (C) 2010 Elsevier B.V. All rights reserved.
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