Geometry and physics of catenanes applied to the study of DNA replication

被引:41
|
作者
Laurie, B
Katritch, V
Sogo, J
Koller, T
Dubochet, J
Stasiak, A
机构
[1] Univ Lausanne, Lab Anal Ultrastruct, CH-1015 Lausanne, Switzerland
[2] AL Digital, London W4 4GB, England
[3] Rutgers State Univ, Dept Chem, New Brunswick, NJ 08903 USA
[4] ETH Honggerberg, Inst Zellbiol, CH-8093 Zurich, Switzerland
关键词
D O I
10.1016/S0006-3495(98)77988-3
中图分类号
Q6 [生物物理学];
学科分类号
071011 ;
摘要
The concept of ideal geometric configurations was recently applied to the classification and characterization of various knots. Different knots in their ideal form (i.e., the one requiring the shortest length of a constant-diameter tube to form a given knot) were shown to have an overall compactness proportional to the time-averaged compactness of thermally agitated knotted polymers forming corresponding knots. This was useful for predicting the relative speed of electrophoretic migration of different DNA knots. Here we characterize the ideal geometric configurations of catenanes (called links by mathematicians), i.e., closed curves in space that are topologically linked to each other. We demonstrate that the ideal configurations of different catenanes show interrelations very similar to those observed in the ideal configurations of knots. By analyzing literature data on electrophoretic separations of the torus-type of DNA catenanes with increasing complexity, we observed that their electrophoretic migration is roughly proportional to the overall compactness of ideal representations of the corresponding catenanes. This correlation does not apply, however, to electrophoretic migration of certain replication intermediates, believed up to now to represent the simplest torus-type catenanes. We propose, therefore, that freshly replicated circular DNA molecules, in addition to forming regular catenanes, may also form hemicatenanes.
引用
收藏
页码:2815 / 2822
页数:8
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