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

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Version: Final published version
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State: Public
Version: Supplementary document
Serval ID
serval:BIB_2DFB1F3E7AC2
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Geometry and physics of catenanes applied to the study of DNA replication.
Journal
Biophysical Journal
Author(s)
Laurie B., Katritch V., Sogo J., Koller T., Dubochet J., Stasiak A.
ISSN
0006-3495
Publication state
Published
Issued date
06/1998
Peer-reviewed
Oui
Volume
74
Number
6
Pages
2815-2822
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
Publication Status: ppublish
Abstract
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.
Keywords
Biophysical Phenomena, Biophysics, DNA/biosynthesis, DNA/chemistry, DNA Replication, DNA, Circular/chemistry, DNA, Circular/ultrastructure, DNA, Viral/chemistry, DNA, Viral/ultrastructure, DNA-Directed DNA Polymerase/metabolism, Mathematics, Microscopy, Electron, Models, Biological, Models, Molecular, Nucleic Acid Conformation, Simian virus 40
Pubmed
Open Access
Yes
Create date
24/01/2008 11:25
Last modification date
20/08/2019 14:12
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