Geometry and Physics of Catenanes Applied to the Study of DNA Replication
| Autor: | Vsevolod Katritch, Jacques Dubochet, Theo Koller, José Sogo, Andrzej Stasiak, Ben Laurie |
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| Rok vydání: | 1998 |
| Předmět: |
DNA Replication
Models Molecular Pure mathematics DNA biosynthesis Catenane Biophysics DNA-Directed DNA Polymerase Simian virus 40 Circular DNA 010402 general chemistry Models Biological 01 natural sciences Biophysical Phenomena 03 medical and health sciences Knot (unit) DNA Catenanes Dna viral 030304 developmental biology Physics DNA/biosynthesis DNA/chemistry DNA Circular/chemistry DNA Circular/ultrastructure DNA Viral/chemistry DNA Viral/ultrastructure DNA-Directed DNA Polymerase/metabolism Mathematics Microscopy Electron Nucleic Acid Conformation 0303 health sciences DNA replication DNA Mathematics::Geometric Topology 0104 chemical sciences Crystallography Compact space DNA Viral DNA Circular Research Article |
| Zdroj: | Biophysical Journal, vol. 74, no. 6, pp. 2815-2822 |
| ISSN: | 0006-3495 |
| DOI: | 10.1016/s0006-3495(98)77988-3 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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