Simulations of Action of DNA Topoisomerases to Investigate Boundaries and Shapes of Spaces of Knots
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| Publicat a: | Biophysical Journal vol. 87, no. 5 (Nov 2004), p. 2968-2975 |
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Biophysical Society
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| 100 | 1 | |a Flammini, Alessandro | |
| 245 | 1 | |a Simulations of Action of DNA Topoisomerases to Investigate Boundaries and Shapes of Spaces of Knots | |
| 260 | |b Biophysical Society |c Nov 2004 | ||
| 513 | |a Evaluation Studies | ||
| 520 | 3 | |a The configuration space available to randomly cyclized polymers is divided into subspaces accessible to individual knot types. A phantom chain utilized in numerical simulations of polymers can explore all subspaces, whereas a real closed chain forming a figure-of-eight knot, for example, is confined to a subspace corresponding to this knot type only. One can conceptually compare the assembly of configuration spaces of various knot types to a complex foam where individual cells delimit the configuration space available to a given knot type. Neighboring cells in the foam harbor knots that can be converted into each other by just one intersegmental passage. Such a segment-segment passage occurring at the level of knotted configurations corresponds to a passage through the interface between neighboring cells in the foamy knot space. Using a DNA topoisomerase-inspired simulation approach we characterize here the effective interface area between neighboring knot spaces as well as the surface-to-volume ratio of individual knot spaces. These results provide a reference system required for better understanding mechanisms of action of various DNA topoisomerases. [PUBLICATION ABSTRACT] The configuration space available to randomly cyclized polymers is divided into subspaces accessible to individual knot types. A phantom chain utilized in numerical simulations of polymers can explore all subspaces, whereas a real closed chain forming a figure-of-eight knot, for example, is confined to a subspace corresponding to this knot type only. One can conceptually compare the assembly of configuration spaces of various knot types to a complex foam where individual cells delimit the configuration space available to a given knot type. Neighboring cells in the foam harbor knots that can be converted into each other by just one intersegmental passage. Such a segment-segment passage occurring at the level of knotted configurations corresponds to a passage through the interface between neighboring cells in the foamy knot space. Using a DNA topoisomerase-inspired simulation approach we characterize here the effective interface area between neighboring knot spaces as well as the surface-to-volume ratio of individual knot spaces. These results provide a reference system required for better understanding mechanisms of action of various DNA topoisomerases. | |
| 650 | 1 | 2 | |a Bacteriophage T4 |x genetics |
| 650 | 2 | 2 | |a Computer Simulation |
| 650 | 1 | 2 | |a DNA, Viral |x chemistry |
| 650 | 1 | 2 | |a Models, Chemical |
| 650 | 1 | 2 | |a Models, Molecular |
| 650 | 2 | 2 | |a Models, Statistical |
| 650 | 2 | 2 | |a Nucleic Acid Conformation |
| 653 | |a Knots | ||
| 653 | |a Cells | ||
| 653 | |a DNA polymerase | ||
| 653 | |a Enzymes | ||
| 653 | |a Molecules | ||
| 653 | |a Physical properties | ||
| 653 | |a Deoxyribonucleic acid--DNA | ||
| 653 | |a Polymers | ||
| 700 | 1 | |a Maritan, Amos | |
| 700 | 1 | |a Stasiak, Andrzej | |
| 773 | 0 | |t Biophysical Journal |g vol. 87, no. 5 (Nov 2004), p. 2968-2975 | |
| 786 | 0 | |d ProQuest |t Science Database | |
| 856 | 4 | 1 | |3 Citation/Abstract |u https://www.proquest.com/docview/89157336/abstract/embedded/6A8EOT78XXH2IG52?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text + Graphics |u https://www.proquest.com/docview/89157336/fulltextwithgraphics/embedded/6A8EOT78XXH2IG52?source=fedsrch |
| 856 | 4 | 0 | |3 Full Text - PDF |u https://www.proquest.com/docview/89157336/fulltextPDF/embedded/6A8EOT78XXH2IG52?source=fedsrch |