It is proposed to develop and refine a computational approach to analyze the conformational properties of supercoiled DNA catenanes, which are topologically linked closed circular DNA molecules. The approach is based on the Metropolis Monte Carlo procedure and allows construction of an equilibrium set of conformations of DNA molecules with specified topology. Variables to be treated include the size of the molecules, the supercoiling density, and the effective DNA diameter, which reflects the ionic strength. The principal parameter to be monitored is the angular distribution of juxtaposed DNA binding sites, since this is apparently the parameter sensed by topoisomerases and recombinases. The simulations will be coordinated with experiments to be carried out by Dr. Nick Cozzarelli's group at Berkeley. Catenanes are efficient model systems for studying the mechanisms of topoisomerases and recombinases. These molecules play critical roles in replication and gene expression, and they are the target of many anticancer and antibacterial drugs. Thus, the significance of the work lies in the opportunity to better understand the interrelationships between DNA topology and the conformation of catenanes, which is important for understanding the mechanisms of topoisomerases and recombinases.
| Vologodskii, Alexander (2011) Unlinking of supercoiled DNA catenanes by type IIA topoisomerases. Biophys J 101:1403-11 |
| Geggier, Stephanie; Kotlyar, Alexander; Vologodskii, Alexander (2011) Temperature dependence of DNA persistence length. Nucleic Acids Res 39:1419-26 |
| Zheng, Xiaozhong; Vologodskii, Alexander (2010) Tightness of knots in a polymer chain. Phys Rev E Stat Nonlin Soft Matter Phys 81:041806 |
| Vologodskii, Alexander (2010) DNA supercoiling helps to unlink sister duplexes after replication. Bioessays 32:9-12 |
| Geggier, Stephanie; Vologodskii, Alexander (2010) Sequence dependence of DNA bending rigidity. Proc Natl Acad Sci U S A 107:15421-6 |
| Vologodskii, Alexander (2009) Determining protein-induced DNA bending in force-extension experiments: theoretical analysis. Biophys J 96:3591-9 |
| Vologodskii, Alexander; Rybenkov, Valentin V (2009) Simulation of DNA catenanes. Phys Chem Chem Phys 11:10543-52 |
| Zheng, Xiaozhong; Vologodskii, Alexander (2009) Theoretical analysis of disruptions in DNA minicircles. Biophys J 96:1341-9 |
| Vologodskii, Alexander (2009) Theoretical models of DNA topology simplification by type IIA DNA topoisomerases. Nucleic Acids Res 37:3125-33 |
| Du, Quan; Kotlyar, Alexander; Vologodskii, Alexander (2008) Kinking the double helix by bending deformation. Nucleic Acids Res 36:1120-8 |
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