Alexander Vologodskii

Research Scholar of Chemistry
M.S. Moscow Physical Technical Institute; Ph.D. Moscow Physical Technical Institute; D.S. Moscow University

Phone: 212-998-3599
Lab Homepage

Areas of Research/Interest
DNA Conformational Properties, Circular DNA, DNA Topology, and DNA-protein interaction

Research Description
Research interests of my group are focused on conformational properties of DNA and DNA-protein interactions. Major attention is paid to topological properties of circular DNA molecules and enzymes which change DNA topology, DNA topoisomerases and site-specific recombinases. Molecular mechanisms of DNA bending became one of the group's major topics in the recent years. A key feature of our research strategy is a complementation between experimental and theoretical approaches. Our theoretical methods are based, mainly, on computer simulation of DNA equilibrium and dynamic properties. In particular, we can simulate properties which determine outcomes of DNA enzymatic transformations and, by this way, calculate distributions of the reaction products. Then we can compare the simulated results with corresponding experimental data to test various models of the enzyme action. This approach, developed in my group, has already brought a new insight in our understanding of the enzyme action.

A. Vologodskii. Theoretical models of DNA topology simplification by type IIA DNA topoisomerases. Nucl. Acids Res., 37, 3125 - 3133 (2009).

A. Vologodskii. Determining protein-induced DNA bending in force-extension experiment: Theoretical analysis. Biophys J., 96, 3591-3599 (2009).

X. Zheng and A. Vologodskii. Theoretical analysis of disruptions in DNA minicircles. Biophys J., 96, 1341-1349 (2009).

Q. Du, A. Kotlyar, and A. Vologodskii. Kinking the double helix by bending deformation. Nucl. Acids Res., 36, 1120-1128 (2008).

Y. S. Polikanov, V. A. Bondarenko, V. Tchernaenko, Y. I. Jiang, L. C. Lutter, A.Vologodskii, and V. M. Studitsky. Probability of the site juxtaposition determines the rate of protein-mediated DNA looping. Biophys. J., 93, 2726-2731 (2007).

Q. Du, A. Livshits, A. Kwiatek, M. Jayaram, and A. Vologodskii. Protein-induced local DNA bends regulate global topological complexity of recombination products. J. Mol. Biol., 368, 170-182 (2007).

A. Vologodskii. Monte Carlo simulation of DNA topological properties. In Topology in Molecular Biology (Monastryrsky, M., ed.), pp. 23-41. Springer, Berlin - Heidelberg - New York (2007).
A. Vologodskii. Simulation of equilibrium and dynamic properties of large DNA molecules. In Computational Studies of DNA and RNA, Eds. F. Lankas and J. Sponer, Springer, pp.579-604 (2006).
A. Vologodskii. Energy transformation in biological molecular motors. Phys. Life Rev., 3, 119-132 (2006).
A. Vologodskii. Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. Biophys. J. 90, 1594-97 (2006).
Q. Du, C. Smith, N. Shiffeldrim, M. Vologodskaia and A. Vologodskii. Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc. Natl. Acad. Sci. USA, 102, 5397-5402 (2005).
Q. Du, M. Vologodskaia, H. Kuhn, M. Frank-Kamenetskii, and A. Vologodskii. Gapped DNA and cyclization of short DNA fragments. Biophys. J. 88, 4137-45 (2005).
G. Charvin, A. Vologodskii, D. Bensimon and V. Croquette. Braiding DNA: experiments, simulations and models. Biophys. J. 88, 4124-36 (2005).
A. Vologodskii. Computational analysis of DNA gyrase action. Biophys. J. 87, 3066-73 (2004).
M. L. Embleton, A. V. Vologodskii and S. E. Halford. Dynamics of DNA loop capture by the SfiI restriction endonuclease on supercoiled and relaxed DNA. J. Mol. Biol. 339, 53-66 (2004).
N. P. Higgins and A. Vologodskii. Topological behavior of plasmid DNA. In Plasmid Biology , G.Phillips, and B. Funnell (eds), p. 181-201, ASM Press, Washington D.C. (2004).
M. D. Stone, Z. Bryant, N. J. Crisona, S. B. Smith, A. Vologodskii , C. Bustamante, and N. R. Cozzarelli. Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases. Proc. Natl. Acad. Sci. USA 100, 8654-59 (2003).

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