Alexander Vologodskii

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

Email:

Research Interests:

DNA Conformational Properties, Circular DNA, DNA Topology, and DNA-protein interaction

Selected Works:

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).

P. Sa-Ardyen, A. V. Vologodskii, and N. C. Seeman. The flexibility of DNA double crossover molecules. Biophys. J. 84, 3829-37 (2003).

I. Grainge, S. Pathania, A. Vologodskii, R. Harshey and M. Jayaram. Symmetric DNA sites are functionally asymmetric within Flp and Cre site-specific DNA recombination synapses. J. Mol. Biol. 320, 515-27 (2002).

M. Y. Vologodskaia and A. V. Vologodskii. Contribution of intrinsic curvature to measured DNA persistence length. J. Mol. Biol. 317:205-13, (2002).

A. V. Vologodskii, W. Zhang, V. V. Rybenkov, A. Podtelezhnikov, D. Subramanian, J. D. Griffith and N. R. Cozzarelli. Mechanism of topology simplification by type II DNA topoisomerases. Proc. Natl. Acad. Sci. U.S.A. 98:3045-49, (2001).

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