Publications

Papers

  1. Q. Du, A. Kotlyar, and A. Vologodskii. Kinking the double helix by bending deformation. Nucl. Acids Res. , in press. (PDF)
  2. 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). http://www.biophysj.org/cgi/content/abstract/93/8/2726?etoc. (PDF)
  3. 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), http://dx.doi.org/10.1016/j.jmb.2007.02.010. (PDF)
  4. A. Vologodskii. Monte Carlo simulation of DNA topological properties. In: Topology in molecular biology, Ed. M. Monastryrsky, Springer, pp. 23-41 (2007). (PDF)
  5. 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). (PDF)
  6. A. Vologodskii. Energy transformation in biological molecular motors. Phys. Life Rev., 3, 119-132 (2006). (PDF)
  7. A. Vologodskii. Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. Biophys. J., 90, 1594-1597 (2006). (PDF)
  8. 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). (PDF)
  9. Q. Du, M. Vologodskaia, H. Kuhn, M. Frank-Kamenetskii, and A. Vologodskii. Gapped DNA and cyclization of short DNA fragments. Biophys. J., 88, 4137-4145 (2005). (PDF)
  10. G. Charvin, A. Vologodskii, D. Bensimon and V. Croquette. Braiding DNA: experiments, simulations and models. Biophys. J., 88, 4124-4136 (2005). (PDF)
  11. A. Vologodskii. Computational Analysis of DNA Gyrase Action. Biophys. J. 87, 3066-3073 (2004). (PDF)
  12. 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). (PDF)
  13. 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). (PDF)
  14. 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, 8654-8659 (2003). (PDF)
  15. P. Sa-Ardyen, A. V. Vologodskii, and N. C. Seeman. The flexibility of DNA double crossover molecules, Biophys. J., 84, 3829-3837 (2003). (PDF)
  16. 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, 515-527 (2002). (PDF)
  17. K. Klenin, J. Langowski and A. Vologodskii. Computational analysis of the chiral action of type II DNA topoisomerases, J. Mol. Biol., 320, 359-367 (2002). (PDF)
  18. M. Y. Vologodskaia and A. V. Vologodskii. Contribution of intrinsic curvature to measured DNA persistence length, J. Mol. Biol., 317, 205-213 (2001). (PDF)
  19. C. A. Olson, E. J. Spek, Z. Shi, A. V. Vologodskii, N. R. Kallenbach. Cooperative helix stabilization by complex Arg-Glu salt bridges, Proteins, 44, 123-132 (2001)
  20. A. V. Vologodskii. Distribution of topological states in circular DNA, Mol. Biol., 35, 285-297 (2001). (PDF)
  21. 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. USA, 98, 3045-3049 (2001). (PDF)
  22. J. Huang, T. Schlick and A. Vologodskii. Dynamics of site juxtaposition in supercoiled DNA, Proc. Natl. Acad. Sci. USA, 98, 968-973 (2001). (PDF)
  23. L. Postow, C. Ullsperger, R. W. Keller, C. Bustamante, A. V. Vologodskii and N. R. Cozzarelli. Positive torsional strain causes the formation of a four-way junction at replication forks, J. Biol. Chem., 276, 2790-2796 (2001). (PDF)
  24. A. A. Podtelezhnikov, C. Mao, N. C. Seeman, and A. Vologodskii. Multimerization-cyclization of DNA fragments as a method of conformational analysis, Biophys. J. 79, 2692-2704 (2000). (PDF)
  25. V. I. Lyamichev, M. W. Kaiser, N. E. Lyamicheva, A. V. Vologodskii, J. G. Hall, W.-P. Ma, H. T. Allawi and B. P. Neri. Experimental and Theoretical Analysis of the Invasive Signal Amplification Reaction, Biochemistry, 39, 9523-9532 (2000).
  26. V. Katritch, W. Olson, A. Vologodskii, J. Dubochet and A. Stasiak. Tightness of random knotting, Phys. Rev. E 61, 5545-5549 (2000). (PDF)
  27. L. P. Reynaldo, A. V. Vologodskii, B. P. Neri and V. I. Lyamichev. The kinetics of oligonucleotide replacements, J. Mol. Biol., 297, 511-520 (2000). (PDF)
  28. A. A. Podtelezhnikov and A. V. Vologodskii. Dynamics of small loops in DNA molecules, Macromolecules, 33, 2767-2771 (2000). (PDF)
  29. A. S. Krasilnikov, A. Podtelezhnikov, A. Vologodskii and S. M. Mirkin. Large-scale effects of transcriptional DNA supercoiling in vivo, J. Mol. Biol. 292, 1149-1160 (1999).
  30. A. I. Alexandrov, N. R. Cozzarelli, V. F. Holmes, A. B. Khodursky, B. J. Peter, L. Postow, V. Rybenkov and A. V. Vologodskii. Mechanisms of separation of the complementary strands of DNA during replication, Genetica, 106, 131-140 (1999). (PDF)
  31. A. A. Podtelezhnikov, N. R. Cozzarelli and A. V. Vologodskii . Equilibrium distributions of topological states in circular DNA: Interplay of supercoiling and knotting, Proc. Natl. Acad. Sci. USA 96, 12974-12979 (1999). (PDF)
  32. A. Vologodskii. Circular DNA, in On-Line Biophysics Textbook, ed. V. Bloomfield, http://www.biophysics.org/education/vologodskii.pdf (1999).
  33. M. Vologodskaia and A. Vologodskii. Effect of magnesium on the cruciform Extrusion in supercoiled DNA, J. Mol. Biol., 289, 851-859 (1999). (PDF)
  34. H. Jian, T. Schlick and A. Vologodskii. Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition, J. Mol. Biol., 284, 287-296 (1998).
  35. J. Yang, K. Zhao, Y. Gong, A. Vologodskii and N. Kallenbach. a-helix nucleation constant in copolypeptides of alanine and ornithine or lysine, J. Am. Chem. Soc., 120, 10646-10652, (1998).
  36. A. V. Vologodskii, N. J. Crisona, B. Laurie, P. Pieranski, V. Katritch, J. Dubochet and A. Stasiak. Sedimentation and electrophoretic migration of DNA knots and catenanes, J. Mol. Biol. 278, 1-3 (1998).
  37. A. V. Vologodskii. Exploiting circular DNA, Proc. Natl. Acad. Sci. USA 95, 4092-4093 (1998).
  38. A. V. Vologodskii, X. Yang, and N. C. Seeman. Non-complementary DNA helical structure induced by positive torsional stress, Nucl. Acids Res. 26, 1503-1508, (1998). (PDF)
  39. X. Yang, A. V. Vologodskii, B. Liu, B. Kemper and N. Seeman. Torsional control of double stranded DNA branch migration, Biopolymers 45, 69-83 (1998).
  40. V. V. Rybenkov, C. Ullsperger, A. V. Vologodskii and N. R. Cozzarelli. Simplification of DNA topology below equilibrium values by type II topoisomerases, Science 277, 690-693 (1997). (PDF)
  41. A. Podtelezhnikov and A. Vologodskii. Simulation of polymer cyclization by Brownian dynamics, Macromolecules 30, 6668-6673 (1997).
  42. H. Jian, A. Vologodskii and T. Schlick. A combined wormlike-chain and bead model for dynamic simulations of long DNA, J. Comp. Phys. 73, 123-132 (1997).
  43. A. V. Vologodskii and J. F. Marko. Extension of torsionally stressed DNA by external force. Biophys. J. 73, 123-132 (1997).
  44. V. V. Rybenkov, A. V. Vologodskii and N. R. Cozzarelli. The effect of ionic conditions on DNA helical repeat, effective diameter, and free energy of supercoiling. Nucl. Acids Res. 25, 1412-1418 (1997). (PDF)
  45. V. V. Rybenkov, A. V. Vologodskii and N. R. Cozzarelli. The effect of ionic conditions on the conformations of supercoiled DNA. II. Equilibrium catenation. J. Mol. Biol. 267, 312-323 (1997). (PDF)
  46. V. V. Rybenkov, A. V. Vologodskii and N. R. Cozzarelli. The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis. J. Mol. Biol. 267, 299-311 (1997). (PDF)
  47. V. Katritch, and A. V. Vologodskii. The effect of intrinsic curvature on conformational properties of circular DNA. Biophys. J. 72, 1070-1079 (1997).
  48. A. V. Vologodskii and N. R. Cozzarelli. Effect of supercoiling on the juxtaposition and relative orientation of DNA sites, Biophys. J. 70, 2548-2556 (1996).
  49. C. J. Ullsperger, A. V. Vologodskii and N. R. Cozzarelli. Unlinking of DNA by topoisomerases during DNA replication, Nucl. Acids Mol. Biol. 9, 115-143 (1995).
  50. A. V. Vologodskii and N. R. Cozzarelli. Modeling of long-range electrostatic interactions in DNA, Biopolymers 35, 289-296 (1995).
  51. A. V. Vologodskii. DNA extension under the action of an external force, Macromolecules 27, 5623-5625 (1994). (PDF)
  52. J. Langowski, U. Kapp, K. Klenin and A. V. Vologodskii. Solution structure and dynamics of DNA topoisomers: dynamic light scattering studies and Monte Carlo simulations, Biopolymers 34, 639-646 (1994).
  53. A. V. Vologodskii and N. R. Cozzarelli.. Supercoiling, knotting, looping, and other large-scale conformational properties of DNA, Curr. Opin. Struct. Biol. 4, 372-375 (1994).
  54. A. V. Vologodskii and N. R. Cozzarelli. Conformational and thermodynamic properties of supercoiled DNA, Ann. Rev. Biophys. Biomol. Struct. 23, 609-643 (1994).
  55. A. A. Podtelezhnikov, A. V. Kurakin, A. V. Vologodskii and D. I. Cherny. Testing the quality of electron microscope mapping data for DNA molecules with sequence-specific ligands, Micron 25, 439-446 (1994).
  56. V. V. Rybenkov, N. R. Cozzarelli, A. V. Vologodskii. The probability of DNA knotting and the effective diameter of the double helix, Proc. Natl. Acad. Sci. USA 90, 5307-5311 (1993). (PDF)
  57. A. V. Vologodskii and N. R. Cozzarelli. Monte Carlo analysis of the conformation of DNA catenanes, J. Mol. Biol. , 232, 1130-1140 (1993).
  58. A. V. Vologodskii, M. D. Frank-Kamenetskii. Modeling DNA Supercoiling, Methods in Enzymology, eds. D. M. J. Lilley & J. Dahlberg, v. 211, pp. 467-480 (1992).
  59. A. V. Vologodskii, S. D. Levene, K. V. Klenin, M. D. Frank-Kamenetskii and N. R. Cozzarelli. Conformational and thermodynamic properties of supercoiled DNA, J. Mol. Biol. 227, 1224-1243 (1992).
  60. V. V. Rybenkov and A. V. Vologodskii. Effective diameter of DNA, Molek. Biol. (Russia) 26, 1433-1439 (1992).
  61. K. V. Klenin, A. V. Vologodskii, V. V. Anshelevich, V. Y. Klishko, A. M. Dykhne and M. D. Frank-Kamenetskii. Computer simulation of DNA supercoiling, J. Mol. Biol. 217, 413-419 (1991).
  62. M. D. Frank-Kamenetskii and A. V. Vologodskii. Conformational properties of circular DNA's, in: Theoretical Biochemistry and Molecular Biophysics, vol. 1: DNA, pp. 117-123, eds. D. L. Beveridge & R. Lavery, Adenin Press, 1991.
  63. K. V. Klenin, A. V. Vologodskii, V. V. Anshelevich, V. Y. Klishko, A. M. Dykhne and M. D. Frank-Kamenetskii. Variance of writhe for wormlike DNA rings with excluded volume, J. Biomol. Struct. Dyn. 6, 707-714 (1989).
  64. V. N. Lyamichev, S. M. Mirkin, V. P. Kumarev, L. V. Baranova, A. V. Vologodskii and M. D. Frank-Kamenetskii. Energetics of the B-H transition in supercoiled DNA carrying d(CT)n×d(AG)n and d(C)n×d(G)n inserts, Nucl. Acids Res. 17, 9417-9423 (1989).
  65. K. V. Klenin, A. V. Vologodskii, V. V. Anshelevich, A. M. Dykhne and M. D. Frank-Kamenetskii. Effect of excluded volume on topological properties of circular DNA, J. Biomol. Struct. Dyn. 5, 1173-1185 (1988).
  66. M. P. Perelroyzen and A. V. Vologodskii. Theoretical analysis of. addressed, chemical modification of DNA, Nucl. Acids Res. 16, 4693-4704 (1988).
  67. V. V. Anshelevich, A. V. Vologodskii and M. D. Frank-Kamenetskii. A theoretical study of formation of DNA noncanonical structures under negative superhelical stress, J. Biomol. Struct. Dyn. 6, 247-259 (1988).
  68. S. M. Mirkin, V. I. Lyamichev, V. P. Kumarev, V. F. Kobzev, V. V. Nosikov and A. V. Vologodskii. The energetics of the B-Z transition in DNA, J. Biomol. Struct. Dyn. , 5, 79-88 (1987).
  69. D. V. Pakhomov and A. V. Vologodskii. A theoretical study of the B-A transition in superhelical DNA, Biopolymers and Cell (Russia), 2, 1005-1012 (1986).
  70. V. V. Anshelevich and A. V. Vologodskii. The effect of sequence heterogeneity on DNA melting kinetics, J. Biomol. Struct. Dyn. , 4, 251-262 (1986).
  71. M. D. Frank-Kamenetskii, A. V. Lukashin and V. V. Anshelevich and A. V. Vologodskii. Torsional and bending rigidity of the double helix from data on small DNA rings, J. Biomol. Struct. Dynam. 2, 1005-1012 (1985).
  72. A. V. Vologodskii. Formation of noncanonical structures in superhelical DNA. Effects of mutual influence of transitions, Molek. Biol. (Russia), 19, 687-692 (1985).
  73. A. V. Vologodskii. A theoretical study of the B-Z transition in DNA with arbitrary sequence, Molek. Biol. (Russia), 19, 1062-1072 (1985).
  74. V. V. Anshelevich, A. V. Vologodskii, A. V. Lukashin and M. D. Frank- Kamenetskii. Slow relaxational processes in the melting of linear biopolymers. A theory and its application to nucleic acids, Biopolymers 23, 39-58 (1984).
  75. M. D. Frank-Kamenetskii and A. V. Vologodskii. Thermodynamics of the B-Z transition in superhelical DNA, Nature 307, 481-482 (1984).
  76. A. V. Vologodskii and M. D. Frank-Kamenetskii. Left-handed Z form in superhelical DNA: a theoretical study, J. Biomol. Struct. Dyn. 1, 1325-1333 (1984).
  77. A. V. Vologodskii, B. R. Amirikyan, Y. L. Lyubchenko, and M. D. Frank-Kamenetskii. Allowance for heterogeneous stacking in the DNA helix-coil transition theory, J. Biomol. Struct. Dyn. 2, 131-148 (1984).
  78. A. V. Vologodskii and M. D. Frank-Kamenetskii. The relaxation time for a cruciform structure in superhelical DNA, FEBS Letters 160, 173-176 (1983).
  79. A. V. Vologodskii and M. D. Frank-Kamenetskii. Theoretical study of cruciform states in superhelical DNA, FEBS Letters 143, 257-260 (1982).
  80. V. V. Anshelevich and A. V. Vologodskii,. Random walk on a one-dimensional ingomogeneous lattice, J. Phys. A, 15, 185-197 (1982).
  81. A. V. Vologodskii and M. D. Frank-Kamenetskii. Premelting of superhelical DNA: an expression for superhelix energy, FEBS Letters 131, 178-180 (1981).
  82. M. D. Frank-Kamenetskii and A. V. Vologodskii. Topological aspects of polymer physics: theory and its biophysical applications, Usp. Phys. Nauk 134, 641-673 (1981) (English translation: Sov. Phys. Usp. 24, 679-695 (1981)).
  83. M. P. Perelroyzen, V. I. Liamichev, Y. A. Kalambet, Y. L. Lyubchenko and A. V. Vologodskii. A study of the reversibility of helix-coil transition in DNA, Nucl. Acids Res. 9, 4043-4059 (1981).
  84. B. R. Amirikian, A. V. Vologodskii and Y. L. Lyubchenko. Determination of DNA cooperativity factor, Nucl. Acids Res. 9, 5469-5482 (1981).
  85. V. V. Anshelevich and A. V. Vologodskii. Laplace operator and random walk on one-dimensional nonhomogeneous lattice, J. Stat. Phys. 25, 419-430 (1981).
  86. G. I. Chogovadze, A. V. Vologodskii and M. D. Frank-Kamenetskii. Influence of additional links stabilizing or destabilizing the double helix on the DNA melting temperature, Molek. Biol. (Russia) 14, 369-374 (1980).
  87. A. V. Vologodskii, A. V. Lukashin, V. V. Anshelevich and M. D. Frank-Kamenetskii. Fluctuations in superhelical DNA, Nucleic Acids Res. 6, 967-982 (1979).
  88. V. V. Anshelevich, A. V. Vologodskii, A. V. Lukashin and M. D. Frank-Kamenetskii. Statistical-mechanical treatment of violations of the double helix in supercoiled DNA, Biopolymers 18, 2733-2744 (1979).
  89. A. V. Vologodskii, V. V. Anshelevich, A. V. Lukashin and M. D. Frank-Kamenetskii. Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix, Nature 280, 294-298 (1979).
  90. Y. L. Lyubchenko, A. V. Vologodskii and M. D. Frank-Kamenetskii. Direct comparison of theoretical and experimental melting profiles for fX174 DNA, Nature 271, 28-31 (1978).
  91. A. V. Vologodskii and M. D. Frank-Kamenetskii. Theoretical melting curves and denaturation maps for DNA with knew sequences: fd DNA, Nucl. Acids Res. 5, 2547-2554 (1978).
  92. G. I. Karataev, V. I. Permogorov, A. V. Vologodskii and M. D. Frank-Kamenetskii. Denaturation maps of DNA: experimental and theoretical maps of fX174, Nucl. Acids Res. 5, 2493-2500 (1978).
  93. M. D. Frank-Kamenetskii and A. V. Vologodskii. The nature of the fine structure of DNA melting curves, Nature 269, 729-730 (1977).
  94. Y. L. Lyubchenko, M. D. Frank-Kamenetskii, A. V. Vologodskii Y. S. Lazurkin and G. G. Gause. Fine structure of DNA melting curves, Biopolymers 15, 1019-1036 (1976).
  95. A. V. Lukashin, A. V. Vologodskii and M. D. Frank-Kamenetskii. Comparison of different theoretical descriptions of helix-coil transition in DNA, Biopolymers 15, 1841-1844 (1976).
  96. A. V. Vologodskii and V. V. Anshelevich. On the character of the thermodynamic properties distribution in DNA molecules inside the melting interval, Nucl. Acids Res. 3, 3377-3382 (1976).
  97. A. V. Lukashin, A. V. Vologodskii, M. D. Frank-Kamenetskii and Y. L. Lyubchenko. Fluctuational opening of the double helix as revealed by theoretical and experimental study of DNA interaction with formaldehyde, J. Mol. Biol. 108, 665-682 (1976).
  98. A. V. Vologodskii, A. V. Lukashin, and M. D. Frank-Kamenetskii. Topological interaction between polymer chains, ZETF 67, 1876-1885 (1974). (English translation: Sov. Phys-JETP 40, 932 (1975)).
  99. M. D. Frank-Kamenetskii, A. V. Lukashin and A. V. Vologodskii. Statistical mechanics and topology of polymer chains, Nature 258, 398-402 (1975).
  100. B. N. Belintsev, A. V. Vologodskii and M. D. Frank-Kamenetskii. Influence of nucleotide sequence on stability of the DNA double helix, Molek. Biol. 10, 764-769 (1975).
  101. A. V. Vologodskii and M. D. Frank-Kamenetskii. Theoretical study of DNA unwinding under the action of formaldehyde, J. Theor. Biol. 55, 153-166 (1975).
  102. A. V. Vologodskii, M. D. Frank-Kamenetskii, A. V. Lukashin. Theory of co-operative formation of defects in DNA molecule under ultraviolet irradiation, J. Theor. Biol. 44, 271-286 (1974).
  103. A. V. Vologodskii, A. V. Lukashin, M. D. Frank-Kamenetskii and V. V. Anshelevich. The knot problem in statistical mechanics of polymer chains, ZETF 66, 2153-2163 (1974). (English translation: Sov. Phys-JETP 39, 327 (1974)).
  104. M. D. Frank-Kamenetskii, A. V. Lukashin and A. V. Vologodskii. Theory of co-operative formation of defects in biopolymer under irradiation, Dokl. USSR Acad. of Sci. 208, 721-724 (1973).

Monograph

A. V. Vologodskii. Topology and physics of circular DNA, CRC Press, Boca Roton, FL, USA, 1992.