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51

The effect of ionic conditions on the conformations of supercoiled DNA. II. equilibrium catenation

Valentin V Rybenkov, Alexander V Vologodskii, Nicholas R Cozzarelli

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 587 KB

english, 1997

52

The effect of ionic conditions on the conformations of supercoiled DNA. I. sedimentation analysis

Valentin V. Rybenkov, Alexander V. Vologodskii, Nicholas R. Cozzarelli

Journal:

Journal of Molecular Biology

Year:

1997

Language:

english

File:

PDF, 389 KB

english, 1997

53

Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition

Hongmei Jian, Tamar Schlick, Alexander Vologodskii

Journal:

Journal of Molecular Biology

Year:

1998

Language:

english

File:

PDF, 314 KB

english, 1998

54

Effect of Magnesium on Cruciform Extrusion in Supercoiled DNA

Maria Y. Vologodskaia, Alexander V. Vologodskii

Journal:

Journal of Molecular Biology

Year:

1999

Language:

english

File:

PDF, 216 KB

english, 1999

55

The kinetics of oligonucleotide replacements

Luis P Reynaldo, Alexander V Vologodskii, Bruce P Neri, Victor I Lyamichev

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 279 KB

english, 2000

56

Contribution of the intrinsic curvature to measured DNA persistence length

Maria Vologodskaia, Alexander Vologodskii

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 264 KB

english, 2002

57

Premelting of superhelical DNA: an expression for superhelical energy

A.V. Vologodskii, M.D. Frank-Kamenetskii

Journal:

Year:

1981

Language:

english

File:

PDF, 167 KB

english, 1981

58

Theoretical study of cruciform states in superhelical DNAs

A.V. Vologodskii, M.D. Frank-Kamenetskii

Journal:

Year:

1982

Language:

english

File:

PDF, 335 KB

english, 1982

59

The relaxation time for a cruciform structure in superhelical DNA

A.V. Vologodskii, M.D. Frank-Kamenetskii

Journal:

Year:

1983

Language:

english

File:

PDF, 380 KB

english, 1983

60

Conformational and thermodynamic properties of supercoiled DNA

Alexander V. Vologodskii, Stephen D. Levene, Konstantin V. Klenin, Maxim Frank-Kamenetskii, Nicholas R. Cozzarelli

Journal:

Journal of Molecular Biology

Year:

1992

Language:

english

File:

PDF, 3.04 MB

english, 1992

61

Dynamics of DNA Loop Capture by the SfiI Restriction Endonuclease on Supercoiled and Relaxed DNA

Michelle L. Embleton, Alexander V. Vologodskii, Stephen E. Halford

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 1.47 MB

english, 2004

62

Protein-induced Local DNA Bends Regulate Global Topology of Recombination Products

Quan Du, Alexei Livshits, Agnieszka Kwiatek, Makkuni Jayaram, Alexander Vologodskii

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 852 KB

english, 2007

63

Computational Analysis of the Chiral Action of Type II DNA Topoisomerases

Konstantin Klenin, Jörg Langowski, Alexander Vologodskii

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 316 KB

english, 2002

64

Symmetric DNA Sites are Functionally Asymmetric Within Flp and Cre Site-specific DNA Recombination Synapses

Ian Grainge, Shailja Pathania, Alexander Vologodskii, Rasika M. Harshey, Makkuni Jayaram

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 503 KB

english, 2002

65

Sequence dependence of DNA bending rigidity

Geggier, S., Vologodskii, A.

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 491 KB

english, 2010

66

Multimerization-Cyclization of DNA Fragments as a Method of Conformational Analysis

Podtelezhnikov, Alexei A., Mao, Chengde, Seeman, Nadrian C., Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2000

Language:

english

File:

PDF, 343 KB

english, 2000

67

The Flexibility of DNA Double Crossover Molecules

Sa-Ardyen, Phiset, Vologodskii, Alexander V., Seeman, Nadrian C.

Journal:

Biophysical Journal

Year:

2003

Language:

english

File:

PDF, 282 KB

english, 2003

68

Computer simulation of DNA supercoiling

Konstantin V. Klenin, Alexander V. Vologodskii, Vadim V. Anshelevich, Alexander M. Dykhne, Maxim D. Frank-Kamenetskii

Journal:

Journal of Molecular Biology

Year:

1991

Language:

english

File:

PDF, 660 KB

english, 1991

69

Theoretical Analysis of Disruptions in DNA Minicircles

Zheng, Xiaozhong, Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 403 KB

english, 2009

70

Determining Protein-Induced DNA Bending in Force-Extension Experiments: Theoretical Analysis

Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 288 KB

english, 2009

71

Temperature Dependence of DNA Persistence Length

Geggier, Stephanie, Kotlyar, Alexander, Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

72

Sequence Dependence of DNA Persistence Length

Geggier, Stephanie, Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 35 KB

english, 2011

73

Unlinking of Supercoiled DNA Catenanes by Type IIA Topoisomerases

Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 847 KB

english, 2011

74

Effect of supercoiling on the juxtaposition and relative orientation of DNA sites

Vologodskii, A., Cozzarelli, N.R.

Journal:

Biophysical Journal

Year:

1996

Language:

english

File:

PDF, 893 KB

english, 1996

75

The effect of intrinsic curvature on conformational properties of circular DNA

Katritch, V., Vologodskii, A.

Journal:

Biophysical Journal

Year:

1997

Language:

english

File:

PDF, 941 KB

english, 1997

76

Fluctuational opening of the double helix as revealed by theoretical and experimental study of DNA interaction with formaldehyde

Alexander V. Lukashin, Alexander V. Vologodskii, Maxim D. Frank-Kamenetskii, Yuril L. Lyubchenko

Journal:

Journal of Molecular Biology

Year:

1976

Language:

english

File:

PDF, 1.10 MB

english, 1976

77

Gapped DNA and Cyclization of Short DNA Fragments

Du, Quan, Vologodskaia, Maria, Kuhn, Heiko, Frank-Kamenetskii, Maxim, Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2005

Language:

english

File:

PDF, 221 KB

english, 2005

78

Braiding DNA: Experiments, Simulations, and Models

Charvin, G., Vologodskii, A., Bensimon, D., Croquette, V.

Journal:

Biophysical Journal

Year:

2005

Language:

english

File:

PDF, 582 KB

english, 2005

79

Brownian Dynamics Simulation of Knot Diffusion along a Stretched DNA Molecule

Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2006

Language:

english

File:

PDF, 106 KB

english, 2006

80

Probability of the Site Juxtaposition Determines the Rate of Protein-Mediated DNA Looping

Polikanov, Yury S., Bondarenko, Vladimir A., Tchernaenko, Vladimir, Jiang, Yong I., Lutter, Leonard C., Vologodskii, Alexander, Studitsky, Vasily M.

Journal:

Biophysical Journal

Year:

2007

Language:

english

File:

PDF, 278 KB

english, 2007

81

Computational Analysis of DNA Gyrase Action

Vologodskii, Alexander

Journal:

Biophysical Journal

Year:

2004

Language:

english

File:

PDF, 353 KB

english, 2004

82

DNA Extension under the Action of an External Force

Vologodskii, Alexander

Journal:

Year:

1994

Language:

english

File:

PDF, 405 KB

english, 1994

83

Conformational and Thermodynamic Properties of Supercoiled DNA

Vologodskii, A V, Cozzarelli, N R

Journal:

Annual Review of Biophysics and Biomolecular Structure

Year:

1994

Language:

english

File:

PDF, 1.11 MB

english, 1994

84

Experimental and Theoretical Analysis of the Invasive Signal Amplification Reaction †

Lyamichev, Victor I., Kaiser, Michael W., Lyamicheva, Natasha E., Vologodskii, Alexander V., Hall, Jeff G., Ma, Wu-Po, Allawi, Hatim T., Neri, Bruce P.

Journal:

Year:

2000

Language:

english

File:

PDF, 137 KB

english, 2000

85

Disruptions of the Regular Structure in DNA Minicircles

Vologodskii, Alexander, Du, Quan, Zheng, Xiaozhong, Kotlyar, Alexander

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 39 KB

english, 2009

86

Supercoiling, knotting, looping and other large-scale conformational properties of DNA

Vologodskii, Alexander V., Cozzarelli, Nicholas R.

Journal:

Current Opinion in Structural Biology

Year:

1994

Language:

english

File:

PDF, 426 KB

english, 1994

87

Exploiting Circular DNA

Alexander Vologodskii

Journal:

Proceedings of the National Academy of Sciences

Year:

1998

Language:

english

File:

PDF, 440 KB

english, 1998

88

Equilibrium Distributions of Topological States in Circular DNA: Interplay of Supercoiling and Knotting

Alexei A. Podtelezhnikov, Nicholas R. Cozzarelli and Alexander V. Vologodskii

Journal:

Proceedings of the National Academy of Sciences

Year:

1999

Language:

english

File:

PDF, 1.43 MB

english, 1999

89

Dynamics of Small Loops in DNA Molecules

Podtelezhnikov, Alexei A., Vologodskii, Alexander V.

Journal:

Year:

2000

Language:

english

File:

PDF, 59 KB

english, 2000

90

Bridged DNA Circles: A New Model System To Study DNA Topology

Vologodskii, Alexander

Journal:

Year:

2012

Language:

english

File:

PDF, 1.43 MB

english, 2012

91

α-Helix Nucleation Constant in Copolypeptides of Alanine and Ornithine or Lysine

Yang, Jianxin, Zhao, Kang, Gong, Youxiang, Vologodskii, Alexander, Kallenbach, Neville R.

Journal:

Journal of the American Chemical Society

Year:

1998

Language:

english

File:

PDF, 84 KB

english, 1998

92

Simulations of Polymer Cyclization by Brownian Dynamics

Podtelezhnikov, Alexei, Vologodskii, Alexander

Journal:

Year:

1997

Language:

english

File:

PDF, 145 KB

english, 1997

93

Strong bending of the DNA double helix

Vologodskii, A., D. Frank-Kamenetskii, M.

Journal:

Nucleic Acids Research

Year:

2013

Language:

english

File:

PDF, 769 KB

english, 2013

94

Temperature dependence of DNA persistence length

Geggier, S., Kotlyar, A., Vologodskii, A.

Journal:

Nucleic Acids Research

Year:

2011

Language:

english

File:

PDF, 1.16 MB

english, 2011

95

Effect of Excluded Volume on Topological Properties of Circular DNA

Klenin, K. V., Vologodskii, A. V., Anshelevich, V. V., Dykhne, A. M., Frank-Kamenetskii, M. D.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

1988

Language:

english

File:

PDF, 581 KB

english, 1988

96

Tightness of knots in a polymer chain

Zheng, Xiaozhong, Vologodskii, Alexander

Journal:

Physical Review E

Year:

2010

Language:

english

File:

PDF, 280 KB

english, 2010

97

Tightness of random knotting

Katritch, Vsevolod, Olson, Wilma K., Vologodskii, Alexander, Dubochet, Jacques, Stasiak, Andrzej

Journal:

Physical Review E

Year:

2000

Language:

english

File:

PDF, 133 KB

english, 2000

98

Sequence dependence of DNA bending rigidity

Stephanie Geggier, Alexander Vologodskii and Michael Levitt

Journal:

Proceedings of the National Academy of Sciences

Year:

2010

Language:

english

File:

PDF, 1.29 MB

english, 2010

99

Bending of short DNA helices

Vologodskii, Alexander, Du, Quan, Frank-Kamenetskii, Maxim D.

Journal:

Artificial DNA PNA & XNA

Year:

2013

Language:

english

File:

PDF, 194 KB

english, 2013

100

A Theoretical Study of Formation of DNA Noncanonical Structures Under Negative Superhelical Stress

Anshelevich, V. V., Vologodskii, A. V., Frank-Kamenetskii, M. D.

Journal:

Journal of Biomolecular Structure and Dynamics

Year:

1988

Language:

english

File:

PDF, 677 KB

english, 1988