-
1
-
-
0024316735
-
DNA gyrase can supercoil DNA circles as small as 174 base-pairs
-
Bates, A. D., and A. Maxwell. 1989. DNA gyrase can supercoil DNA circles as small as 174 base-pairs. EMBO J. 8:1861-1866.
-
(1989)
EMBO J.
, vol.8
, pp. 1861-1866
-
-
Bates, A.D.1
Maxwell, A.2
-
2
-
-
0019578292
-
Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition
-
Brian, A. A., H. L. Frisch, and L. S. Lerman. 1981. Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition. Biopolymers. 20:1305-1328.
-
(1981)
Biopolymers
, vol.20
, pp. 1305-1328
-
-
Brian, A.A.1
Frisch, H.L.2
Lerman, L.S.3
-
3
-
-
0018666498
-
A sign inversion mechanism for enzymatic supercoiling of DNA
-
Brown, P. O., and N. R. Cozzarelli. 1979. A sign inversion mechanism for enzymatic supercoiling of DNA. Science. 206:1081-1083.
-
(1979)
Science
, vol.206
, pp. 1081-1083
-
-
Brown, P.O.1
Cozzarelli, N.R.2
-
4
-
-
2442611949
-
The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold
-
Corbett, K. D., R. K. Shultzaberger, and J. M. Berger. 2004. The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Proc. Natl. Acad. Sci. USA. 101:7293-7298.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 7293-7298
-
-
Corbett, K.D.1
Shultzaberger, R.K.2
Berger, J.M.3
-
5
-
-
0019591164
-
Site-specific interaction of DNA gyrase with DNA
-
Fisher, L. M., K. Mizuuchi, M. H. O'Dea, H. Ohmori, and M. Gellert. 1981. Site-specific interaction of DNA gyrase with DNA. Proc. Natl. Acad. Sci. USA. 78:4165-4169.
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 4165-4169
-
-
Fisher, L.M.1
Mizuuchi, K.2
O'Dea, M.H.3
Ohmori, H.4
Gellert, M.5
-
7
-
-
0000576165
-
DNA gyrase: An enzyme that introduces superhelical turns into DNA
-
Gellert, M., K. Mizuuchi, M. H. O'Dea, and H. A. Nash. 1976. DNA gyrase: an enzyme that introduces superhelical turns into DNA. Proc. Natl. Acad. Sci. USA. 73:3872-3876.
-
(1976)
Proc. Natl. Acad. Sci. USA
, vol.73
, pp. 3872-3876
-
-
Gellert, M.1
Mizuuchi, K.2
O'Dea, M.H.3
Nash, H.A.4
-
8
-
-
0036317910
-
Symmetric DNA sites are functionally asymmetric within Flp and Cre site-specific DNA recombination synapses
-
Grainge, I., S. Pathania, A. Vologodskii, R. Harshey, and M. Jayaram. 2002. Symmetric DNA sites are functionally asymmetric within Flp and Cre site-specific DNA recombination synapses. J. Mol. Biol. 320:515-527.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 515-527
-
-
Grainge, I.1
Pathania, S.2
Vologodskii, A.3
Harshey, R.4
Jayaram, M.5
-
9
-
-
0019588074
-
Investigation of the flexibility of DNA using transient electric birefringence
-
Hagerman, P. J. 1981. Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers. 20:1503-1535.
-
(1981)
Biopolymers
, vol.20
, pp. 1503-1535
-
-
Hagerman, P.J.1
-
11
-
-
0025312950
-
Sequence-directed curvature of DNA
-
Hagerman, P. J. 1990. Sequence-directed curvature of DNA. Annu. Rev. Biochem. 59:755-781.
-
(1990)
Annu. Rev. Biochem.
, vol.59
, pp. 755-781
-
-
Hagerman, P.J.1
-
12
-
-
84985720098
-
Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains
-
Hagerman, P. J., and B. H. Zimm. 1981. Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains. Biopolymers. 20:1481-1502.
-
(1981)
Biopolymers
, vol.20
, pp. 1481-1502
-
-
Hagerman, P.J.1
Zimm, B.H.2
-
13
-
-
0031793539
-
Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations
-
Hammermann, M., N. Brun, K. V. Kienin, R. May, K. Toth, and J. Langowski. 1998. Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations. Biophys. J. 75:3057-3063.
-
(1998)
Biophys. J.
, vol.75
, pp. 3057-3063
-
-
Hammermann, M.1
Brun, N.2
Kienin, K.V.3
May, R.4
Toth, K.5
Langowski, J.6
-
14
-
-
0030844210
-
Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamic
-
Hammermann, M., C. Stainmaier, H. Merlitz, U. Kapp, W. Waldeck, G. Chirico, and J. Langowski. 1997. Salt effects on the structure and internal dynamics of superhelical DNAs studied by light scattering and Brownian dynamic. Biophys. J. 73:2674-2687.
-
(1997)
Biophys. J.
, vol.73
, pp. 2674-2687
-
-
Hammermann, M.1
Stainmaier, C.2
Merlitz, H.3
Kapp, U.4
Waldeck, W.5
Chirico, G.6
Langowski, J.7
-
15
-
-
1542328858
-
Nucleotide binding to DNA gyrase causes loss of DNA wrap
-
Heddle, J. G., S. Mitelheiser, A. Maxwell, and N. H. Thomson. 2004. Nucleotide binding to DNA gyrase causes loss of DNA wrap. J. Mol. Biol. 337:597-610.
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 597-610
-
-
Heddle, J.G.1
Mitelheiser, S.2
Maxwell, A.3
Thomson, N.H.4
-
16
-
-
0021320555
-
Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling
-
Horowitz, D. S., and J. C. Wang. 1984. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J. Mol. Biol. 173:75-91.
-
(1984)
J. Mol. Biol.
, vol.173
, pp. 75-91
-
-
Horowitz, D.S.1
Wang, J.C.2
-
18
-
-
0019435921
-
Mapping the topography of DNA wrapped around gyrase by nucleolytic and chemical probing of complexes of unique DNA sequences
-
Kirkegaard, K., and J. C. Wang. 1981. Mapping the topography of DNA wrapped around gyrase by nucleolytic and chemical probing of complexes of unique DNA sequences. Cell. 23:721-729.
-
(1981)
Cell
, vol.23
, pp. 721-729
-
-
Kirkegaard, K.1
Wang, J.C.2
-
19
-
-
0033902554
-
Modeling dynamic light scattering of supercoiled DNA
-
Klenin, K., M. Hammermann, and J. Langowski. 2000. Modeling dynamic light scattering of supercoiled DNA. Macromolecules. 33:1459-1466.
-
(2000)
Macromolecules
, vol.33
, pp. 1459-1466
-
-
Klenin, K.1
Hammermann, M.2
Langowski, J.3
-
20
-
-
0036299103
-
Computational analysis of the chiral action of type II DNA topoisomerases
-
Klenin, K., J. Langowski, and A. Vologodskii. 2002. Computational analysis of the chiral action of type II DNA topoisomerases. J. Mol. Biol. 320:359-367.
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 359-367
-
-
Klenin, K.1
Langowski, J.2
Vologodskii, A.3
-
21
-
-
0024021097
-
Effect of excluded volume on topological properties of circular DNA
-
Klenin, K. V., A. V. Vologodskii, V. V. Anshelevich, A. M. Dykhne, and M. D. Frank-Kamenetskii. 1988. Effect of excluded volume on topological properties of circular DNA. J. Biomol. Struct. Dyn. 5:1173-1185.
-
(1988)
J. Biomol. Struct. Dyn.
, vol.5
, pp. 1173-1185
-
-
Klenin, K.V.1
Vologodskii, A.V.2
Anshelevich, V.V.3
Dykhne, A.M.4
Frank-Kamenetskii, M.D.5
-
22
-
-
0025969098
-
Computer simulation of DNA super-coiling
-
Klenin, K. V., A. V. Vologodskii, V. V. Anshelevich, A. M. Dykhne, and M. D. Frank-Kamenetskii. 1991. Computer simulation of DNA super-coiling. J. Mol. Biol. 217:413-419.
-
(1991)
J. Mol. Biol.
, vol.217
, pp. 413-419
-
-
Klenin, K.V.1
Vologodskii, A.V.2
Anshelevich, V.V.3
Dykhne, A.M.4
Frank-Kamenetskii, M.D.5
-
23
-
-
0024580766
-
Variance of writhe for wormlike DNA rings with excluded volume
-
Klenin, K. V., A. V. Vologodskii, V. V. Anshelevich, V. Y. Klisko, A. M. Dykhne, and M. D. Frank-Kamenetskii. 1989. Variance of writhe for wormlike DNA rings with excluded volume. J. Biomol. Struct. Dyn. 6:707-714.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 707-714
-
-
Klenin, K.V.1
Vologodskii, A.V.2
Anshelevich, V.V.3
Klisko, V.Y.4
Dykhne, A.M.5
Frank-Kamenetskii, M.D.6
-
24
-
-
0018835270
-
Formation and resolution of DNA catenanes by DNA gyrase
-
Kreuzer, K. N., and N. R. Cozzarelli. 1980. Formation and resolution of DNA catenanes by DNA gyrase. Cell. 20:245-254.
-
(1980)
Cell
, vol.20
, pp. 245-254
-
-
Kreuzer, K.N.1
Cozzarelli, N.R.2
-
25
-
-
0023042216
-
Topological distributions and the torsional rigidity of DNA. A Monte Carlo study of DNA circles
-
Levene, S. D., and D. M. Crothers. 1986. Topological distributions and the torsional rigidity of DNA. A Monte Carlo study of DNA circles. J. Mol. Biol. 189:73-83.
-
(1986)
J. Mol. Biol.
, vol.189
, pp. 73-83
-
-
Levene, S.D.1
Crothers, D.M.2
-
26
-
-
0032189275
-
DNA gyrase and topoisomerase. IV. Biochemical activities, physiological roles during chromosome replication, and drug sensitivities
-
Levine, C., H. Hiasa, and K. J. Marians. 1998. DNA gyrase and topoisomerase. IV. Biochemical activities, physiological roles during chromosome replication, and drug sensitivities. Biochim. Biophys. Acta. 1400:29-43.
-
(1998)
Biochim. Biophys. Acta
, vol.1400
, pp. 29-43
-
-
Levine, C.1
Hiasa, H.2
Marians, K.J.3
-
27
-
-
0018039318
-
DNA-DNA gyrase complex: The wrapping of the DNA duplex outside the enzyme
-
Liu, L. F., and J. C. Wang. 1978a. DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme. Cell. 15:979-984.
-
(1978)
Cell
, vol.15
, pp. 979-984
-
-
Liu, L.F.1
Wang, J.C.2
-
28
-
-
0017968152
-
Micrococcus luteus DNA gyrase: Active components and a model for its supercoiling of DNA
-
Liu, L. F., and J. C. Wang. 1978b. Micrococcus luteus DNA gyrase: active components and a model for its supercoiling of DNA. Proc. Natl. Acad. Sci. USA. 75:2098-2102.
-
(1978)
Proc. Natl. Acad. Sci. USA
, vol.75
, pp. 2098-2102
-
-
Liu, L.F.1
Wang, J.C.2
-
29
-
-
0023664670
-
DNA gyrase-catalyzed decatenation of multiply linked DNA dimers
-
Marians, K. J. 1987. DNA gyrase-catalyzed decatenation of multiply linked DNA dimers. J. Biol. Chem. 262:10362-10368.
-
(1987)
J. Biol. Chem.
, vol.262
, pp. 10362-10368
-
-
Marians, K.J.1
-
30
-
-
0012127194
-
DNA gyrase action involves the introduction of transient double-strand breaks into DNA
-
Mizuuchi, K., L. M. Fisher, M. H. O'Dea, and M. Gellert. 1980. DNA gyrase action involves the introduction of transient double-strand breaks into DNA. Proc. Natl. Acad. Sci. USA. 77:1847-1851.
-
(1980)
Proc. Natl. Acad. Sci. USA
, vol.77
, pp. 1847-1851
-
-
Mizuuchi, K.1
Fisher, L.M.2
O'Dea, M.H.3
Gellert, M.4
-
31
-
-
0019542484
-
Contacts between DNA gyrase and its binding site on DNA: Features of symmetry and asymmetry revealed by protection from nucleases
-
Morrison, A., and N. R. Cozzarelli. 1981. Contacts between DNA gyrase and its binding site on DNA: features of symmetry and asymmetry revealed by protection from nucleases. Proc. Natl. Acad. Sci. USA. 78:1416-1420.
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 1416-1420
-
-
Morrison, A.1
Cozzarelli, N.R.2
-
33
-
-
0028233250
-
Evidence for a conformational change in the DNA gyrase-DNA complex from hydroxyl radical footprinting
-
Orphanides, G., and A. Maxwell. 1994. Evidence for a conformational change in the DNA gyrase-DNA complex from hydroxyl radical footprinting. Nucleic Acids Res. 22:1567-1575.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 1567-1575
-
-
Orphanides, G.1
Maxwell, A.2
-
34
-
-
0028806614
-
The interaction of Escherichia coli topoisomerase IV with DNA
-
Peng, H., and K. J. Marians. 1995. The interaction of Escherichia coli topoisomerase IV with DNA. J. Biol. Chem. 270:25286-25290.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 25286-25290
-
-
Peng, H.1
Marians, K.J.2
-
36
-
-
0027279063
-
Probability of DNA knotting and the effective diameter of the DNA double helix
-
Rybenkov, V. V., N. R. Cozzarelli, and A. V. Vologodskii. 1993. Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. USA. 90:5307-5311.
-
(1993)
Proc. Natl. Acad. Sci. USA
, vol.90
, pp. 5307-5311
-
-
Rybenkov, V.V.1
Cozzarelli, N.R.2
Vologodskii, A.V.3
-
37
-
-
0030758268
-
Simplification of DNA topology below equilibrium values by type II topoisomerases
-
Rybenkov, V. V., C. Ullsperger, A. V. Vologodskii, and N. R. Cozzarelli. 1997a. Simplification of DNA topology below equilibrium values by type II topoisomerases. Science. 277:690-693.
-
(1997)
Science
, vol.277
, pp. 690-693
-
-
Rybenkov, V.V.1
Ullsperger, C.2
Vologodskii, A.V.3
Cozzarelli, N.R.4
-
38
-
-
0030740986
-
The effect of ionic conditions on DNA helical repeat, effective diameter, and free energy of supercoiling
-
Rybenkov, V. V., A. V. Vologodskii, and N. R. Cozzarelli. 1997b. The effect of ionic conditions on DNA helical repeat, effective diameter, and free energy of supercoiling. Nucleic Acids Res. 25:1412-1418.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 1412-1418
-
-
Rybenkov, V.V.1
Vologodskii, A.V.2
Cozzarelli, N.R.3
-
39
-
-
0031588905
-
The effect of ionic conditions on the conformations of supercoiled DNA. II. Equilibrium catenation
-
Rybenkov, V. V., A. V. Vologodskii, and N. R. Cozzarelli. 1997c. The effect of ionic conditions on the conformations of supercoiled DNA. II. Equilibrium catenation. J. Mol. Biol. 267:312-323.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 312-323
-
-
Rybenkov, V.V.1
Vologodskii, A.V.2
Cozzarelli, N.R.3
-
40
-
-
0030977220
-
The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis
-
Rybenkov, V. V., A. V. Vologoskii, and N. R. Cozzarelli. 1997d. The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis. J. Mol. Biol. 267:299-311.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 299-311
-
-
Rybenkov, V.V.1
Vologoskii, A.V.2
Cozzarelli, N.R.3
-
41
-
-
0027200062
-
Knotting of a DNA chain during ring closure
-
Shaw, S. Y., and J. C. Wang. 1993. Knotting of a DNA chain during ring closure. Science. 260:533-536.
-
(1993)
Science
, vol.260
, pp. 533-536
-
-
Shaw, S.Y.1
Wang, J.C.2
-
42
-
-
0017389770
-
Interactions of highly charged colloidal cylinders with applications to double-stranded DNA
-
Stigter, D. 1977. Interactions of highly charged colloidal cylinders with applications to double-stranded DNA. Biopolymers. 16:1435-1448.
-
(1977)
Biopolymers
, vol.16
, pp. 1435-1448
-
-
Stigter, D.1
-
43
-
-
0025355712
-
Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat
-
Taylor, W. H., and P. J. Hagerman. 1990. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212:363-376.
-
(1990)
J. Mol. Biol.
, vol.212
, pp. 363-376
-
-
Taylor, W.H.1
Hagerman, P.J.2
-
44
-
-
0029856729
-
Contrasting enzymatic activities of topoisomerase IV and DNA gyrase from Escherichia coli
-
Ullsperger, C., and N. R. Cozzarelli. 1996. Contrasting enzymatic activities of topoisomerase IV and DNA gyrase from Escherichia coli. J. Biol. Chem. 271:31549-31555.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 31549-31555
-
-
Ullsperger, C.1
Cozzarelli, N.R.2
-
45
-
-
0028495164
-
DNA extension under the action of an external force
-
Vologodskii, A. V. 1994. DNA extension under the action of an external force. Macromolecules. 27:5623-5625.
-
(1994)
Macromolecules
, vol.27
, pp. 5623-5625
-
-
Vologodskii, A.V.1
-
46
-
-
0027171352
-
Monte Carlo analysis of the conformation of DNA catenanes
-
Vologodskii, A. V., and N. R. Cozzarelli. 1993. Monte Carlo analysis of the conformation of DNA catenanes. J. Mol. Biol. 232:1130-1140.
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 1130-1140
-
-
Vologodskii, A.V.1
Cozzarelli, N.R.2
-
47
-
-
0029159251
-
Modeling of long-range electrostatic interactions in DNA
-
Vologodskii, A. V., and N. R. Cozzarelli. 1995. Modeling of long-range electrostatic interactions in DNA. Biopolymers. 35:289-296.
-
(1995)
Biopolymers
, vol.35
, pp. 289-296
-
-
Vologodskii, A.V.1
Cozzarelli, N.R.2
-
48
-
-
0026489194
-
Conformational and thermodynamic properties of supercoiled DNA
-
Vologodskii, A. V., S. D. Levene, K. V. Klenin, M. D. Frank-Kamenetskii, and N. R. Cozzarelli. 1992. Conformational and thermodynamic properties of supercoiled DNA. J. Mol. Biol. 227:1224-1243.
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 1224-1243
-
-
Vologodskii, A.V.1
Levene, S.D.2
Klenin, K.V.3
Frank-Kamenetskii, M.D.4
Cozzarelli, N.R.5
-
50
-
-
0000487792
-
Problem of knots in statistical mechanics of polymer chains
-
Vologodskii, A. V., A. V. Lukashin, M. D. Frank-Kamenetskii, and V. V. Anshelevich. 1974. Problem of knots in statistical mechanics of polymer chains. Sov. Phys. JETP. 39:1059-1063.
-
(1974)
Sov. Phys. JETP
, vol.39
, pp. 1059-1063
-
-
Vologodskii, A.V.1
Lukashin, A.V.2
Frank-Kamenetskii, M.D.3
Anshelevich, V.V.4
-
51
-
-
0030973367
-
Extension of torsionally stressed DNA by external force
-
Vologodskii, A. V., and J. F. Marko. 1997. Extension of torsionally stressed DNA by external force. Biophys. J. 73:123-132.
-
(1997)
Biophys. J.
, vol.73
, pp. 123-132
-
-
Vologodskii, A.V.1
Marko, J.F.2
-
52
-
-
0036293430
-
Contribution of the intrinsic curvature to measured DNA persistence length
-
Vologodskaia, M., and A. Vologodskii. 2002. Contribution of the intrinsic curvature to measured DNA persistence length. J. Mol. Biol. 317:205-213.
-
(2002)
J. Mol. Biol.
, vol.317
, pp. 205-213
-
-
Vologodskaia, M.1
Vologodskii, A.2
-
53
-
-
0035853134
-
Mechanism of topology simplification by type II DNA topoisomerases
-
Vologodskii, A. V., W. Zhang, V. V. Rybenkov, A. A. Podtelezhnikov, D. Subramanian, J. D. Griffith, and N. R. Cozzarelli. 2001. Mechanism of topology simplification by type II DNA topoisomerases. Proc. Natl. Acad. Sci. USA. 98:3045-3049.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 3045-3049
-
-
Vologodskii, A.V.1
Zhang, W.2
Rybenkov, V.V.3
Podtelezhnikov, A.A.4
Subramanian, D.5
Griffith, J.D.6
Cozzarelli, N.R.7
-
54
-
-
0030014783
-
DNA topoisomerases
-
Wang, J. C. 1996. DNA topoisomerases. Annu. Rev. Biochem. 65:635-695.
-
(1996)
Annu. Rev. Biochem.
, vol.65
, pp. 635-695
-
-
Wang, J.C.1
-
55
-
-
0031695155
-
Moving one DNA double helix through another by a type II DNA topoisomerase: The story of a simple molecular machine
-
Wang, J. C. 1998. Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine. Quart. Rev. Biophys. 31:107-144.
-
(1998)
Quart. Rev. Biophys.
, vol.31
, pp. 107-144
-
-
Wang, J.C.1
|