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Volumn 87, Issue 5, 2004, Pages 3066-3073

Computational analysis of DNA gyrase action

Author keywords

[No Author keywords available]

Indexed keywords

CIRCULAR DNA; DNA; DNA TOPOISOMERASE (ATP HYDROLYSING); GUANOSINE; THYMIDINE; BACTERIAL DNA;

EID: 16344371468     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.042994     Document Type: Article
Times cited : (2)

References (55)
  • 1
    • 0024316735 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 7
  • 8
    • 0036317910 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 16
    • 0021320555 scopus 로고
    • 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
  • 17
    • 0033587704 scopus 로고    scopus 로고
    • A model for the mechanism of strand passage by DNA gyrase
    • Kampranis, S. C., A. D. Bates, and A. Maxwell. 1999. A model for the mechanism of strand passage by DNA gyrase. Proc. Natl. Acad. Sci. USA. 96:8414-8419.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 8414-8419
    • Kampranis, S.C.1    Bates, A.D.2    Maxwell, A.3
  • 18
    • 0019435921 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 24
    • 0018835270 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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
  • 51
    • 0030973367 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 54
    • 0030014783 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


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