메뉴 건너뛰기




Volumn 154, Issue 7 SPEC. ISS., 2007, Pages 1381-1397

Random state transitions of knots: a first step towards modeling unknotting by type II topoisomerases

Author keywords

BFACF algorithm; DNA knots; Polymer models; Random knotting; Topoisomerase II

Indexed keywords


EID: 33847743923     PISSN: 01668641     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.topol.2006.05.010     Document Type: Article
Times cited : (32)

References (59)
  • 1
    • 0020719315 scopus 로고
    • A new Monte Carlo approach to the critical properties of self-avoiding random walks
    • Arãgao de Carvalho C., and Caracciolo S. A new Monte Carlo approach to the critical properties of self-avoiding random walks. J. Phys. (Paris) 44 (1983) 323-331
    • (1983) J. Phys. (Paris) , vol.44 , pp. 323-331
    • Arãgao de Carvalho, C.1    Caracciolo, S.2
  • 3
    • 0037117517 scopus 로고    scopus 로고
    • Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids
    • Arsuaga J., Vazquez M., Trigueros S., de Sumners W., and Roca J. Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids. Proc. Natl. Acad. Sci. USA 99 (2002) 5373-5377
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 5373-5377
    • Arsuaga, J.1    Vazquez, M.2    Trigueros, S.3    de Sumners, W.4    Roca, J.5
  • 4
    • 0000935544 scopus 로고
    • Random paths and random surfaces on a digital computer
    • Berg B., and Foerster D. Random paths and random surfaces on a digital computer. Phys. Lett. B 106 4 (1981) 323-326
    • (1981) Phys. Lett. B , vol.106 , Issue.4 , pp. 323-326
    • Berg, B.1    Foerster, D.2
  • 5
    • 0030045003 scopus 로고    scopus 로고
    • Structure and mechanism of DNA topoisomerase II
    • Berger J.M., Gamblin S.J., Harrison S.C., and Wang J.C. Structure and mechanism of DNA topoisomerase II. Nature 379 (1996) 225-232
    • (1996) Nature , vol.379 , pp. 225-232
    • Berger, J.M.1    Gamblin, S.J.2    Harrison, S.C.3    Wang, J.C.4
  • 6
    • 0029911698 scopus 로고    scopus 로고
    • Recent developments in DNA topoisomerase II structure and mechanism
    • Berger J.M., and Wang J.C. Recent developments in DNA topoisomerase II structure and mechanism. Curr. Opin. Struct. Biol. 6 (1996) 84-90
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , pp. 84-90
    • Berger, J.M.1    Wang, J.C.2
  • 7
    • 3242754359 scopus 로고    scopus 로고
    • DNA disentangling by type-2 topoisomerases
    • Buck G.R., and Zechiedrich E.L. DNA disentangling by type-2 topoisomerases. J. Mol. Biol. 340 (2004) 933-939
    • (2004) J. Mol. Biol. , vol.340 , pp. 933-939
    • Buck, G.R.1    Zechiedrich, E.L.2
  • 8
  • 9
    • 4243636725 scopus 로고
    • A general limitation on Monte Carlo algorithms of Metropolis type
    • Caracciolo S., Pelissetto A., and Sokal A.D. A general limitation on Monte Carlo algorithms of Metropolis type. Phys. Rev. Lett. 72 2 (1994) 179-182
    • (1994) Phys. Rev. Lett. , vol.72 , Issue.2 , pp. 179-182
    • Caracciolo, S.1    Pelissetto, A.2    Sokal, A.D.3
  • 10
    • 0034923502 scopus 로고    scopus 로고
    • DNA topoisomerases: structures, function, and mechanism
    • Champloux J.J. DNA topoisomerases: structures, function, and mechanism. Annu. Rev. Biochem. 70 (2001) 369-413
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 369-413
    • Champloux, J.J.1
  • 11
    • 23044520009 scopus 로고    scopus 로고
    • Rational tangle distances on knots and links
    • Darcy I. Rational tangle distances on knots and links. Math. Proc. Cambridge Philos. Soc. 128 (2000) 497-510
    • (2000) Math. Proc. Cambridge Philos. Soc. , vol.128 , pp. 497-510
    • Darcy, I.1
  • 12
    • 0035627462 scopus 로고    scopus 로고
    • Biological distances on DNA knots and links: applications to XER recombination
    • Knots in Hellas 2, 1998, Delphi
    • Darcy I. Biological distances on DNA knots and links: applications to XER recombination. Knots in Hellas 2, 1998, Delphi. J. Knot Theory Ramifications 10 2 (2001) 269-294
    • (2001) J. Knot Theory Ramifications , vol.10 , Issue.2 , pp. 269-294
    • Darcy, I.1
  • 13
    • 0001321818 scopus 로고
    • A statistical study of random knotting using the Vassiliev invariants, random knotting and linking
    • Deguchi T., and Tsurasaki K. A statistical study of random knotting using the Vassiliev invariants, random knotting and linking. J. Knot Theory Ramifications 3 (1994) 321-353
    • (1994) J. Knot Theory Ramifications , vol.3 , pp. 321-353
    • Deguchi, T.1    Tsurasaki, K.2
  • 14
    • 0035868644 scopus 로고    scopus 로고
    • Topoisomerase IV, alone, unknots DNA in E. Coli
    • Deibler R.W., Rahmati S., and Zechiedrich E.L. Topoisomerase IV, alone, unknots DNA in E. Coli. Genes Dev. 15 (2001) 748-761
    • (2001) Genes Dev. , vol.15 , pp. 748-761
    • Deibler, R.W.1    Rahmati, S.2    Zechiedrich, E.L.3
  • 16
    • 84972274704 scopus 로고
    • A calculus for rational tangles: applications to DNA recombination
    • Ernst C., and Sumners D.W. A calculus for rational tangles: applications to DNA recombination. Math. Proc. Cambridge Philos. Soc. 108 3 (1990) 489-515
    • (1990) Math. Proc. Cambridge Philos. Soc. , vol.108 , Issue.3 , pp. 489-515
    • Ernst, C.1    Sumners, D.W.2
  • 17
    • 0042682250 scopus 로고    scopus 로고
    • Ewing B., and Millett K.C. (Eds), Hermann, Paris
    • In: Ewing B., and Millett K.C. (Eds). Computational Algorithms and the Complexity of Link Polynomials. Progress in Knot Theory and Related Topics. Travaux en Cours vol. 56 (1997), Hermann, Paris
    • (1997) Progress in Knot Theory and Related Topics. Travaux en Cours , vol.56
  • 18
    • 13244285443 scopus 로고    scopus 로고
    • Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots
    • Flammini A., Maritan A., and Stasiak A. Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots. Biophys. J. 87 (2004) 2968-2975
    • (2004) Biophys. J. , vol.87 , pp. 2968-2975
    • Flammini, A.1    Maritan, A.2    Stasiak, A.3
  • 21
    • 0346906092 scopus 로고    scopus 로고
    • Computer evaluation of Homfly polynomials by using Gauss codes, with a skein-template algorithm
    • Gouesbet G., Meunier-Guttin-Cluzel S., and Letellier C. Computer evaluation of Homfly polynomials by using Gauss codes, with a skein-template algorithm. Appl. Math. Comput. 105 2-3 (1999) 271-289
    • (1999) Appl. Math. Comput. , vol.105 , Issue.2-3 , pp. 271-289
    • Gouesbet, G.1    Meunier-Guttin-Cluzel, S.2    Letellier, C.3
  • 24
    • 0021099687 scopus 로고
    • Knotting of the circular duplex DNA by type II DNA topoisomerase from Drosophilla melanogaster
    • Hsieh T. Knotting of the circular duplex DNA by type II DNA topoisomerase from Drosophilla melanogaster. J. Biol. Chem. 258 (1983) 8413-8420
    • (1983) J. Biol. Chem. , vol.258 , pp. 8413-8420
    • Hsieh, T.1
  • 26
    • 0019517763 scopus 로고
    • Novel topologically knotted DNA from bacteriophage P4 capsids: studies with DNA topoisomerases
    • Liu L.F., Davis J.L., and Calendar R. Novel topologically knotted DNA from bacteriophage P4 capsids: studies with DNA topoisomerases. Nucleic Acids Res. 9 (1981) 3979-3989
    • (1981) Nucleic Acids Res. , vol.9 , pp. 3979-3989
    • Liu, L.F.1    Davis, J.L.2    Calendar, R.3
  • 28
    • 0030458354 scopus 로고    scopus 로고
    • T7 RNA polymerase cannot transcribe through a highly knotted DNA template
    • Portugal J., and Rodriguez-Campos A. T7 RNA polymerase cannot transcribe through a highly knotted DNA template. Nucleic Acids Res. 24 (1996) 4890-4894
    • (1996) Nucleic Acids Res. , vol.24 , pp. 4890-4894
    • Portugal, J.1    Rodriguez-Campos, A.2
  • 31
    • 27844543323 scopus 로고    scopus 로고
    • Minimal Lattice Knots
    • World Scientific, Singapore
    • van Rensburg E.J. Minimal Lattice Knots. Ideal Knots vol. 19 (1998), World Scientific, Singapore
    • (1998) Ideal Knots , vol.19
    • van Rensburg, E.J.1
  • 33
    • 0028949206 scopus 로고
    • The mechanisms of DNA topoisomerases
    • Roca J. The mechanisms of DNA topoisomerases. Trends Biochem. Sci. 20 (1995) 156-160
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 156-160
    • Roca, J.1
  • 34
    • 0035910283 scopus 로고    scopus 로고
    • Varying levels of positive and negative supercoiling differently affect the efficiency with which topoisomerase II catenates and decatenates DNA
    • Roca J. Varying levels of positive and negative supercoiling differently affect the efficiency with which topoisomerase II catenates and decatenates DNA. J. Mol. Biol. 305 (2001) 441-450
    • (2001) J. Mol. Biol. , vol.305 , pp. 441-450
    • Roca, J.1
  • 35
    • 0029961651 scopus 로고    scopus 로고
    • DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism
    • Roca J., Berger J.M., Harrison S.C., and Wang J.C. DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. Proc. Natl. Acad. Sci. USA 93 (1996) 4057-4062
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 4057-4062
    • Roca, J.1    Berger, J.M.2    Harrison, S.C.3    Wang, J.C.4
  • 36
    • 17544380168 scopus 로고    scopus 로고
    • DNA knotting abolishes in vitro chromatin assembly
    • Rodriguez-Campos A. DNA knotting abolishes in vitro chromatin assembly. J. Biol. Chem. 271 (1996) 14150-14155
    • (1996) J. Biol. Chem. , vol.271 , pp. 14150-14155
    • Rodriguez-Campos, A.1
  • 38
    • 0027279063 scopus 로고
    • Probability of DNA knotting and the effective diameter of the DNA double helix
    • Rybenkov V.V., Cozzarelli N.R., and Vologodskii A.V. Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. USA 90 (1993) 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
  • 39
    • 0030758268 scopus 로고    scopus 로고
    • Simplification of DNA topology below equilibrium values by type II topoisomerases
    • Rybenkov V.V., Ullsperger C., Vologodskii A.V., and Cozzarelli N.R. Simplification of DNA topology below equilibrium values by type II topoisomerases. Science 277 (1997) 690-693
    • (1997) Science , vol.277 , pp. 690-693
    • Rybenkov, V.V.1    Ullsperger, C.2    Vologodskii, A.V.3    Cozzarelli, N.R.4
  • 41
    • 0027200062 scopus 로고
    • Knotting of a DNA chain during ring closure
    • Shaw S.Y., and Wang J.C. Knotting of a DNA chain during ring closure. Science 260 (1993) 533-536
    • (1993) Science , vol.260 , pp. 533-536
    • Shaw, S.Y.1    Wang, J.C.2
  • 42
    • 0024791187 scopus 로고
    • The presence of the region on pBR322 that encodes resistance to tetracycline is responsible for high levels of plasmid DNA knotting in Escherichia coli DNA topoisomerase I deletion mutant
    • Shishido K., Ishii S., and Komiyama N. The presence of the region on pBR322 that encodes resistance to tetracycline is responsible for high levels of plasmid DNA knotting in Escherichia coli DNA topoisomerase I deletion mutant. Nucleic Acids Res. 17 (1989) 9749-9759
    • (1989) Nucleic Acids Res. , vol.17 , pp. 9749-9759
    • Shishido, K.1    Ishii, S.2    Komiyama, N.3
  • 44
    • 0024364817 scopus 로고
    • Site-specific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions
    • Stark W.M., Sherratt D.J., and Boocock M.R. Site-specific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions. Cell 58 (1989) 779-790
    • (1989) Cell , vol.58 , pp. 779-790
    • Stark, W.M.1    Sherratt, D.J.2    Boocock, M.R.3
  • 45
    • 0034644125 scopus 로고    scopus 로고
    • DNA topology: feeling the pulse of a topoisomerase
    • Stasiak A. DNA topology: feeling the pulse of a topoisomerase. Curr. Biol. 10 (2000) 526-528
    • (2000) Curr. Biol. , vol.10 , pp. 526-528
    • Stasiak, A.1
  • 48
    • 33847757436 scopus 로고    scopus 로고
    • M. Szafron, Monte Carlo simulations of strand-passage in unknotted self-avoiding polygons, Masters thesis, University of Saskatoon, 2000
  • 49
    • 1542501878 scopus 로고    scopus 로고
    • Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology
    • Trigueros S., Salceda J., Bermudez I., Fernandez X., and Roca J. Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology. J. Mol. Biol. 335 (2004) 723-731
    • (2004) J. Mol. Biol. , vol.335 , pp. 723-731
    • Trigueros, S.1    Salceda, J.2    Bermudez, I.3    Fernandez, X.4    Roca, J.5
  • 51
    • 2542521543 scopus 로고    scopus 로고
    • Tangle analysis of Gin site-specific recombination
    • Vazquez M., and Sumners D.W. Tangle analysis of Gin site-specific recombination. Math. Proc. Cambridge Philos. Soc. 136 3 (2004) 565-582
    • (2004) Math. Proc. Cambridge Philos. Soc. , vol.136 , Issue.3 , pp. 565-582
    • Vazquez, M.1    Sumners, D.W.2
  • 52
    • 0018579392 scopus 로고
    • Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix
    • Vologodskii A.V., Anshelevich V.V., Lukashin A.V., and Frank-Kamenetskii M.D. Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix. Nature 280 (1979) 294-298
    • (1979) Nature , vol.280 , pp. 294-298
    • Vologodskii, A.V.1    Anshelevich, V.V.2    Lukashin, A.V.3    Frank-Kamenetskii, M.D.4
  • 53
    • 0027171352 scopus 로고
    • Monte Carlo analysis of the conformation of DNA catenates
    • Vologodskii A.V., and Cozzarelli N.R. Monte Carlo analysis of the conformation of DNA catenates. J. Mol. Biol. 232 (1993) 1130-1140
    • (1993) J. Mol. Biol. , vol.232 , pp. 1130-1140
    • Vologodskii, A.V.1    Cozzarelli, N.R.2
  • 57
    • 0022518195 scopus 로고
    • Biochemical topology: applications to DNA recombination and replication
    • Wasserman S.R., and Cozzarelli N.R. Biochemical topology: applications to DNA recombination and replication. Science 232 (1986) 951-960
    • (1986) Science , vol.232 , pp. 951-960
    • Wasserman, S.R.1    Cozzarelli, N.R.2
  • 58
    • 0033613387 scopus 로고    scopus 로고
    • A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases
    • Yan J., Magnasco M.O., and Marko J.F. A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases. Nature 401 (1999) 932-935
    • (1999) Nature , vol.401 , pp. 932-935
    • Yan, J.1    Magnasco, M.O.2    Marko, J.F.3
  • 59
    • 0030771373 scopus 로고    scopus 로고
    • Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli
    • Zechiedrich E.L., Khodursky A.B., and Cozzarelli N.R. Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli. Genes Dev. 11 (1997) 2580-2592
    • (1997) Genes Dev. , vol.11 , pp. 2580-2592
    • Zechiedrich, E.L.1    Khodursky, A.B.2    Cozzarelli, N.R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.