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Volumn 464, Issue 2099, 2008, Pages 2811-2829

Single-molecule magnetic tweezer tests on DNA: Bounds on topoisomerase relaxation

Author keywords

Magnetic tweezers; Plectoneme mechanics; Single molecule experiments; Supercoiling of DNA; Topoisomerase

Indexed keywords

CHEMOTHERAPY; DNA; GENES; HEALTH; MECHANICS; MOLECULES; NUCLEIC ACIDS; PARAMETER ESTIMATION; SPEED;

EID: 52949152472     PISSN: 13645021     EISSN: 14712946     Source Type: Journal    
DOI: 10.1098/rspa.2008.0132     Document Type: Article
Times cited : (7)

References (40)
  • 1
  • 2
    • 34447323073 scopus 로고    scopus 로고
    • Energy coupling in type II topoisomerases: Why do they hydrolyze ATP?
    • doi:10.1021/bi700789g
    • Bates, A. D. & Maxwell, A. 2007 Energy coupling in type II topoisomerases: why do they hydrolyze ATP? Biochemistry 46, 7929-7941. (doi:10.1021/bi700789g)
    • (2007) Biochemistry , vol.46 , pp. 7929-7941
    • Bates, A.D.1    Maxwell, A.2
  • 3
    • 34548576981 scopus 로고    scopus 로고
    • Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases
    • doi:10.1093/nar/gkm532
    • Burnier, Y., Weber, C., Flammini, A. & Stasiak, A. 2007 Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases. Nucleic Acids Res. 35, 5223-5231. (doi:10.1093/nar/gkm532)
    • (2007) Nucleic Acids Res , vol.35 , pp. 5223-5231
    • Burnier, Y.1    Weber, C.2    Flammini, A.3    Stasiak, A.4
  • 4
    • 85015087906 scopus 로고    scopus 로고
    • Ten years of tension: Single-molecule DNA mechanics
    • doi:10.1038/nature01405
    • Bustamante, C., Bryant, Z. & Smith, S. B. 2003 Ten years of tension: single-molecule DNA mechanics. Nature 421, 423-427. (doi:10.1038/nature01405)
    • (2003) Nature , vol.421 , pp. 423-427
    • Bustamante, C.1    Bryant, Z.2    Smith, S.B.3
  • 6
    • 0002979277 scopus 로고
    • L'intégral de Gauss at l'analyse des noeuds tridimensionnels.
    • Cǎlugǎreanu, G. 1959 L'intégral de Gauss at l'analyse des noeuds tridimensionnels. Rev. Math. Pures Appl. 4, 5-20.
    • (1959) Rev. Math. Pures Appl , vol.4 , pp. 5-20
    • Cǎlugǎreanu, G.1
  • 7
    • 0001443491 scopus 로고
    • Sur les classes d'isotopie des noeuds tridimensionnels et leurs invariants.
    • Cǎlugǎreanu, G. 1961 Sur les classes d'isotopie des noeuds tridimensionnels et leurs invariants. Czechoslovak Math. J. 11, 588-625.
    • (1961) Czechoslovak Math. J , vol.11 , pp. 588-625
    • Cǎlugǎreanu, G.1
  • 8
    • 33746703799 scopus 로고    scopus 로고
    • A multiplicity of localized buckling modes for twisted rod equations
    • doi:10.1098/rspa.1996.0132
    • Champneys, A. R. & Thompson, J. M. T. 1996 A multiplicity of localized buckling modes for twisted rod equations. Proc. R. Soc. A 452, 2467-2491. (doi:10.1098/rspa.1996.0132)
    • (1996) Proc. R. Soc. A , vol.452 , pp. 2467-2491
    • Champneys, A.R.1    Thompson, J.M.T.2
  • 9
    • 3142583750 scopus 로고    scopus 로고
    • Spatially complex localization after one-twist-per-wave equilibria in twisted circular rods with initial curvature
    • doi:10.1098/rsta.1997.0115
    • Champneys, A. R., van der Heijden, G. H. M. & Thompson, J. M. T. 1997 Spatially complex localization after one-twist-per-wave equilibria in twisted circular rods with initial curvature. Phil. Trans. R. Soc. A 355, 2151-2174. (doi:10.1098/rsta.1997.0115)
    • (1997) Phil. Trans. R. Soc. A , vol.355 , pp. 2151-2174
    • Champneys, A.R.1    van der Heijden, G.H.M.2    Thompson, J.M.T.3
  • 10
    • 43249124469 scopus 로고    scopus 로고
    • Analytical results for the plectonemic response of supercoiled DNA
    • doi:10.1007/s10820-007-9072-y
    • Clauvelin, N., Audoly, B. & Neikirch, S. 2007 Analytical results for the plectonemic response of supercoiled DNA. J. Comput. Aided Mater. Des. 14, 95-101. (doi:10.1007/s10820-007-9072-y)
    • (2007) J. Comput. Aided Mater. Des , vol.14 , pp. 95-101
    • Clauvelin, N.1    Audoly, B.2    Neikirch, S.3
  • 11
    • 0034965398 scopus 로고    scopus 로고
    • Theory of supercoiled elastic rings with self-contact and its application to DNA plasmids
    • doi:10.1023/A:1010911113919
    • Coleman, B. D. & Swigon, D. 2000 Theory of supercoiled elastic rings with self-contact and its application to DNA plasmids. J. Elasticity 60, 173-221. (doi:10.1023/A:1010911113919)
    • (2000) J. Elasticity , vol.60 , pp. 173-221
    • Coleman, B.D.1    Swigon, D.2
  • 13
    • 0015040327 scopus 로고
    • The writhing number of a space curve
    • doi:10.1073/pnas.68.4.815
    • Fuller, F. B. 1971 The writhing number of a space curve. Proc. Natl Acad. Sci. USA 68, 815-819. (doi:10.1073/pnas.68.4.815)
    • (1971) Proc. Natl Acad. Sci. USA , vol.68 , pp. 815-819
    • Fuller, F.B.1
  • 14
    • 0017886919 scopus 로고
    • Decomposition of the linking of a closed ribbon: A problem from molecular biology
    • doi:10.1073/pnas.75.8.3557
    • Fuller, F. B. 1978 Decomposition of the linking of a closed ribbon: a problem from molecular biology. Proc. Natl Acad. Sci. USA 75, 3557-3561. (doi:10.1073/pnas.75.8.3557)
    • (1978) Proc. Natl Acad. Sci. USA , vol.75 , pp. 3557-3561
    • Fuller, F.B.1
  • 15
    • 24144475221 scopus 로고    scopus 로고
    • Experiments on snap buckling, hysteresis and loop formation in twisted rods
    • doi:10.1007/BF02428182
    • Goss, V. G. A., van der Heijden, G. H. M., Thompson, J. M. T. & Neukirch, S. 2005 Experiments on snap buckling, hysteresis and loop formation in twisted rods. Exp. Mech. 45, 101-111. (doi:10.1007/BF02428182)
    • (2005) Exp. Mech , vol.45 , pp. 101-111
    • Goss, V.G.A.1    van der Heijden, G.H.M.2    Thompson, J.M.T.3    Neukirch, S.4
  • 16
    • 31444452335 scopus 로고    scopus 로고
    • Buckling in space and time
    • doi:10.1007/s11071-006-0748-8
    • Hunt, G. W. 2006 Buckling in space and time. Nonlin. Dyn. 43, 29-46. (doi:10.1007/s11071-006-0748-8)
    • (2006) Nonlin. Dyn , vol.43 , pp. 29-46
    • Hunt, G.W.1
  • 17
    • 0007859149 scopus 로고
    • Structural localization phenomena and the dynamical phase-space analogy
    • doi:10.1098/rspa.1989.0105
    • Hunt, G. W., Bolt, H. M. & Thompson, J. M. T. 1989 Structural localization phenomena and the dynamical phase-space analogy. Proc. R. Soc. A 425, 245-267. (doi:10.1098/rspa.1989.0105)
    • (1989) Proc. R. Soc. A , vol.425 , pp. 245-267
    • Hunt, G.W.1    Bolt, H.M.2    Thompson, J.M.T.3
  • 18
    • 0027659796 scopus 로고
    • Maxwell critical loads for axially loaded cylindrical-shells
    • doi:10.1115/1.2900861
    • Hunt, G. W. & Neto, E. L. 1993 Maxwell critical loads for axially loaded cylindrical-shells. J. Appl. Mech. 60, 702-706. (doi:10.1115/1.2900861)
    • (1993) J. Appl. Mech , vol.60 , pp. 702-706
    • Hunt, G.W.1    Neto, E.L.2
  • 20
    • 28844493513 scopus 로고    scopus 로고
    • Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases
    • doi:10.1042/BST20051460
    • Maxwell, A., Costenaro, L., Mitelheiser, S. & Bates, A. D. 2005 Coupling ATP hydrolysis to DNA strand passage in type IIA DNA topoisomerases. Biochem. Soc. Trans. 33, 1460-1464. (doi:10.1042/BST20051460)
    • (2005) Biochem. Soc. Trans , vol.33 , pp. 1460-1464
    • Maxwell, A.1    Costenaro, L.2    Mitelheiser, S.3    Bates, A.D.4
  • 21
    • 0023817889 scopus 로고
    • Spatially complex equilibria of buckled rods
    • doi:10.1007/ BF00251491
    • Mielke, A. & Holmes, P. 1988 Spatially complex equilibria of buckled rods. Arch. Ration. Mech. Anal. 101, 319-348. (doi:10.1007/ BF00251491)
    • (1988) Arch. Ration. Mech. Anal , vol.101 , pp. 319-348
    • Mielke, A.1    Holmes, P.2
  • 22
    • 0000807788 scopus 로고
    • Helicity and the Cǎlugǎreanu invariant
    • doi:10.1098/rspa.1992.0159
    • Moffatt, H. K. & Ricca, R. L. 1992 Helicity and the Cǎlugǎreanu invariant. Proc. R. Soc. A 439, 411-429. (doi:10.1098/rspa.1992.0159)
    • (1992) Proc. R. Soc. A , vol.439 , pp. 411-429
    • Moffatt, H.K.1    Ricca, R.L.2
  • 23
    • 19744364369 scopus 로고    scopus 로고
    • Extracting DNA twist rigidity from experimental supercoiling data
    • doi:10.1103/PhysRevLett.93.198107
    • Neukirch, S. 2004 Extracting DNA twist rigidity from experimental supercoiling data. Phys. Rev. Lett. 93, 198 107. (doi:10.1103/PhysRevLett.93.198107)
    • (2004) Phys. Rev. Lett , vol.93 , pp. 198-107
    • Neukirch, S.1
  • 24
    • 33746675190 scopus 로고    scopus 로고
    • Single-molecule experiments in biological physics
    • doi:10.1088/0953-8984/18/32/ R01
    • Ritort, F. 2006 Single-molecule experiments in biological physics. J. Phys. Condens. Matter 18, R531-R583. (doi:10.1088/0953-8984/18/32/ R01)
    • (2006) J. Phys. Condens. Matter , vol.18
    • Ritort, F.1
  • 25
    • 0030758268 scopus 로고    scopus 로고
    • Simplification of DNA topology below equilibrium values by type II topoisomerases
    • doi:10.1126/science.277. 5326.690
    • Rybenkov, V. V., Ullsperger, C., Vologodskii, A. V. & Cozzarelli, N. R. 1997 Simplification of DNA topology below equilibrium values by type II topoisomerases. Science 277, 690-693. (doi:10.1126/science.277. 5326.690)
    • (1997) Science , vol.277 , pp. 690-693
    • Rybenkov, V.V.1    Ullsperger, C.2    Vologodskii, A.V.3    Cozzarelli, N.R.4
  • 26
    • 0037849836 scopus 로고    scopus 로고
    • Tracking enzymatic steps of DNA topoisomerases using single-molecule micromanipulation
    • doi:10.1016/S1631-0705(02)01347-6
    • Strick, T. R., Charvin, G., Dekker, N. H., Allemand, J., Bensimon, D. & Croquette, V. 2002 Tracking enzymatic steps of DNA topoisomerases using single-molecule micromanipulation. C. R. Phys. 3, 595-618. (doi:10.1016/S1631-0705(02)01347-6)
    • (2002) C. R. Phys , vol.3 , pp. 595-618
    • Strick, T.R.1    Charvin, G.2    Dekker, N.H.3    Allemand, J.4    Bensimon, D.5    Croquette, V.6
  • 28
    • 35548950309 scopus 로고    scopus 로고
    • Topoisomerase V relaxes supercoiled DNA by a constrained swivelling mechanism
    • doi:10.1073/pnas.0701989104
    • Taneja, B., Schnurr, B., Slesarev, A., Marko, J. F. & Mondragon, A. 2007 Topoisomerase V relaxes supercoiled DNA by a constrained swivelling mechanism. Proc. Natl Acad. Sci. USA 104, 14 670-14 675. (doi:10.1073/pnas.0701989104)
    • (2007) Proc. Natl Acad. Sci. USA , vol.104
    • Taneja, B.1    Schnurr, B.2    Slesarev, A.3    Marko, J.F.4    Mondragon, A.5
  • 29
    • 0002189162 scopus 로고
    • Stability predictions through a succession of folds
    • doi:10.1098/rsta.1979. 0043
    • Thompson, J. M. T. 1979 Stability predictions through a succession of folds. Phil. Trans. R. Soc. A 292, 1-23. (doi:10.1098/rsta.1979. 0043)
    • (1979) Phil. Trans. R. Soc. A , vol.292 , pp. 1-23
    • Thompson, J.M.T.1
  • 30
    • 85020778253 scopus 로고    scopus 로고
    • Cutting DNA: Mechanics of the topoisomerase
    • In press
    • Thompson, J. M. T. In press. Cutting DNA: mechanics of the topoisomerase. Eur. Phys. J.
    • Eur. Phys. J
    • Thompson, J.M.T.1
  • 31
    • 0000111802 scopus 로고    scopus 로고
    • From helix to localized writhing in the torsional post-buckling of elastic rods
    • doi:10.1098/rspa.1996.0007
    • Thompson, J. M. T. & Champneys, A. R. 1996 From helix to localized writhing in the torsional post-buckling of elastic rods. Proc. R. Soc. A 452, 117-138. (doi:10.1098/rspa.1996.0007)
    • (1996) Proc. R. Soc. A , vol.452 , pp. 117-138
    • Thompson, J.M.T.1    Champneys, A.R.2
  • 33
    • 5144231541 scopus 로고    scopus 로고
    • Supercoiling of DNA plasmids: Mechanics of the generalized ply
    • doi:10.1098/rspa.2001.0901
    • Thompson, J. M. T., van der Heijden, G. H. M. & Neukirch, S. 2002 Supercoiling of DNA plasmids: mechanics of the generalized ply. Proc. R. Soc. A 458, 959-985. (doi:10.1098/rspa.2001.0901)
    • (2002) Proc. R. Soc. A , vol.458 , pp. 959-985
    • Thompson, J.M.T.1    van der Heijden, G.H.M.2    Neukirch, S.3
  • 34
    • 0033764926 scopus 로고    scopus 로고
    • Elastic stability of DNA configurations. I. General theory
    • doi:10.1103/PhysRevE.61.747
    • Tobias, I., Swigon, D. & Coleman, B. D. 2000 Elastic stability of DNA configurations. I. General theory. Phys. Rev. E 61, 747-758. (doi:10.1103/PhysRevE.61.747)
    • (2000) Phys. Rev. E , vol.61 , pp. 747-758
    • Tobias, I.1    Swigon, D.2    Coleman, B.D.3
  • 35
    • 3042623396 scopus 로고    scopus 로고
    • An introduction to the mechanics of DNA
    • doi:10.1098/rsta.2004.1392
    • Travers, A. A. & Thompson, J. M. T. 2004 An introduction to the mechanics of DNA. Phil. Trans. R. Soc. A 362, 1265-1279. (doi:10.1098/rsta.2004.1392)
    • (2004) Phil. Trans. R. Soc. A , vol.362 , pp. 1265-1279
    • Travers, A.A.1    Thompson, J.M.T.2
  • 36
    • 0033903070 scopus 로고    scopus 로고
    • Helical and localised buckling in twisted rods: A unified analysis of the symmetric case
    • doi:10.1023/A:1008310425967
    • van der Heijden, G. H. M. & Thompson, J. M. T. 2000 Helical and localised buckling in twisted rods: a unified analysis of the symmetric case. Nonlin. Dyn. 21, 71-99. (doi:10.1023/A:1008310425967)
    • (2000) Nonlin. Dyn , vol.21 , pp. 71-99
    • van der Heijden, G.H.M.1    Thompson, J.M.T.2
  • 37
    • 0037119523 scopus 로고    scopus 로고
    • The chaotic instability of a slowly spinning asymmetric top
    • doi:10.1016/S0895-7177(02)00130-9
    • van der Heijden, G. H. M. & Thompson, J. M. T. 2002 The chaotic instability of a slowly spinning asymmetric top. Math. Comput. Model. 36, 359-369. (doi:10.1016/S0895-7177(02)00130-9)
    • (2002) Math. Comput. Model , vol.36 , pp. 359-369
    • van der Heijden, G.H.M.1    Thompson, J.M.T.2
  • 38
    • 0037187257 scopus 로고    scopus 로고
    • Spatially complex localisation in twisted elastic rods constrained to a cylinder
    • doi:10.1016/S0020-7683(01)00234-7
    • van der Heijden, G. H. M., Champneys, A. R. & Thompson, J. M. T. 2002 Spatially complex localisation in twisted elastic rods constrained to a cylinder. Int. J. Solids Struct. 39, 1863-1883. (doi:10.1016/S0020-7683(01)00234-7)
    • (2002) Int. J. Solids Struct , vol.39 , pp. 1863-1883
    • van der Heijden, G.H.M.1    Champneys, A.R.2    Thompson, J.M.T.3
  • 39
    • 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
    • doi:10.1017/S0033583598003424
    • Wang, J. C. 1998 Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine. Q. Rev. Biophys. 31, 107-144. (doi:10.1017/S0033583598003424)
    • (1998) Q. Rev. Biophys , vol.31 , pp. 107-144
    • Wang, J.C.1
  • 40
    • 0000751914 scopus 로고
    • Self-linking and the Gauss integral in higher dimensions
    • doi:10.2307/2373348
    • White, J. H. 1969 Self-linking and the Gauss integral in higher dimensions. Am. J. Math. 91, 693-728. (doi:10.2307/2373348)
    • (1969) Am. J. Math , vol.91 , pp. 693-728
    • White, J.H.1


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