-
1
-
-
0024791187
-
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. (1989) 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, 9749-9759.
-
(1989)
Nucleic Acids Res
, vol.17
, pp. 9749-9759
-
-
Shishido, K.1
Ishii, S.2
Komiyama, N.3
-
2
-
-
0033605230
-
Formation of knots in partially replicated DNA molecules
-
Sogo,J.M., Stasiak,A., Martinez-Robles,M.L., Krimer,D.B., Hernandez,P. and Schvartzman,J.B. (1999) Formation of knots in partially replicated DNA molecules. J. Mol. Biol., 286, 637-643.
-
(1999)
J. Mol. Biol
, vol.286
, pp. 637-643
-
-
Sogo, J.M.1
Stasiak, A.2
Martinez-Robles, M.L.3
Krimer, D.B.4
Hernandez, P.5
Schvartzman, J.B.6
-
3
-
-
21544474118
-
DNA knots reveal a chiral organization of DNA in phage capsids
-
Arsuaga,J., Vazquez,M., McGuirk,P., Trigueros,S., Sumners,D.W. and Roca,J. (2005) DNA knots reveal a chiral organization of DNA in phage capsids. Proc. Natl Acad. Sci. USA, 102, 9165-9169.
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 9165-9169
-
-
Arsuaga, J.1
Vazquez, M.2
McGuirk, P.3
Trigueros, S.4
Sumners, D.W.5
Roca, J.6
-
4
-
-
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. Q. Rev. Biophys., 31, 107-144.
-
(1998)
Q. Rev. Biophys
, vol.31
, pp. 107-144
-
-
Wang, J.C.1
-
5
-
-
2442599792
-
Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases
-
Corbett,K.D. and Berger,J.M. (2004) Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases. Annu. Rev. Biophys. Biomol. Struct., 33, 95-118.
-
(2004)
Annu. Rev. Biophys. Biomol. Struct
, vol.33
, pp. 95-118
-
-
Corbett, K.D.1
Berger, J.M.2
-
6
-
-
0003564812
-
-
2nd edn. Oxford University Press, Oxford
-
Bates,A.D. and Maxwell,A. (2005) DNA Topology, 2nd edn. Oxford University Press, Oxford.
-
(2005)
DNA Topology
-
-
Bates, A.D.1
Maxwell, A.2
-
7
-
-
0034677898
-
Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli
-
Zechiedrich,E.L., Khodursky,A.B., Bachellier,S., Schneider,R., Chen,D., Lilley,D.M. and Cozzarelli,N.R. (2000) Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J. Biol. Chem., 275, 8103-8113.
-
(2000)
J. Biol. Chem
, vol.275
, pp. 8103-8113
-
-
Zechiedrich, E.L.1
Khodursky, A.B.2
Bachellier, S.3
Schneider, R.4
Chen, D.5
Lilley, D.M.6
Cozzarelli, N.R.7
-
8
-
-
3142665836
-
A topological view of the replicon
-
Schvartzman,J.B. and Stasiak,A. (2004) A topological view of the replicon. EMBO Rep., 5, 256-261.
-
(2004)
EMBO Rep
, vol.5
, pp. 256-261
-
-
Schvartzman, J.B.1
Stasiak, A.2
-
9
-
-
0021846984
-
Duplex DNA knots produced by Escherichia coli topoisomerase I. Structure and requirements for formation
-
Dean,F.B., Stasiak,A., Koller,T. and Cozzarelli,N.R. (1985) Duplex DNA knots produced by Escherichia coli topoisomerase I. Structure and requirements for formation. J. Biol. Chem., 260, 4975-4983.
-
(1985)
J. Biol. Chem
, vol.260
, pp. 4975-4983
-
-
Dean, F.B.1
Stasiak, A.2
Koller, T.3
Cozzarelli, N.R.4
-
10
-
-
0020571715
-
Determination of the absolute handedness of knots and catenanes of DNA
-
Krasnow,M.A., Stasiak,A., Spengler,S.J., Dean,F., Koller,T. and Cozzarelli,N.R. (1983) Determination of the absolute handedness of knots and catenanes of DNA. Nature, 304, 559-560.
-
(1983)
Nature
, vol.304
, pp. 559-560
-
-
Krasnow, M.A.1
Stasiak, A.2
Spengler, S.J.3
Dean, F.4
Koller, T.5
Cozzarelli, N.R.6
-
11
-
-
0025789990
-
Supercoiled DNA-directed knotting by T4 topoisomerase
-
Wasserman,S.A. and Cozzarelli,N.R. (1991) Supercoiled DNA-directed knotting by T4 topoisomerase. J. Biol. Chem., 266, 20567-20573.
-
(1991)
J. Biol. Chem
, vol.266
, pp. 20567-20573
-
-
Wasserman, S.A.1
Cozzarelli, N.R.2
-
12
-
-
17544380168
-
DNA knotting abolishes in vitro chromatin assembly
-
Rodriguez-Campos,A. (1996) DNA knotting abolishes in vitro chromatin assembly. J. Biol. Chem., 271, 14150-14155.
-
(1996)
J. Biol. Chem
, vol.271
, pp. 14150-14155
-
-
Rodriguez-Campos, A.1
-
13
-
-
0030758268
-
Simplification of DNA topology below equilibrium values by type II topoisomerases
-
Rybenkov,V.V., Ullsperger,C., Vologodskii,A.V. and Cozzarelli,N.R. (1997) 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
-
14
-
-
0033613387
-
A kinetic proof-reading mechanism for disentanglement of DNA by topoisomerases
-
Yan,J., Magnasco,M.O. and Marko,J.F. (1999) A kinetic proof-reading mechanism for disentanglement of DNA by topoisomerases. Nature, 401, 932-935.
-
(1999)
Nature
, vol.401
, pp. 932-935
-
-
Yan, J.1
Magnasco, M.O.2
Marko, J.F.3
-
15
-
-
0035853134
-
Mechanism of topology simplification by type II DNA topoisomerases
-
Vologodskii,A.V., Zhang,W., Rybenkov,V.V., Podtelezhnikov,A.A., Subramanian,D., Griffith,J.D. and Cozzarelli,N.R, (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
-
16
-
-
1542501878
-
Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology
-
Trigueros,S., Salceda,J., Bermudez,I., Fernandez,X. and Roca,J. (2004) Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology. J. Mol. Biol., 335, 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
-
17
-
-
3242754359
-
DNA disentangling by type-2 topoisomerases
-
Buck,G.R. and Zechiedrich,E.L. (2004) DNA disentangling by type-2 topoisomerases. J. Mol. Biol., 340, 933-939.
-
(2004)
J. Mol. Biol
, vol.340
, pp. 933-939
-
-
Buck, G.R.1
Zechiedrich, E.L.2
-
18
-
-
33746253988
-
Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases
-
Liu,Z., Mann,J.K., Zechiedrich,E.L. and Chan,H.S. (2006) Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases. J. Mol. Biol., 361, 268-285.
-
(2006)
J. Mol. Biol
, vol.361
, pp. 268-285
-
-
Liu, Z.1
Mann, J.K.2
Zechiedrich, E.L.3
Chan, H.S.4
-
19
-
-
34548576981
-
Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topoisomerases
-
Burnier,Y., Weber,C., Flammini,A. and 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.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 5223-5231
-
-
Burnier, Y.1
Weber, C.2
Flammini, A.3
Stasiak, A.4
-
20
-
-
0034669232
-
Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements
-
Crisona,N.J., Strick,T.R., Bensimon,D., Croquette,V. and Cozzarelli,N.R. (2000) Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. Genes Dev., 14, 2881-2892.
-
(2000)
Genes Dev
, vol.14
, pp. 2881-2892
-
-
Crisona, N.J.1
Strick, T.R.2
Bensimon, D.3
Croquette, V.4
Cozzarelli, N.R.5
-
21
-
-
0003740339
-
-
Publish or Perish Inc, Houston, TX
-
Rolfsen,D. (1990) Knots and Links. Publish or Perish Inc., Houston, TX.
-
(1990)
Knots and Links
-
-
Rolfsen, D.1
-
22
-
-
0004192246
-
-
W.H. Freeman and Company, New York
-
Adams,C.C. (1994) The Knot Book. W.H. Freeman and Company, New York.
-
(1994)
The Knot Book
-
-
Adams, C.C.1
-
24
-
-
46349093852
-
-
3 (Las Vegas, NV, 2001). Contemp. Math. Series, 304, American Mathematical Society Providence, Rhode Island, pp. 223-259.
-
3 (Las Vegas, NV, 2001). Contemp. Math. Series, 304, American Mathematical Society Providence, Rhode Island, pp. 223-259.
-
-
-
-
25
-
-
33745637556
-
On the classification of rational knots
-
Kauffman,L.H. and Lambropoulou,S. (2003) On the classification of rational knots. Enseign. Math. II, 49, 357-410.
-
(2003)
Enseign. Math. II
, vol.49
, pp. 357-410
-
-
Kauffman, L.H.1
Lambropoulou, S.2
-
26
-
-
3342978849
-
On the classification of rational tangles
-
Kauffman,L.H. and Lambropoulou,S. (2004) On the classification of rational tangles. Adv. Appl. Math., 33, 199-237.
-
(2004)
Adv. Appl. Math
, vol.33
, pp. 199-237
-
-
Kauffman, L.H.1
Lambropoulou, S.2
-
28
-
-
30444445119
-
Solving unoriented tangle equations involving 4- plats
-
Darcy,I.K. (2005) Solving unoriented tangle equations involving 4- plats. J. Knot Theory Ramif., 14, 993-1005.
-
(2005)
J. Knot Theory Ramif
, vol.14
, pp. 993-1005
-
-
Darcy, I.K.1
-
29
-
-
33747879673
-
TopoICE-R: 3D visualization modeling the topology of DNA recombination
-
Darcy,I.K. and Scharein,R.G. (2006) TopoICE-R: 3D visualization modeling the topology of DNA recombination. Bioinformatics, 22, 1790-1791.
-
(2006)
Bioinformatics
, vol.22
, pp. 1790-1791
-
-
Darcy, I.K.1
Scharein, R.G.2
-
30
-
-
0003578872
-
-
PhD thesis. The University of British Columbia, Vancouver
-
Scharein,R.G. (1998) Interactive Topological Drawing, PhD thesis. The University of British Columbia, Vancouver.
-
(1998)
Interactive Topological Drawing
-
-
Scharein, R.G.1
-
31
-
-
33646175146
-
DNA reshaping by MukB. Right-handed knotting, left-handed supercoiling
-
Petrushenko,Z.M., Lai,C.H., Rai,R. and Rybenkov,V.V. (2006) DNA reshaping by MukB. Right-handed knotting, left-handed supercoiling. J. Biol. Chem., 281, 4606-4615.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 4606-4615
-
-
Petrushenko, Z.M.1
Lai, C.H.2
Rai, R.3
Rybenkov, V.V.4
-
33
-
-
1842319108
-
Energy coupling in DNA gyrase and the mechanism of action of novobiocin
-
Sugino,A., Higgins,N.P., Brown,P.O., Peebles,C.L. and Cozzarelli,N.R. (1978) Energy coupling in DNA gyrase and the mechanism of action of novobiocin. Proc. Natl Acad. Sci. USA, 75, 4838-4842.
-
(1978)
Proc. Natl Acad. Sci. USA
, vol.75
, pp. 4838-4842
-
-
Sugino, A.1
Higgins, N.P.2
Brown, P.O.3
Peebles, C.L.4
Cozzarelli, N.R.5
-
34
-
-
0021099884
-
DNA topoisomerase II from Drosophila melanogaster. Relaxation of supercoiled DNA
-
Osheroff,N., Shelton,E.R. and Brutlag,D.L. (1983) DNA topoisomerase II from Drosophila melanogaster. Relaxation of supercoiled DNA. J. Biol. Chem., 258, 9536-9543.
-
(1983)
J. Biol. Chem
, vol.258
, pp. 9536-9543
-
-
Osheroff, N.1
Shelton, E.R.2
Brutlag, D.L.3
-
35
-
-
0028334718
-
DNA transport by a type II DNA topoisomerase: Evidence in favor of a two-gate mechanism
-
Roca,J. and Wang,J.C. (1994) DNA transport by a type II DNA topoisomerase: Evidence in favor of a two-gate mechanism. Cell, 77, 609-616.
-
(1994)
Cell
, vol.77
, pp. 609-616
-
-
Roca, J.1
Wang, J.C.2
-
36
-
-
13244285443
-
Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots
-
Flammini,A., Maritan,A. and Stasiak,A. (2004) Simulations of action of DNA topoisomerases to investigate boundaries and shapes of spaces of knots. Biophys. J., 87, 2968-2975.
-
(2004)
Biophys. J
, vol.87
, pp. 2968-2975
-
-
Flammini, A.1
Maritan, A.2
Stasiak, A.3
-
37
-
-
33847743923
-
Random state transitions of knots: A first step towards modeling unknotting by type II topoisomerases
-
Hua,X., Nguyen,D., Raghavan,B., Arsuaga,J. and Vazquez,M. (2007) Random state transitions of knots: A first step towards modeling unknotting by type II topoisomerases. Topol. Appl., 154, 1381-1397.
-
(2007)
Topol. Appl
, vol.154
, pp. 1381-1397
-
-
Hua, X.1
Nguyen, D.2
Raghavan, B.3
Arsuaga, J.4
Vazquez, M.5
-
38
-
-
34548589210
-
Unknotting by type II topoisomerases
-
994-992--187
-
Mann,J.K., Deibler,R.W., Sumners,D.W. and Zechiedrich,E.L. (2004) Unknotting by type II topoisomerases. Abstracts of papers presented to the American Mathematical Society, 25, 994-992--187.
-
(2004)
Abstracts of papers presented to the American Mathematical Society
, vol.25
-
-
Mann, J.K.1
Deibler, R.W.2
Sumners, D.W.3
Zechiedrich, E.L.4
-
39
-
-
0033597962
-
13S condensin actively reconfigures DNA by introducing global positive writhe: Implications for chromosome condensation
-
Kimura,K., Rybenkov,V.V., Crisona,N.J., Hirano,T. and Cozzarelli,N.R. (1999) 13S condensin actively reconfigures DNA by introducing global positive writhe: Implications for chromosome condensation. Cell, 98, 239-248.
-
(1999)
Cell
, vol.98
, pp. 239-248
-
-
Kimura, K.1
Rybenkov, V.V.2
Crisona, N.J.3
Hirano, T.4
Cozzarelli, N.R.5
-
40
-
-
0034685618
-
Geometry of site alignment during int family recombination: Antiparallel synapsis by the Flp recombinase
-
Grainge,I., Buck,D. and Jayaram,M. (2000) Geometry of site alignment during int family recombination: Antiparallel synapsis by the Flp recombinase. J. Mol. Biol., 298, 749-764.
-
(2000)
J. Mol. Biol
, vol.298
, pp. 749-764
-
-
Grainge, I.1
Buck, D.2
Jayaram, M.3
-
41
-
-
0035937189
-
Chromosome condensation by a human condensin complex in Xenopus egg extracts
-
Kimura,K., Cuvier,O. and Hirano,T. (2001) Chromosome condensation by a human condensin complex in Xenopus egg extracts. J. Biol. Chem., 276, 5417-5420.
-
(2001)
J. Biol. Chem
, vol.276
, pp. 5417-5420
-
-
Kimura, K.1
Cuvier, O.2
Hirano, T.3
-
42
-
-
0037492126
-
Biochemical analysis of the yeast condensin Smc2/4 complex: An ATPase that promotes knotting of circular DNA
-
Stray,J.E. and Lindsley,J.E. (2003) Biochemical analysis of the yeast condensin Smc2/4 complex: An ATPase that promotes knotting of circular DNA. J. Biol. Chem., 278, 26238-26248.
-
(2003)
J. Biol. Chem
, vol.278
, pp. 26238-26248
-
-
Stray, J.E.1
Lindsley, J.E.2
-
43
-
-
27144546805
-
The Saccharomyces cerevisiae Smc2/4 condensin compacts DNA into (+) chiral structures without net supercoiling
-
Stray,J.E., Crisona,N.J., Belotserkovskii,B.P., Lindsley,J.E. and Cozzarelli,N.R. (2005) The Saccharomyces cerevisiae Smc2/4 condensin compacts DNA into (+) chiral structures without net supercoiling. J. Biol. Chem., 280, 34723-34734.
-
(2005)
J. Biol. Chem
, vol.280
, pp. 34723-34734
-
-
Stray, J.E.1
Crisona, N.J.2
Belotserkovskii, B.P.3
Lindsley, J.E.4
Cozzarelli, N.R.5
-
44
-
-
0036464531
-
Supercoiling, knotting and replication fork reversal in partially replicated plasmids
-
Olavarrieta,L., Martinez-Robles,M.L., Sogo,J.M., Stasiak,A., Hernandez,P., Krimer,D.B. and Schvartzman,J.B. (2002) Supercoiling, knotting and replication fork reversal in partially replicated plasmids. Nucleic Acids Res., 30, 656-666.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 656-666
-
-
Olavarrieta, L.1
Martinez-Robles, M.L.2
Sogo, J.M.3
Stasiak, A.4
Hernandez, P.5
Krimer, D.B.6
Schvartzman, J.B.7
-
45
-
-
0029792919
-
An RNA topoisomerase
-
Wang,H., Di Gate,R.J. and Seeman,N.C. (1996) An RNA topoisomerase. Proc. Natl Acad. Sci. USA, 93, 9477-9482.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 9477-9482
-
-
Wang, H.1
Di Gate, R.J.2
Seeman, N.C.3
-
46
-
-
0028151069
-
Processive recombination by wild-type gin and an enhancer-independent mutant. Insight into the mechanisms of recombination selectivity and strand exchange
-
Crisona,N.J., Kanaar,R., Gonzalez,T.N., Zechiedrich,E.L., Klippel,A. and Cozzarelli,N.R. (1994) Processive recombination by wild-type gin and an enhancer-independent mutant. Insight into the mechanisms of recombination selectivity and strand exchange. J. Mol. Biol., 243, 437-457.
-
(1994)
J. Mol. Biol
, vol.243
, pp. 437-457
-
-
Crisona, N.J.1
Kanaar, R.2
Gonzalez, T.N.3
Zechiedrich, E.L.4
Klippel, A.5
Cozzarelli, N.R.6
-
47
-
-
1442325402
-
Topological analysis of Hin-catalysed DNA recombination in vivo and in vitro
-
Merickel,S.K. and Johnson,R.C. (2004) Topological analysis of Hin-catalysed DNA recombination in vivo and in vitro. Mol. Microbiol. 51, 1143-1154.
-
(2004)
Mol. Microbiol
, vol.51
, pp. 1143-1154
-
-
Merickel, S.K.1
Johnson, R.C.2
-
48
-
-
34347368460
-
Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation
-
Deibler,R.W., Mann,J.K., Sumners,D.W. and Zechiedrich,L. (2007) Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Mol. Biol., 8, 44.
-
(2007)
BMC Mol. Biol
, vol.8
, pp. 44
-
-
Deibler, R.W.1
Mann, J.K.2
Sumners, D.W.3
Zechiedrich, L.4
-
49
-
-
21544474118
-
-
Arsuaga.J., Vazquez,M., McGuirk,P., Trigueros,S., Sumners,D.W. and Roca,J. (2005) DNA knots reveal a chiral organization of DNA in phage capsids. Proc. Natl Acad. Sci. USA, 102, 9165-9169.
-
Arsuaga.J., Vazquez,M., McGuirk,P., Trigueros,S., Sumners,D.W. and Roca,J. (2005) DNA knots reveal a chiral organization of DNA in phage capsids. Proc. Natl Acad. Sci. USA, 102, 9165-9169.
-
-
-
-
50
-
-
16144365192
-
Electrophoretic mobility of DNA knots
-
Stasiak,A., Katritch,V., Bednar,J., Michoud,D. and Dubochet,J. (1996) Electrophoretic mobility of DNA knots. Nature, 384, 122.
-
(1996)
Nature
, vol.384
, pp. 122
-
-
Stasiak, A.1
Katritch, V.2
Bednar, J.3
Michoud, D.4
Dubochet, J.5
-
51
-
-
0032562742
-
Sedimentation and electrophoretic migration of DNA knots and catenanes
-
Vologodskii,A.V., Crisona,N.J., Laurie,B., Pieranski,P., Katritch,V., Dubochet,J. and Stasiak,A. (1998) Sedimentation and electrophoretic migration of DNA knots and catenanes. J. Mol. Biol., 278, 1-3.
-
(1998)
J. Mol. Biol
, vol.278
, pp. 1-3
-
-
Vologodskii, A.V.1
Crisona, N.J.2
Laurie, B.3
Pieranski, P.4
Katritch, V.5
Dubochet, J.6
Stasiak, A.7
-
52
-
-
0031043014
-
Chirality of DNA trefoils: Implications in intramolecular synapsis of distant DNA segments
-
Shaw,S.Y. and Wang,J.C. (1997) Chirality of DNA trefoils: Implications in intramolecular synapsis of distant DNA segments. Proc. Natl Acad. Sci. USA, 94, 1692-1697.
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 1692-1697
-
-
Shaw, S.Y.1
Wang, J.C.2
|