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Volumn 339, Issue 1, 2004, Pages 53-66

Dynamics of DNA loop capture by the SfiI restriction endonuclease on supercoiled and relaxed DNA

Author keywords

DNA looping; DNA supercoiling; DNA protein interaction; restriction enzyme; SC, supercoiled; transient kinetics

Indexed keywords

DNA; MAGNESIUM CHLORIDE; RESTRICTION ENDONUCLEASE;

EID: 2342538957     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.03.046     Document Type: Article
Times cited : (16)

References (58)
  • 4
    • 0035066617 scopus 로고    scopus 로고
    • Transcriptional regulation at a distance in bacteria
    • Xu H., Hoover T.R. Transcriptional regulation at a distance in bacteria. Curr. Opin. Microbiol. 4:2001;138-144
    • (2001) Curr. Opin. Microbiol. , vol.4 , pp. 138-144
    • Xu, H.1    Hoover, T.R.2
  • 5
    • 0037311664 scopus 로고    scopus 로고
    • Eukaryotic transcriptional regulatory complexes: Cooperativity from near and afar
    • Ogata K., Sato K., Tahirov T. Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar. Curr. Opin. Struct. Biol. 13:2003;40-48
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 40-48
    • Ogata, K.1    Sato, K.2    Tahirov, T.3
  • 6
    • 0003873979 scopus 로고    scopus 로고
    • N.L. Craig, R. Craigie, M. Gellert, & A.M. Lambowitz. Washington, DC: ASM Press
    • Craig N.L., Craigie R., Gellert M., Lambowitz A.M. Mobile DNA II. 2002;ASM Press, Washington, DC
    • (2002) Mobile DNA II
  • 7
    • 0034877122 scopus 로고    scopus 로고
    • Hopping, jumping and looping by restriction enzymes
    • Halford S.E. Hopping, jumping and looping by restriction enzymes. Biochem. Soc. Trans. 29:2001;363-373
    • (2001) Biochem. Soc. Trans. , vol.29 , pp. 363-373
    • Halford, S.E.1
  • 8
    • 0035883536 scopus 로고    scopus 로고
    • Nucleoside triphosphate-dependent restriction enzymes
    • Dryden D.T.F., Murray N.E., Rao D.N. Nucleoside triphosphate-dependent restriction enzymes. Nucl. Acids Res. 29:2001;3728-3741
    • (2001) Nucl. Acids Res. , vol.29 , pp. 3728-3741
    • Dryden, D.T.F.1    Murray, N.E.2    Rao, D.N.3
  • 9
    • 0036880785 scopus 로고    scopus 로고
    • Complex restriction enzymes: NTP-driven molecular motors
    • Bourniquel A.A., Bickle T.A. Complex restriction enzymes: NTP-driven molecular motors. Biochimie. 84:2002;1047-1059
    • (2002) Biochimie , vol.84 , pp. 1047-1059
    • Bourniquel, A.A.1    Bickle, T.A.2
  • 10
    • 0035902832 scopus 로고    scopus 로고
    • DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites
    • Embleton M.L., Siksnys V., Halford S.E. DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol. 311:2001;503-514
    • (2001) J. Mol. Biol. , vol.311 , pp. 503-514
    • Embleton, M.L.1    Siksnys, V.2    Halford, S.E.3
  • 11
    • 0344011130 scopus 로고    scopus 로고
    • Diversity of type II restriction endonucleases that require two DNA recognition sites
    • Mucke M., Kruger D.H., Reuter M. Diversity of type II restriction endonucleases that require two DNA recognition sites. Nucl. Acids Res. 31:2003;6079-6084
    • (2003) Nucl. Acids Res. , vol.31 , pp. 6079-6084
    • Mucke, M.1    Kruger, D.H.2    Reuter, M.3
  • 14
    • 0028819366 scopus 로고
    • Modulation of intramolecular interactions in superhelical DNA by curved sequences: A Monte Carlo simulation study
    • Klenin K.V., Frank-Kamenetskii M.D., Langowski J. Modulation of intramolecular interactions in superhelical DNA by curved sequences: a Monte Carlo simulation study. Biophys. J. 68:1995;81-88
    • (1995) Biophys. J. , vol.68 , pp. 81-88
    • Klenin, K.V.1    Frank-Kamenetskii, M.D.2    Langowski, J.3
  • 15
    • 0030058275 scopus 로고    scopus 로고
    • Effects of supercoiling on the juxtaposition and relative orientation of two DNA sites
    • Vologodskii A., Cozzarelli N.R. Effects of supercoiling on the juxtaposition and relative orientation of two DNA sites. Biophys. J. 70:1996;2548-2556
    • (1996) Biophys. J. , vol.70 , pp. 2548-2556
    • Vologodskii, A.1    Cozzarelli, N.R.2
  • 16
    • 0028184699 scopus 로고
    • Kinetics of DNA supercoiling studied by Brownian dynamics simulation
    • Chirico G., Langowski J. Kinetics of DNA supercoiling studied by Brownian dynamics simulation. Biopolymers. 34:1994;415-433
    • (1994) Biopolymers , vol.34 , pp. 415-433
    • Chirico, G.1    Langowski, J.2
  • 17
    • 0031880930 scopus 로고    scopus 로고
    • Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation
    • Merlitz H., Rippe K., Klenin K.V., Langowski J. Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. Biophys. J. 74:1998;773-779
    • (1998) Biophys. J. , vol.74 , pp. 773-779
    • Merlitz, H.1    Rippe, K.2    Klenin, K.V.3    Langowski, J.4
  • 18
    • 0032573605 scopus 로고    scopus 로고
    • Internal motion of supercoiled DNA: Brownian dynamic simulations of site juxtaposition
    • Jian H., Schlick T., Vologodskii A. Internal motion of supercoiled DNA: Brownian dynamic simulations of site juxtaposition. J. Mol. Biol. 284:1998;287-296
    • (1998) J. Mol. Biol. , vol.284 , pp. 287-296
    • Jian, H.1    Schlick, T.2    Vologodskii, A.3
  • 20
    • 0034815621 scopus 로고    scopus 로고
    • Intrachain reactions of supercoiled DNA simulated by Brownian dynamics
    • Klenin K.V., Langowski J. Intrachain reactions of supercoiled DNA simulated by Brownian dynamics. Biophys. J. 81:2001;1924-1929
    • (2001) Biophys. J. , vol.81 , pp. 1924-1929
    • Klenin, K.V.1    Langowski, J.2
  • 21
    • 0036392202 scopus 로고    scopus 로고
    • Kinetics of site-site interactions in supercoiled DNA with bent sequences
    • Bussiek M., Klenin K., Langowski J. Kinetics of site-site interactions in supercoiled DNA with bent sequences. J. Mol. Biol. 322:2002;707-718
    • (2002) J. Mol. Biol. , vol.322 , pp. 707-718
    • Bussiek, M.1    Klenin, K.2    Langowski, J.3
  • 22
    • 0031577319 scopus 로고    scopus 로고
    • Communications between distant sites on supercoiled DNA from the non-exponential kinetics of DNA synapsis by resolvase
    • Oram M., Marko J.F., Halford S.E. Communications between distant sites on supercoiled DNA from the non-exponential kinetics of DNA synapsis by resolvase. J. Mol. Biol. 270:1997;396-412
    • (1997) J. Mol. Biol. , vol.270 , pp. 396-412
    • Oram, M.1    Marko, J.F.2    Halford, S.E.3
  • 24
    • 0036301458 scopus 로고    scopus 로고
    • Interactions of protein complexes on supercoiled DNA: The mechanism of selective synapsis by Tn3 resolvase
    • Brown J.L., He J., Sherratt D.J., Stark W.M., Boocock M.R. Interactions of protein complexes on supercoiled DNA: the mechanism of selective synapsis by Tn3 resolvase. J. Mol. Biol. 319:2002;371-383
    • (2002) J. Mol. Biol. , vol.319 , pp. 371-383
    • Brown, J.L.1    He, J.2    Sherratt, D.J.3    Stark, W.M.4    Boocock, M.R.5
  • 25
    • 0028988946 scopus 로고
    • The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence
    • Wentzell L.M., Nobbs T.J., Halford S.E. The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. J. Mol. Biol. 248:1995;581-595
    • (1995) J. Mol. Biol. , vol.248 , pp. 581-595
    • Wentzell, L.M.1    Nobbs, T.J.2    Halford, S.E.3
  • 26
    • 0029091376 scopus 로고
    • DNA cleavage at two recognition sites by the SfiI restriction endonuclease: Salt dependence of cis and trans interactions between distant DNA sites
    • Nobbs T.J., Halford S.E. DNA cleavage at two recognition sites by the SfiI restriction endonuclease: salt dependence of cis and trans interactions between distant DNA sites. J. Mol. Biol. 252:1995;399-411
    • (1995) J. Mol. Biol. , vol.252 , pp. 399-411
    • Nobbs, T.J.1    Halford, S.E.2
  • 27
    • 0029978713 scopus 로고    scopus 로고
    • Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease
    • Szczelkun M.D., Halford S.E. Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease. EMBO J. 15:1996;1460-1469
    • (1996) EMBO J. , vol.15 , pp. 1460-1469
    • Szczelkun, M.D.1    Halford, S.E.2
  • 28
    • 0032555293 scopus 로고    scopus 로고
    • DNA looping by the SfiI restriction endonuclease
    • Wentzell L.M., Halford S.E. DNA looping by the SfiI restriction endonuclease. J. Mol. Biol. 281:1998;433-444
    • (1998) J. Mol. Biol. , vol.281 , pp. 433-444
    • Wentzell, L.M.1    Halford, S.E.2
  • 30
  • 31
    • 0034607553 scopus 로고    scopus 로고
    • Alternative geometries of DNA looping: An analysis using the SfiI endonuclease
    • Watson M.A., Gowers D.M., Halford S.E. Alternative geometries of DNA looping: an analysis using the SfiI endonuclease. J. Mol. Biol. 298:2000;461-475
    • (2000) J. Mol. Biol. , vol.298 , pp. 461-475
    • Watson, M.A.1    Gowers, D.M.2    Halford, S.E.3
  • 32
    • 0035902776 scopus 로고    scopus 로고
    • Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites
    • Milsom S.E., Halford S.E., Embleton M.L., Szczelkun M.D. Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol. 311:2001;515-527
    • (2001) J. Mol. Biol. , vol.311 , pp. 515-527
    • Milsom, S.E.1    Halford, S.E.2    Embleton, M.L.3    Szczelkun, M.D.4
  • 33
    • 0036302286 scopus 로고    scopus 로고
    • Communications between catalytic sites in the protein-DNA synapse by the SfiI endonuclease
    • Williams S.A., Halford S.E. Communications between catalytic sites in the protein-DNA synapse by the SfiI endonuclease. J. Mol. Biol. 318:2002;387-394
    • (2002) J. Mol. Biol. , vol.318 , pp. 387-394
    • Williams, S.A.1    Halford, S.E.2
  • 34
    • 0033818703 scopus 로고    scopus 로고
    • Tetrameric restriction enzyme trapped in action: Structure of NgoMIV endonuclease in complex with cognate DNA
    • Deibert M., Grazulis S., Siksnys V., Huber R. Tetrameric restriction enzyme trapped in action: structure of NgoMIV endonuclease in complex with cognate DNA. Nature Struct. Biol. 7:2000;792-799
    • (2000) Nature Struct. Biol. , vol.7 , pp. 792-799
    • Deibert, M.1    Grazulis, S.2    Siksnys, V.3    Huber, R.4
  • 35
    • 0035668536 scopus 로고    scopus 로고
    • Making contacts on a nucleic acid polymer
    • Rippe K. Making contacts on a nucleic acid polymer. Trends Biochem. Sci. 26:2001;733-740
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 733-740
    • Rippe, K.1
  • 37
    • 0037082418 scopus 로고    scopus 로고
    • Crystal structure of the Bse634I restriction endonuclease: Comparison of two enzymes recognizing the same DNA sequence
    • Grazulis S., Deibert M., Rimeseliene R., Skirgaila R., Sasnauskas G., Lagunavicius A., et al. Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. Nucl. Acids Res. 30:2002;876-885
    • (2002) Nucl. Acids Res. , vol.30 , pp. 876-885
    • Grazulis, S.1    Deibert, M.2    Rimeseliene, R.3    Skirgaila, R.4    Sasnauskas, G.5    Lagunavicius, A.6
  • 38
    • 0037040190 scopus 로고    scopus 로고
    • The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence
    • Gormley N., Hillberg A.L., Halford S.E. The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence. J. Biol. Chem. 277:2002;4034-4041
    • (2002) J. Biol. Chem. , vol.277 , pp. 4034-4041
    • Gormley, N.1    Hillberg, A.L.2    Halford, S.E.3
  • 39
    • 0037470637 scopus 로고    scopus 로고
    • Subunit assembly for DNA cleavage by the restriction endonuclease SgrAI
    • Daniels L.E., Wood K.M., Scott D.J., Halford S.E. Subunit assembly for DNA cleavage by the restriction endonuclease SgrAI. J. Mol. Biol. 327:2003;579-591
    • (2003) J. Mol. Biol. , vol.327 , pp. 579-591
    • Daniels, L.E.1    Wood, K.M.2    Scott, D.J.3    Halford, S.E.4
  • 40
    • 0029938053 scopus 로고    scopus 로고
    • Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
    • Lewis M., Chang G., Horton N.C., Kercher M.A., Pace H.C., Schumacher M.A., et al. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science. 271:1996;1247-1254
    • (1996) Science , vol.271 , pp. 1247-1254
    • Lewis, M.1    Chang, G.2    Horton, N.C.3    Kercher, M.A.4    Pace, H.C.5    Schumacher, M.A.6
  • 41
    • 0035968257 scopus 로고    scopus 로고
    • Sau3AI - A monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops
    • Friedhoff P., Lurz R., Lueder G., Pingoud A. Sau3AI - a monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops. J. Biol. Chem. 276:2001;23581-23588
    • (2001) J. Biol. Chem. , vol.276 , pp. 23581-23588
    • Friedhoff, P.1    Lurz, R.2    Lueder, G.3    Pingoud, A.4
  • 42
    • 0021760476 scopus 로고
    • A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus
    • Qiang B.-Q., Schildkraut I. A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus. Nucl. Acids Res. 12:1984;4507-4515
    • (1984) Nucl. Acids Res. , vol.12 , pp. 4507-4515
    • Qiang, B.-Q.1    Schildkraut, I.2
  • 43
    • 0035297698 scopus 로고    scopus 로고
    • SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site
    • Williams S.A., Halford S.E. SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site. Nucl. Acids Res. 29:2001;1476-1483
    • (2001) Nucl. Acids Res. , vol.29 , pp. 1476-1483
    • Williams, S.A.1    Halford, S.E.2
  • 44
    • 0034387984 scopus 로고    scopus 로고
    • One- and three-dimensional pathways for proteins to reach specific DNA sites
    • Stanford N.P., Szczelkun M.D., Marko J.F., Halford S.E. One- and three-dimensional pathways for proteins to reach specific DNA sites. EMBO J. 19:2000;6546-6557
    • (2000) EMBO J. , vol.19 , pp. 6546-6557
    • Stanford, N.P.1    Szczelkun, M.D.2    Marko, J.F.3    Halford, S.E.4
  • 45
    • 0037451299 scopus 로고    scopus 로고
    • Protein motion from non-specific to specific DNA sites by three-dimensional routes facilitated by supercoiling
    • Gowers D.M., Halford S.E. Protein motion from non-specific to specific DNA sites by three-dimensional routes facilitated by supercoiling. EMBO J. 22:2003;1410-1418
    • (2003) EMBO J. , vol.22 , pp. 1410-1418
    • Gowers, D.M.1    Halford, S.E.2
  • 46
    • 0035936703 scopus 로고    scopus 로고
    • Anatomy of a preferred target site for the bacterial insertion sequence IS903
    • Hu W.Y., Thompson W., Lawrence C.E., Derbyshire K.M. Anatomy of a preferred target site for the bacterial insertion sequence IS903. J. Mol. Biol. 306:2001;403-416
    • (2001) J. Mol. Biol. , vol.306 , pp. 403-416
    • Hu, W.Y.1    Thompson, W.2    Lawrence, C.E.3    Derbyshire, K.M.4
  • 48
    • 0021022977 scopus 로고
    • Energetics of DNA twisting. I. Relation between twist and cyclization probability
    • Shore D., Baldwin R.L. Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol. 170:1983;957-981
    • (1983) J. Mol. Biol. , vol.170 , pp. 957-981
    • Shore, D.1    Baldwin, R.L.2
  • 49
    • 0030740986 scopus 로고    scopus 로고
    • The effects of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling
    • Rybenkov V.V., Vologodskii A.V., Cozzarelli N.R. The effects of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. Nucl. Acids Res. 25:1997;1412-14185
    • (1997) Nucl. Acids Res. , vol.25 , pp. 1412-14185
    • Rybenkov, V.V.1    Vologodskii, A.V.2    Cozzarelli, N.R.3
  • 50
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • Monod J., Wyman J., Changeux J.-P. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12:1965;88-103
    • (1965) J. Mol. Biol. , vol.12 , pp. 88-103
    • Monod, J.1    Wyman, J.2    Changeux, J.-P.3
  • 51
    • 0022381905 scopus 로고
    • Facilitated diffusion during catalysis by EcoRI endonuclease
    • Terry B.J., Jack W.E., Modrich P. Facilitated diffusion during catalysis by EcoRI endonuclease. J. Biol. Chem. 260:1985;13130-13137
    • (1985) J. Biol. Chem. , vol.260 , pp. 13130-13137
    • Terry, B.J.1    Jack, W.E.2    Modrich, P.3
  • 52
    • 0033729723 scopus 로고    scopus 로고
    • Multimerization-cyclization of DNA fragments as a method of conformational analysis
    • Podtelezhnikov A.A., Mao C., Seeman N.C., Vologodskii A. Multimerization-cyclization of DNA fragments as a method of conformational analysis. Biophys. J. 79:2000;2692-2704
    • (2000) Biophys. J. , vol.79 , pp. 2692-2704
    • Podtelezhnikov, A.A.1    Mao, C.2    Seeman, N.C.3    Vologodskii, A.4
  • 54
    • 0001973959 scopus 로고
    • On diffusion-controlled dissociation
    • Berg O.G. On diffusion-controlled dissociation. Chem. Phys. 31:1978;47-57
    • (1978) Chem. Phys. , vol.31 , pp. 47-57
    • Berg, O.G.1
  • 55
    • 0028000456 scopus 로고
    • Fluctuations and supercoiling of DNA
    • Marko J., Siggia E. Fluctuations and supercoiling of DNA. Science. 265:1994;506-508
    • (1994) Science , vol.265 , pp. 506-508
    • Marko, J.1    Siggia, E.2


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