메뉴 건너뛰기




Volumn 40, Issue 11, 2012, Pages 4977-4987

DNA looping by FokI: The impact of synapse geometry on loop topology at varied site orientations

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RESTRICTION ENDONUCLEASE; RESTRICTION ENDONUCLEASE FOKI; UNCLASSIFIED DRUG;

EID: 84862178378     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks183     Document Type: Article
Times cited : (10)

References (55)
  • 1
    • 0025148348 scopus 로고
    • Nucleoprotein structures initiating DNA replication transcription, and site-specific recombination
    • Echols, H. (1990) Nucleoprotein structures initiating DNA replication, transcription, and site-specific recombination. J. Biol. Chem., 265, 14697-14700.
    • (1990) J. Biol. Chem. , vol.265 , pp. 14697-14700
    • Echols, H.1
  • 2
    • 77956640375 scopus 로고    scopus 로고
    • Regulation of replication termination by Reb1 protein-mediated action at a distance
    • Singh, S.K., Sabatinos, S., Forsburg, S. and Bastia, D. (2010) Regulation of replication termination by Reb1 protein-mediated action at a distance. Cell, 142, 868-878.
    • (2010) Cell , vol.142 , pp. 868-878
    • Singh, S.K.1    Sabatinos, S.2    Forsburg, S.3    Bastia, D.4
  • 4
    • 0030721538 scopus 로고    scopus 로고
    • Transposition and site-specific recombination: Adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements
    • DOI 10.1016/S0168-6445(97)00055-7, PII S0168644597000557
    • Hallet, B. and Sherratt, D.J. (1997) Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements. FEMS Microbiol. Rev., 21, 157-178. (Pubitemid 27455843)
    • (1997) FEMS Microbiology Reviews , vol.21 , Issue.2 , pp. 157-178
    • Hallet, B.1    Sherratt, D.J.2
  • 5
    • 33746382212 scopus 로고    scopus 로고
    • Mechanisms of site-specific recombination
    • DOI 10.1146/annurev.biochem.73.011303.073908
    • Grindley, N.D.F., Whiteson, K.L. and Rice, P.A. (2006) Mechanisms of site-specific recombination. Annu. Rev. Biochem., 75, 567-605. (Pubitemid 44118044)
    • (2006) Annual Review of Biochemistry , vol.75 , pp. 567-605
    • Grindley, N.D.F.1    Whiteson, K.L.2    Rice, P.A.3
  • 7
    • 0028956979 scopus 로고
    • Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules
    • Finzi, L. and Gelles, J. (1995) Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules. Science, 267, 378-380.
    • (1995) Science , vol.267 , pp. 378-380
    • Finzi, L.1    Gelles, J.2
  • 8
    • 20444387232 scopus 로고    scopus 로고
    • A gamut of loops: Meandering DNA
    • DOI 10.1016/j.tibs.2005.04.009, PII S0968000405001179, Celebrating 50 Years of the IUBMB
    • Semsey, S., Virnik, K. and Adhya, S. (2005) A gamut of loops: meandering DNA. Trends Biochem. Sci., 30, 334-341. (Pubitemid 40799052)
    • (2005) Trends in Biochemical Sciences , vol.30 , Issue.6 , pp. 334-341
    • Semsey, S.1    Virnik, K.2    Adhya, S.3
  • 9
    • 77953512028 scopus 로고    scopus 로고
    • Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription
    • Finzi, L. and Dunlap, D.D. (2010) Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription. J. Biol. Chem., 285, 18973-18978.
    • (2010) J. Biol. Chem. , vol.285 , pp. 18973-18978
    • Finzi, L.1    Dunlap, D.D.2
  • 10
    • 0035883536 scopus 로고    scopus 로고
    • Nucleoside triphosphate-dependent restriction enzymes
    • Dryden, D.T.F., Murray, N.E. and Rao, D.N. (2001) Nucleoside triphosphate-dependent restriction enzymes. Nucleic Acids Res., 29, 3728-3741. (Pubitemid 32910515)
    • (2001) Nucleic Acids Research , vol.29 , Issue.18 , pp. 3728-3741
    • Dryden, D.T.F.1    Murray, N.E.2    Rao, D.N.3
  • 11
    • 0344011130 scopus 로고    scopus 로고
    • Diversity of Type II restriction endonucleases that require two DNA recognition sites
    • DOI 10.1093/nar/gkg836
    • Mucke, M., Kruger, D.H. and Reuter, M. (2003) Diversity of type II restriction endonucleases that require two DNA recognition sites. Nucleic Acids Res., 31, 6079-6084. (Pubitemid 37442335)
    • (2003) Nucleic Acids Research , vol.31 , Issue.21 , pp. 6079-6084
    • Mucke, M.1    Kruger, D.H.2    Reuter, M.3
  • 14
    • 77952727817 scopus 로고    scopus 로고
    • Maintaining a sense of direction during long-range communication on DNA
    • Szczelkun, M.D., Friedhoff, P. and Seidel, R. (2010) Maintaining a sense of direction during long-range communication on DNA. Biochem. Soc. Trans., 38, 404-409.
    • (2010) Biochem. Soc. Trans. , vol.38 , pp. 404-409
    • Szczelkun, M.D.1    Friedhoff, P.2    Seidel, R.3
  • 16
    • 0032555293 scopus 로고    scopus 로고
    • DNA looping by the SfiI restriction endonuclease
    • DOI 10.1006/jmbi.1998.1967
    • Wentzell, L.M. and Halford, S.E. (1998) DNA looping by the SfiI restriction endonuclease. J. Mol. Biol., 281, 433-444. (Pubitemid 28372121)
    • (1998) Journal of Molecular Biology , vol.281 , Issue.3 , pp. 433-444
    • Wentzell, L.M.1    Halford, S.E.2
  • 17
    • 14244254599 scopus 로고    scopus 로고
    • Analysis of type II restriction endonucleases that interact with two recognition sites
    • Pingoud, A. (ed.) Springer, Berlin
    • Welsh, A.J., Halford, S.E. and Scott, D.J. (2004) Analysis of type II restriction endonucleases that interact with two recognition sites. In: Pingoud, A. (ed.), Nucleic Acids and Molecular Biology, Restriction Endonucleases, Vol. 14. Springer, Berlin, pp. 297-317.
    • (2004) Nucleic Acids and Molecular Biology, Restriction Endonucleases , vol.14 , pp. 297-317
    • Welsh, A.J.1    Halford, S.E.2    Scott, D.J.3
  • 18
    • 31544452261 scopus 로고    scopus 로고
    • Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
    • DOI 10.1093/nar/gkj432
    • Van den Broek, B., Vanzi, F., Normanno, D., Pavone, F.S. and Wuite, G.J.L. (2006) Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res., 34, 167-174. (Pubitemid 43160041)
    • (2006) Nucleic Acids Research , vol.34 , Issue.1 , pp. 167-174
    • Van Den Broek, B.1    Vanzi, F.2    Normanno, D.3    Pavone, F.S.4    Wuite, G.J.L.5
  • 20
    • 75549086595 scopus 로고    scopus 로고
    • REBASE - A database for DNA restriction and modification: Enzymes, genes and genomes
    • Roberts, R.J., Vincze, T., Posfai, J. and Macelis, D. (2010) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res., 38, D234-D236.
    • (2010) Nucleic Acids Res. , vol.38
    • Roberts, R.J.1    Vincze, T.2    Posfai, J.3    MacElis, D.4
  • 21
    • 0028932881 scopus 로고
    • Structure and function of restriction endonucleases
    • Aggarwal, A.K. (1995) Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol., 5, 11-19.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 11-19
    • Aggarwal, A.K.1
  • 22
    • 17044403057 scopus 로고    scopus 로고
    • Type II restriction endonucleases: Structure and mechanism
    • Pingoud, A., Fuxreiter, M., Pingoud, V. and Wende, W. (2005) Type II restriction endonucleases: structure and mechanism. Cell. Mol. Life Sci., 62, 685-707.
    • (2005) Cell. Mol. Life Sci. , vol.62 , pp. 685-707
    • Pingoud, A.1    Fuxreiter, M.2    Pingoud, V.3    Wende, W.4
  • 23
    • 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. and Halford, S.E. (1995) The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. J. Mol. Biol., 248, 581-595.
    • (1995) J. Mol. Biol. , vol.248 , pp. 581-595
    • Wentzell, L.M.1    Nobbs, T.J.2    Halford, S.E.3
  • 24
    • 0037470637 scopus 로고    scopus 로고
    • Subunit assembly for DNA cleavage by restriction endonuclease SgrAI
    • DOI 10.1016/S0022-2836(03)00143-8
    • Daniels, L.E., Wood, K.M., Scott, D.J. and Halford, S.E. (2003) Subunit assembly for DNA cleavage by restriction endonuclease SgrAI. J. Mol. Biol., 327, 579-591. (Pubitemid 36299065)
    • (2003) Journal of Molecular Biology , vol.327 , Issue.3 , pp. 579-591
    • Daniels, L.E.1    Wood, K.M.2    Scott, D.J.3    Halford, S.E.4
  • 25
  • 26
    • 0033818703 scopus 로고    scopus 로고
    • Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA
    • Deibert, M., Grazulis, S., Sasnauskas, G., Siksnys, V. and Huber, R. (2000) Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat. Struct. Biol., 7, 792-799.
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 792-799
    • Deibert, M.1    Grazulis, S.2    Sasnauskas, G.3    Siksnys, V.4    Huber, R.5
  • 27
    • 28644435380 scopus 로고    scopus 로고
    • A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA
    • DOI 10.1038/sj.emboj.7600880
    • Vanamee, E.S., Viadiu, H., Kucera, R., Dorner, L., Picone, S., Schildkraut, I. and Aggarwal, A.K. (2005) A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. EMBO J., 24, 4198-4208. (Pubitemid 41752888)
    • (2005) EMBO Journal , vol.24 , Issue.23 , pp. 4198-4208
    • Vanamee, E.S.1    Viadiu, H.2    Kucera, R.3    Dorner, L.4    Picone, S.5    Schildkraut, I.6    Aggarwal, A.K.7
  • 29
    • 0034607553 scopus 로고    scopus 로고
    • Alternative geometries of DNA looping: An analysis using the SfiI endonuclease
    • Watson, M.A., Gowers, D.M. and Halford, S.E. (2000) Alternative geometries of DNA looping: an analysis using the SfiI endonuclease. J. Mol. Biol., 298, 461-475.
    • (2000) J. Mol. Biol. , vol.298 , pp. 461-475
    • Watson, M.A.1    Gowers, D.M.2    Halford, S.E.3
  • 30
    • 0019768975 scopus 로고
    • New restriction endonucleases from Flavobacterium okeanokoites (FokI) and Micrococcus luteus (MluI)
    • DOI 10.1016/0378-1119(81)90062-7
    • Sugisaki, H. and Kanazawa, S. (1981) New restriction endonucleases from Flavobacterium okeanokoites (FokI) and Micrococcus luteus (MluI). Gene, 16, 73-78. (Pubitemid 12132036)
    • (1981) Gene , vol.16 , Issue.1-3 , pp. 73-78
    • Sugisaki, H.1    Kanazawa, S.2
  • 31
    • 0035946911 scopus 로고    scopus 로고
    • FokI requires two specific DNA sites for cleavage
    • DOI 10.1006/jmbi.2001.4635
    • Vanamee, E.S., Santagata, S. and Aggarwal, A.K. (2001) FokI requires two specific DNA sites for cleavage. J. Mol. Biol., 309, 69-78. (Pubitemid 32553508)
    • (2001) Journal of Molecular Biology , vol.309 , Issue.1 , pp. 69-78
    • Vanamee, E.S.1    Santagata, S.2    Aggarwal, A.K.3
  • 32
  • 33
    • 0037040271 scopus 로고    scopus 로고
    • Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA
    • DOI 10.1074/jbc.M108441200
    • Bath, A.J., Milsom, S.E., Gormley, N.A. and Halford, S.E. (2002) Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA. J. Biol. Chem., 277, 4024-4033. (Pubitemid 34968658)
    • (2002) Journal of Biological Chemistry , vol.277 , Issue.6 , pp. 4024-4033
    • Bath, A.J.1    Milsom, S.E.2    Gormley, N.A.3    Halford, S.E.4
  • 34
    • 33847162746 scopus 로고    scopus 로고
    • Restriction Endonucleases that Bridge and Excise Two Recognition Sites from DNA
    • DOI 10.1016/j.jmb.2006.12.070, PII S0022283606017694
    • Marshall, J.J.T., Gowers, D.M. and Halford, S.E. (2007) Restriction endonucleases that bridge and excise two recognition sites from DNA. J. Mol. Biol., 367, 419-431. (Pubitemid 46295428)
    • (2007) Journal of Molecular Biology , vol.367 , Issue.2 , pp. 419-431
    • Marshall, J.J.T.1    Gowers, D.M.2    Halford, S.E.3
  • 35
    • 0024450479 scopus 로고
    • Purification and characterization of the FokI restriction endonuclease
    • DOI 10.1016/0378-1119(89)90285-0
    • Kaczorowski, T., Skowron, P. and Podhajska, A.J. (1989) Purification and characterization of the FokI restriction endonuclease. Gene, 80, 209-216. (Pubitemid 19226577)
    • (1989) Gene , vol.80 , Issue.2 , pp. 209-216
    • Kaczorowski, T.1    Skowron, P.2    Podhajska, A.J.3
  • 36
    • 0026511244 scopus 로고
    • Functional domains in Fok i restriction endonuclease
    • Li, L., Wu, L.P. and Chandrasegaran, S. (1992) Functional domains in Fok I restriction endonuclease. Proc. Natl Acad. Sci. USA, 89, 4275-4279.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 4275-4279
    • Li, L.1    Wu, L.P.2    Chandrasegaran, S.3
  • 37
    • 0028091729 scopus 로고
    • Insertion and deletion mutants of FokI restriction endonuclease
    • Kim, Y.G., Li, L. and Chandrasegaran, S. (1994) Insertion and deletion mutants of FokI restriction endonuclease. J. Biol. Chem., 269, 31978-31982. (Pubitemid 24379576)
    • (1994) Journal of Biological Chemistry , vol.269 , Issue.50 , pp. 31978-31982
    • Kim, Y.-G.1    Li, L.2    Chandrasegaran, S.3
  • 39
    • 0030790696 scopus 로고    scopus 로고
    • Structure of the multimodular endonuclease FokI bound to DNA
    • DOI 10.1038/40446
    • Wah, D.A., Hirsch, J.A., Dorner, L.F., Schildkraut, I. and Aggarwal, A.K. (1997) Structure of the multimodular endonuclease FokI bound to DNA. Nature, 388, 97-100. (Pubitemid 27283896)
    • (1997) Nature , vol.388 , Issue.6637 , pp. 97-100
    • Wah, D.A.1    Hirsch, J.A.2    Dorner, L.F.3    Schildkraut, I.4    Aggarwal, A.K.5
  • 42
    • 65549139378 scopus 로고    scopus 로고
    • Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands
    • Sanders, K.L., Catto, L.E., Bellamy, S.R.W. and Halford, S.E. (2009) Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands. Nucleic Acids Res., 37, 2105-2115.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 2105-2115
    • Sanders, K.L.1    Catto, L.E.2    Bellamy, S.R.W.3    Halford, S.E.4
  • 43
    • 84856895490 scopus 로고    scopus 로고
    • Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer
    • Pernstich, C. and Halford, S.E. (2012) Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer. Nucleic Acids Res., 40, 1203-1213.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 1203-1213
    • Pernstich, C.1    Halford, S.E.2
  • 44
    • 50849106997 scopus 로고    scopus 로고
    • Dynamics and consequences of DNA looping by the FokI restriction endonuclease
    • Catto, L.E., Bellamy, S.R.W., Retter, S.E. and Halford, S.E. (2008) Dynamics and consequences of DNA looping by the FokI restriction endonuclease. Nucleic Acids Res., 36, 5122-5122.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5122-5122
    • Catto, L.E.1    Bellamy, S.R.W.2    Retter, S.E.3    Halford, S.E.4
  • 45
    • 34249660654 scopus 로고    scopus 로고
    • An EM view of the FokI synaptic complex by single particle analysis
    • DOI 10.1016/j.jmb.2007.04.066, PII S002228360700575X
    • Vanamee, E.S., Berriman, J. and Aggarwal, A.K. (2007) An EM view of the FokI synaptic complex by single particle analysis. J. Mol. Biol., 370, 207-212. (Pubitemid 46829217)
    • (2007) Journal of Molecular Biology , vol.370 , Issue.2 , pp. 207-212
    • Vanamee, E.S.1    Berriman, J.2    Aggarwal, A.K.3
  • 46
    • 0037306915 scopus 로고    scopus 로고
    • Fluorescence resonance energy transfer over ∼130 basepairs in hyperstable Lac repressor-DNA loops
    • Edelman, L.M., Cheong, R. and Kahn, J.D. (2003) Fluorescence resonance energy transfer over-130 basepairs in hyperstable Lac repressor-DNA loops. Biophys. J., 84, 1131-1145. (Pubitemid 36133436)
    • (2003) Biophysical Journal , vol.84 , Issue.2 , pp. 1131-1145
    • Edelman, L.M.1    Cheong, R.2    Kahn, J.D.3
  • 47
    • 84862178413 scopus 로고    scopus 로고
    • DNA looping by FokI: The impact of twisting and bending rigidity on protein-induced looping dynamics
    • Laurens, N., Rusling, D.A., Pernstich, C., Brouwer, I., Halford, S.E. and Wuite, G.J.L. (2012) DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics. Nucleic Acids Res., 40, 4988-4997.
    • (2012) Nucleic Acids Res. , vol.40 , pp. 4988-4997
    • Laurens, N.1    Rusling, D.A.2    Pernstich, C.3    Brouwer, I.4    Halford, S.E.5    Wuite, G.J.L.6
  • 51
    • 33644676435 scopus 로고    scopus 로고
    • Volume-exclusion effects in tethered-particle experiments: Bead size matters
    • Segall, D.E., Nelson, P.C. and Phillips, R. (2006) Volume-exclusion effects in tethered-particle experiments: bead size matters. Phys. Rev. Lett., 96, 088306.
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 088306
    • Segall, D.E.1    Nelson, P.C.2    Phillips, R.3
  • 54
    • 0025817867 scopus 로고
    • Dynamics of long-range interactions on DNA: The speed of synapsis during site-specific recombination by resolvase
    • Parker, C.N. and Halford, S.E. (1991) Dynamics of long-range interactions in DNA: the speed of synapsis during site-specific recombination by resolvase. Cell, 66, 781-791. (Pubitemid 121001711)
    • (1991) Cell , vol.66 , Issue.4 , pp. 781-791
    • Parker, C.N.1    Halford, S.E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.