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Volumn 38, Issue 20, 2010, Pages 7142-7154

DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; ARGININE; DIMER; DNA FRAGMENT; MUTANT PROTEIN; RESTRICTION ENDONUCLEASE; TETRAMER;

EID: 78651299353     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq560     Document Type: Article
Times cited : (23)

References (53)
  • 1
    • 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
  • 2
    • 46349101158 scopus 로고    scopus 로고
    • Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses
    • Orlowski, J. and Bujnicki, J. M. (2008) Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res., 36, 3552-3569.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 3552-3569
    • Orlowski, J.1    Bujnicki, J.M.2
  • 5
    • 0038652096 scopus 로고    scopus 로고
    • How the BfiI restriction enzyme uses one active site to cut two DNA strands
    • Sasnauskas, G., Halford, S. E. and Siksnys, V. (2003) How the BfiI restriction enzyme uses one active site to cut two DNA strands. Proc. Natl Acad. Sci. USA, 100, 6410-6415.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 6410-6415
    • Sasnauskas, G.1    Halford, S.E.2    Siksnys, V.3
  • 6
    • 0035883723 scopus 로고    scopus 로고
    • Structure and function of type II restriction endonucleases
    • Pingoud, A. and Jeltsch, A. (2001) Structure and function of type II restriction endonucleases. Nucleic Acids Res., 29, 3705-3727.
    • (2001) Nucleic Acids Res. , vol.29 , pp. 3705-3727
    • Pingoud, A.1    Jeltsch, A.2
  • 7
    • 14244262078 scopus 로고    scopus 로고
    • Structure and function of the tetrameric restriction enzymes
    • Pingoud, A. ed., Springer, Berlin
    • Siksnys, V., Grazulis, S. and Huber, R. (2004) Structure and function of the tetrameric restriction enzymes. In Pingoud, A. (ed.), Restriction Endonucleases, Vol. 14. Springer, Berlin, pp. 237-259.
    • (2004) Restriction Endonucleases , vol.14 , pp. 237-259
    • Siksnys, V.1    Grazulis, S.2    Huber, R.3
  • 8
    • 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
  • 9
    • 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
  • 12
    • 16244422033 scopus 로고    scopus 로고
    • Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: Oligomeric structure-stability-function correlations
    • Zaremba, M., Sasnauskas, G., Urbanke, C. and Siksnys, V. (2005) Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: oligomeric structure-stability-function correlations. J. Mol. Biol., 348, 459-478.
    • (2005) J. Mol. Biol. , vol.348 , pp. 459-478
    • Zaremba, M.1    Sasnauskas, G.2    Urbanke, C.3    Siksnys, V.4
  • 13
    • 35148841533 scopus 로고    scopus 로고
    • A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease
    • Bellamy, S. R., Milsom, S. E., Kovacheva, Y. S., Sessions, R. B. and Halford, S. E. (2007) A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease. J. Mol. Biol., 373, 1169-1183.
    • (2007) J. Mol. Biol. , vol.373 , pp. 1169-1183
    • Bellamy, S.R.1    Milsom, S.E.2    Kovacheva, Y.S.3    Sessions, R.B.4    Halford, S.E.5
  • 14
    • 55149091759 scopus 로고    scopus 로고
    • Fidelity of DNA sequence recognition by the SfiI restriction endonuclease is determined by communications between its two DNA-binding sites
    • Bellamy, S. R., Mina, P., Retter, S. E. and Halford, S. E. (2008) Fidelity of DNA sequence recognition by the SfiI restriction endonuclease is determined by communications between its two DNA-binding sites. J. Mol. Biol., 384, 557-563.
    • (2008) J. Mol. Biol. , vol.384 , pp. 557-563
    • Bellamy, S.R.1    Mina, P.2    Retter, S.E.3    Halford, S.E.4
  • 16
    • 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. 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.3    Halford, S.E.4
  • 19
    • 0037470637 scopus 로고    scopus 로고
    • Subunit assembly for DNA cleavage by restriction endonuclease SgrAI
    • 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.
    • (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
  • 20
    • 20444368444 scopus 로고    scopus 로고
    • Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI
    • Wood, K. M., Daniels, L. E. and Halford, S. E. (2005) Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI. J. Mol. Biol., 350, 240-253.
    • (2005) J. Mol. Biol. , vol.350 , pp. 240-253
    • Wood, K.M.1    Daniels, L.E.2    Halford, S.E.3
  • 24
    • 71049141657 scopus 로고    scopus 로고
    • Structural mechanisms for the 50-CCWGG sequence recognition by the N-and C-terminal domains of EcoRII
    • Golovenko, D., Manakova, E., Tamulaitiene, G., Grazulis, S. and Siksnys, V. (2009) Structural mechanisms for the 50-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII. Nucleic Acids Res., 37, 6613-6624.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 6613-6624
    • Golovenko, D.1    Manakova, E.2    Tamulaitiene, G.3    Grazulis, S.4    Siksnys, V.5
  • 25
    • 0032478624 scopus 로고    scopus 로고
    • Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites
    • Reuter, M., Kupper, D., Meisel, A., Schroeder, C. and Kruger, D. H. (1998) Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J. Biol. Chem., 273, 8294-8300.
    • (1998) J. Biol. Chem. , vol.273 , pp. 8294-8300
    • Reuter, M.1    Kupper, D.2    Meisel, A.3    Schroeder, C.4    Kruger, D.H.5
  • 26
    • 0037531222 scopus 로고    scopus 로고
    • PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: Structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes
    • Pingoud, V., Conzelmann, C., Kinzebach, S., Sudina, A., Metelev, V., Kubareva, E., Bujnicki, J. M., Lurz, R., Luder, G., Xu, S. Y. et al. (2003) PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes. J. Mol. Biol., 329, 913-929.
    • (2003) J. Mol. Biol. , vol.329 , pp. 913-929
    • Pingoud, V.1    Conzelmann, C.2    Kinzebach, S.3    Sudina, A.4    Metelev, V.5    Kubareva, E.6    Bujnicki, J.M.7    Lurz, R.8    Luder, G.9    Xu, S.Y.10
  • 27
    • 33344465796 scopus 로고    scopus 로고
    • Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes
    • Tamulaitis, G., Mucke, M. and Siksnys, V. (2006) Biochemical and mutational analysis of EcoRII functional domains reveals evolutionary links between restriction enzymes. FEBS Lett., 580, 1665-1671.
    • (2006) FEBS Lett. , vol.580 , pp. 1665-1671
    • Tamulaitis, G.1    Mucke, M.2    Siksnys, V.3
  • 28
    • 0037042192 scopus 로고    scopus 로고
    • Alternative arrangements of catalytic residues at the active sites of restriction enzymes
    • Tamulaitis, G., Solonin, A. S. and Siksnys, V. (2002) Alternative arrangements of catalytic residues at the active sites of restriction enzymes. FEBS Lett., 518, 17-22.
    • (2002) FEBS Lett. , vol.518 , pp. 17-22
    • Tamulaitis, G.1    Solonin, A.S.2    Siksnys, V.3
  • 30
    • 59749090938 scopus 로고    scopus 로고
    • AFM for analysis of structure and dynamics of DNA and protein-DNA complexes
    • Lyubchenko, Y. L. and Shlyakhtenko, L. S. (2009) AFM for analysis of structure and dynamics of DNA and protein-DNA complexes. Methods, 47, 206-213.
    • (2009) Methods , vol.47 , pp. 206-213
    • Lyubchenko, Y.L.1    Shlyakhtenko, L.S.2
  • 31
    • 67649099651 scopus 로고    scopus 로고
    • Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: Silatrane surface chemistry
    • Lyubchenko, Y. L., Shlyakhtenko, L. S. and Gall, A. A. (2009) Atomic force microscopy imaging and probing of DNA, proteins, and protein DNA complexes: silatrane surface chemistry. Methods Mol. Biol., 543, 337-351.
    • (2009) Methods Mol. Biol. , vol.543 , pp. 337-351
    • Lyubchenko, Y.L.1    Shlyakhtenko, L.S.2    Gall, A.A.3
  • 32
    • 33646119884 scopus 로고    scopus 로고
    • Simultaneous binding of three recognition sites is necessary for a concerted plasmid DNA cleavage by EcoRII restriction endonuclease
    • Tamulaitis, G., Sasnauskas, G., Mucke, M. and Siksnys, V. (2006) Simultaneous binding of three recognition sites is necessary for a concerted plasmid DNA cleavage by EcoRII restriction endonuclease. J. Mol. Biol., 358, 406-419.
    • (2006) J. Mol. Biol. , vol.358 , pp. 406-419
    • Tamulaitis, G.1    Sasnauskas, G.2    Mucke, M.3    Siksnys, V.4
  • 33
    • 34547862040 scopus 로고    scopus 로고
    • Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence
    • Tamulaitis, G., Zaremba, M., Szczepanowski, R. H., Bochtler, M. and Siksnys, V. (2007) Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence. Nucleic Acids Res., 35, 4792-4799.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 4792-4799
    • Tamulaitis, G.1    Zaremba, M.2    Szczepanowski, R.H.3    Bochtler, M.4    Siksnys, V.5
  • 34
    • 0037841390 scopus 로고    scopus 로고
    • Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials
    • Shlyakhtenko, L. S., Gall, A. A., Filonov, A., Cerovac, Z., Lushnikov, A. and Lyubchenko, Y. L. (2003) Silatrane-based surface chemistry for immobilization of DNA, protein-DNA complexes and other biological materials. Ultramicroscopy, 97, 279-287.
    • (2003) Ultramicroscopy , vol.97 , pp. 279-287
    • Shlyakhtenko, L.S.1    Gall, A.A.2    Filonov, A.3    Cerovac, Z.4    Lushnikov, A.5    Lyubchenko, Y.L.6
  • 35
    • 59749090938 scopus 로고    scopus 로고
    • AFM for analysis of structure and dynamics of DNA and protein-DNA complexes
    • Lyubchenko, Y. L. and Shlyakhtenko, L. S. (2009) AFM for analysis of structure and dynamics of DNA and protein-DNA complexes. Methods, 47, 206-213.
    • (2009) Methods , vol.47 , pp. 206-213
    • Lyubchenko, Y.L.1    Shlyakhtenko, L.S.2
  • 36
    • 0035235288 scopus 로고    scopus 로고
    • Atomic force microscopy of DNA and protein-DNA complexes using functionalized mica substrates
    • Lyubchenko, Y. L., Gall, A. A. and Shlyakhtenko, L. S. (2001) Atomic force microscopy of DNA and protein-DNA complexes using functionalized mica substrates. Methods Mol. Biol., 148, 569-578.
    • (2001) Methods Mol. Biol. , vol.148 , pp. 569-578
    • Lyubchenko, Y.L.1    Gall, A.A.2    Shlyakhtenko, L.S.3
  • 37
    • 30144437474 scopus 로고    scopus 로고
    • DNA strand arrangement within the SfiI-DNA complex: Atomic force microscopy analysis
    • Lushnikov, A. Y., Potaman, V. N., Oussatcheva, E. A., Sinden, R. R. and Lyubchenko, Y. L. (2006) DNA strand arrangement within the SfiI-DNA complex: atomic force microscopy analysis. Biochemistry, 45, 152-158.
    • (2006) Biochemistry , vol.45 , pp. 152-158
    • Lushnikov, A.Y.1    Potaman, V.N.2    Oussatcheva, E.A.3    Sinden, R.R.4    Lyubchenko, Y.L.5
  • 38
    • 69049097259 scopus 로고    scopus 로고
    • Dynamics of nucleosomes revealed by time-lapse atomic force microscopy
    • Shlyakhtenko, L. S., Lushnikov, A. Y. and Lyubchenko, Y. L. (2009) Dynamics of nucleosomes revealed by time-lapse atomic force microscopy. Biochemistry, 48, 7842-7848.
    • (2009) Biochemistry , vol.48 , pp. 7842-7848
    • Shlyakhtenko, L.S.1    Lushnikov, A.Y.2    Lyubchenko, Y.L.3
  • 40
    • 0001774017 scopus 로고
    • Fitting and statistical analysis of single-channel records
    • Sakmann, B. and Neher, E. eds, Plenum Press, New York and London
    • Colquhoun, D. and Sigworth, F. J. (1983) Fitting and statistical analysis of single-channel records. In Sakmann, B. and Neher, E. (eds), Single channel recording. Plenum Press, New York and London, pp. 191-263.
    • (1983) Single Channel Recording , pp. 191-263
    • Colquhoun, D.1    Sigworth, F.J.2
  • 41
    • 0036386075 scopus 로고    scopus 로고
    • KyPlot - A user-oriented tool for statistical data analysis and visualization
    • Yoshioka, K. (2002) KyPlot - a user-oriented tool for statistical data analysis and visualization. CompStat., 17, 425-437.
    • (2002) CompStat. , vol.17 , pp. 425-437
    • Yoshioka, K.1
  • 42
    • 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
  • 43
    • 70449416758 scopus 로고    scopus 로고
    • Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy
    • Gilmore, J. L., Suzuki, Y., Tamulaitis, G., Siksnys, V., Takeyasu, K. and Lyubchenko, Y. L. (2009) Single-molecule dynamics of the DNA-EcoRII protein complexes revealed with high-speed atomic force microscopy. Biochemistry, 48, 10492-10498.
    • (2009) Biochemistry , vol.48 , pp. 10492-10498
    • Gilmore, J.L.1    Suzuki, Y.2    Tamulaitis, G.3    Siksnys, V.4    Takeyasu, K.5    Lyubchenko, Y.L.6
  • 45
    • 31544452261 scopus 로고    scopus 로고
    • Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
    • van den Broek, B., Vanzi, F., Normanno, D., Pavone, F. S. and Wuite, G. J. (2006) Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res., 34, 167-174.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 167-174
    • Van Den Broek, B.1    Vanzi, F.2    Normanno, D.3    Pavone, F.S.4    Wuite, G.J.5
  • 46
    • 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
  • 47
    • 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. and Halford, S. E. (2001) DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol., 311, 503-514.
    • (2001) J. Mol. Biol. , vol.311 , pp. 503-514
    • Embleton, M.L.1    Siksnys, V.2    Halford, S.E.3
  • 48
    • 33749579918 scopus 로고    scopus 로고
    • Allosteric communication network in the tetrameric restriction endonuclease Bse634I
    • Zaremba, M., Sasnauskas, G., Urbanke, C. and Siksnys, V. (2006) Allosteric communication network in the tetrameric restriction endonuclease Bse634I. J. Mol. Biol., 363, 800-812.
    • (2006) J. Mol. Biol. , vol.363 , pp. 800-812
    • Zaremba, M.1    Sasnauskas, G.2    Urbanke, C.3    Siksnys, V.4
  • 49
    • 0037470599 scopus 로고    scopus 로고
    • The metal-independent type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre
    • Lagunavicius, A., Sasnauskas, G., Halford, S. E. and Siksnys, V. (2003) The metal-independent type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre. J. Mol. Biol., 326, 1051-1064.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1051-1064
    • Lagunavicius, A.1    Sasnauskas, G.2    Halford, S.E.3    Siksnys, V.4
  • 50
    • 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. and Halford, S. E. (1995) 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, 399-411.
    • (1995) J. Mol. Biol. , vol.252 , pp. 399-411
    • Nobbs, T.J.1    Halford, S.E.2
  • 51
    • 70349258664 scopus 로고    scopus 로고
    • Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: Implications for DNA looping
    • Bellamy, S. R., Kovacheva, Y. S., Zulkipli, I. H. and Halford, S. E. (2009) Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: implications for DNA looping. Nucleic Acids Res., 37, 5443-5453.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 5443-5453
    • Bellamy, S.R.1    Kovacheva, Y.S.2    Zulkipli, I.H.3    Halford, S.E.4
  • 53
    • 56049119613 scopus 로고    scopus 로고
    • How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets
    • Tamulaitis, G., Zaremba, M., Szczepanowski, R. H., Bochtler, M. and Siksnys, V. (2008) How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets. Nucleic Acids Res., 36, 6101-6108.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 6101-6108
    • Tamulaitis, G.1    Zaremba, M.2    Szczepanowski, R.H.3    Bochtler, M.4    Siksnys, V.5


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