메뉴 건너뛰기




Volumn 36, Issue 12, 2008, Pages 4118-4127

Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; RESTRICTION ENDONUCLEASE; SODIUM CHLORIDE;

EID: 47249153641     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn376     Document Type: Article
Times cited : (181)

References (48)
  • 1
    • 0014945567 scopus 로고
    • The lac repressor-operator interaction. 3. Kinetic studies
    • Riggs,A.D., Bourgeois,S. and Cohn,M. (1970) The lac repressor-operator interaction. 3. Kinetic studies. J. Mol. Biol., 53, 401-417.
    • (1970) J. Mol. Biol , vol.53 , pp. 401-417
    • Riggs, A.D.1    Bourgeois, S.2    Cohn, M.3
  • 2
    • 0019887628 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
    • Berg,O.G., Winter,R.B. and von Hippel,P.H. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry, 20, 6929-6948.
    • (1981) Biochemistry , vol.20 , pp. 6929-6948
    • Berg, O.G.1    Winter, R.B.2    von Hippel, P.H.3
  • 3
    • 0019867850 scopus 로고
    • Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor - operator interaction: Kinetic measurements and conclusions
    • Winter,R.B., Berg,O.G. and von Hippel,P.H. (1981) Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor - operator interaction: Kinetic measurements and conclusions. Biochemistry, 20, 6961-6977.
    • (1981) Biochemistry , vol.20 , pp. 6961-6977
    • Winter, R.B.1    Berg, O.G.2    von Hippel, P.H.3
  • 4
    • 0024531901 scopus 로고
    • Facilitated target location in biological systems
    • von Hippel,P. and Berg,O. (1989) Facilitated target location in biological systems. J. Biol. Chem., 264, 675-678.
    • (1989) J. Biol. Chem , vol.264 , pp. 675-678
    • von Hippel, P.1    Berg, O.2
  • 5
    • 0034877122 scopus 로고    scopus 로고
    • Hopping, jumping and looping by restriction enzymes
    • Halford,S.E. (2001) Hopping, jumping and looping by restriction enzymes. Biochem. Soc. Trans., 29, 363-373.
    • (2001) Biochem. Soc. Trans , vol.29 , pp. 363-373
    • Halford, S.E.1
  • 6
    • 3042579602 scopus 로고    scopus 로고
    • How do site-specific DNA-binding proteins find their targets?
    • Halford,S.E. and Marko,J.F. (2004) How do site-specific DNA-binding proteins find their targets? Nucleic Acids Res., 32, 3040-3052.
    • (2004) Nucleic Acids Res , vol.32 , pp. 3040-3052
    • Halford, S.E.1    Marko, J.F.2
  • 7
    • 28044460036 scopus 로고    scopus 로고
    • Target site localization by site-specific, DNA-binding proteins
    • Widom,J. (2005) Target site localization by site-specific, DNA-binding proteins. Proc. Natl Acad. Sci. USA, 102, 16909-16910.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 16909-16910
    • Widom, J.1
  • 8
    • 0032986554 scopus 로고    scopus 로고
    • One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements
    • Shimamoto,N. (1999) One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements. J. Biol. Chem., 274, 15293-15296.
    • (1999) J. Biol. Chem , vol.274 , pp. 15293-15296
    • Shimamoto, N.1
  • 10
    • 0016302334 scopus 로고
    • Diffusion controlled reaction rates in spheroidal geometry. Application to repressor - operator association and membrane bound enzymes
    • Richter,P.H. and Eigen,M. (1974) Diffusion controlled reaction rates in spheroidal geometry. Application to repressor - operator association and membrane bound enzymes. Biophys. Chem., 2, 255-263.
    • (1974) Biophys. Chem , vol.2 , pp. 255-263
    • Richter, P.H.1    Eigen, M.2
  • 13
    • 33645807371 scopus 로고    scopus 로고
    • A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA
    • Blainey,P.C., van Oijen,A.M., Banerjee,A., Verdine,G.L. and Xie,X.S. (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc. Natl Acad. Sci. USA 103, 5752-5757.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 5752-5757
    • Blainey, P.C.1    van Oijen, A.M.2    Banerjee, A.3    Verdine, G.L.4    Xie, X.S.5
  • 14
    • 33746649820 scopus 로고    scopus 로고
    • Single molecule measurements of repressor protein 1D diffusion on DNA
    • Wang,Y.M., Austin,R.H. and Cox,E.C. (2006) Single molecule measurements of repressor protein 1D diffusion on DNA. Phys. Rev. Lett., 97 048302.
    • (2006) Phys. Rev. Lett , vol.97 , pp. 048302
    • Wang, Y.M.1    Austin, R.H.2    Cox, E.C.3
  • 15
    • 34547138714 scopus 로고    scopus 로고
    • Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules
    • Kim,J.H. and Larson,R.G. (2007) Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules. Nucleic Acids Res., 35, 3848-3858.
    • (2007) Nucleic Acids Res , vol.35 , pp. 3848-3858
    • Kim, J.H.1    Larson, R.G.2
  • 16
    • 35649018595 scopus 로고    scopus 로고
    • Gorman,J., Chowdhury,A., Surtees,J.A., Shimada.J., Reichman,D.R., Alani,E. and Greene,E.C. (2007) Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol. Cell, 28, 359-370.
    • Gorman,J., Chowdhury,A., Surtees,J.A., Shimada.J., Reichman,D.R., Alani,E. and Greene,E.C. (2007) Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. Mol. Cell, 28, 359-370.
  • 17
    • 34249932435 scopus 로고    scopus 로고
    • Probing transcription factor dynamics at the single-molecule level in a living cell
    • Elf,J., Li,G.W. and Xie,X.S. (2007) Probing transcription factor dynamics at the single-molecule level in a living cell. Science, 316, 1191-1194.
    • (2007) Science , vol.316 , pp. 1191-1194
    • Elf, J.1    Li, G.W.2    Xie, X.S.3
  • 18
    • 27644460480 scopus 로고    scopus 로고
    • Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA
    • Gowers,D.M., Wilson,G.G. and Halford,S.E. (2005) Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc. Natl Acad. Sci. USA, 102, 15883-15888.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 15883-15888
    • Gowers, D.M.1    Wilson, G.G.2    Halford, S.E.3
  • 19
    • 0037126028 scopus 로고    scopus 로고
    • Physical constraints and functional characteristics of transcription factor-DNA interaction
    • Gerland,U., Moroz,J.D. and Hwa,T. (2002) Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc. Natl Acad. Sci. USA, 99, 12015-12020.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 12015-12020
    • Gerland, U.1    Moroz, J.D.2    Hwa, T.3
  • 20
    • 33646945653 scopus 로고    scopus 로고
    • Strong physical constraints on sequence-specific target location by proteins on DNA molecules
    • Flyvbjerg,H., Keatch,S.A. and Dryden,D.T.F. (2006) Strong physical constraints on sequence-specific target location by proteins on DNA molecules. Nucleic Acids Res., 34, 2550-2557.
    • (2006) Nucleic Acids Res , vol.34 , pp. 2550-2557
    • Flyvbjerg, H.1    Keatch, S.A.2    Dryden, D.T.F.3
  • 21
    • 10044223573 scopus 로고    scopus 로고
    • Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential
    • Slutsky,M. and Mirny,L.A. (2004) Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential. Biophys. J., 87, 4021-4035.
    • (2004) Biophys. J , vol.87 , pp. 4021-4035
    • Slutsky, M.1    Mirny, L.A.2
  • 22
    • 4444236055 scopus 로고    scopus 로고
    • Kinetics of target site localization of a protein on DNA: A stochastic approach
    • Coppey,M., Bénichou,O., Voituriez,R. and Moreau,M. (2004) Kinetics of target site localization of a protein on DNA: A stochastic approach. Biophys. J., 87, 1640-1649.
    • (2004) Biophys. J , vol.87 , pp. 1640-1649
    • Coppey, M.1    Bénichou, O.2    Voituriez, R.3    Moreau, M.4
  • 23
    • 30344463841 scopus 로고    scopus 로고
    • Optimal target search on a fast-folding polymer chain with volume exchange
    • Lomholt,M.A., Ambjornsson,T. and Metzler,R. (2005) Optimal target search on a fast-folding polymer chain with volume exchange. Phys. Rev. Lett., 95, 260603.
    • (2005) Phys. Rev. Lett , vol.95 , pp. 260603
    • Lomholt, M.A.1    Ambjornsson, T.2    Metzler, R.3
  • 24
    • 33645816459 scopus 로고    scopus 로고
    • How proteins search for their specific sites on DNA: The role of DNA conformation
    • Hu,T., Grosberg,A.Y. and Shklovskii,B.I. (2006) How proteins search for their specific sites on DNA: The role of DNA conformation. Biophys. J., 90, 2731-2744.
    • (2006) Biophys. J , vol.90 , pp. 2731-2744
    • Hu, T.1    Grosberg, A.Y.2    Shklovskii, B.I.3
  • 28
    • 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
  • 29
    • 0025889005 scopus 로고
    • EcoRV restriction endonuclease binds all DNA sequences with equal affinity
    • Taylor,J.D., Badcoe,I.G., Clarke,A.R. and Halford,S.E. (1991) EcoRV restriction endonuclease binds all DNA sequences with equal affinity. Biochemistry, 30, 8743-8753.
    • (1991) Biochemistry , vol.30 , pp. 8743-8753
    • Taylor, J.D.1    Badcoe, I.G.2    Clarke, A.R.3    Halford, S.E.4
  • 30
    • 0032562139 scopus 로고    scopus 로고
    • Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA
    • Jeltsch,A. and Pingoud,A. (1998) Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA. Biochemistry 37, 2160-2169.
    • (1998) Biochemistry , vol.37 , pp. 2160-2169
    • Jeltsch, A.1    Pingoud, A.2
  • 31
    • 0029790522 scopus 로고    scopus 로고
    • Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme
    • Jeltsch,A., Wenz,C., Stahl,F. and Pingoud,A. (1996) Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme. EMBO J., 15, 5104-5111.
    • (1996) EMBO J , vol.15 , pp. 5104-5111
    • Jeltsch, A.1    Wenz, C.2    Stahl, F.3    Pingoud, A.4
  • 33
    • 0032538889 scopus 로고    scopus 로고
    • Crosslinking the EcoRV restriction endonuclease across the DNA-binding site reveals transient intermediates and conformational changes of the enzyme during DNA binding and catalytic turnover
    • Schulze,C., Jeltsch,A., Franke,I., Urbanke,C. and Pingoud,A. (1998) Crosslinking the EcoRV restriction endonuclease across the DNA-binding site reveals transient intermediates and conformational changes of the enzyme during DNA binding and catalytic turnover. EMBO J., 17 6757-6766.
    • (1998) EMBO J , vol.17 , pp. 6757-6766
    • Schulze, C.1    Jeltsch, A.2    Franke, I.3    Urbanke, C.4    Pingoud, A.5
  • 34
    • 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. and Halford,S.E. (2000) One- and three-dimensional pathways for proteins to reach specific DNA sites. EMBO J., 19, 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
  • 36
    • 0037451299 scopus 로고    scopus 로고
    • Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling
    • Gowers,D.M. and Halford,S.E. (2003) Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling. EMBO J., 22, 1410-1418.
    • (2003) EMBO J , vol.22 , pp. 1410-1418
    • Gowers, D.M.1    Halford, S.E.2
  • 38
    • 19444384194 scopus 로고    scopus 로고
    • DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway
    • van den Broek,B., Noom,M.C. and Wuite,G.J. (2005) DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway. Nucleic Acids Res., 33, 2676-2684.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2676-2684
    • van den Broek, B.1    Noom, M.C.2    Wuite, G.J.3
  • 39
    • 33744546367 scopus 로고    scopus 로고
    • DNA looping by two-site restriction endonucleases: Heterogeneous probability distributions for loop size and unbinding force
    • Gemmen,G.J., Millin,R. and Smith,D.E. (2006) DNA looping by two-site restriction endonucleases: Heterogeneous probability distributions for loop size and unbinding force. Nucleic Acids Res., 34, 2864-2877.
    • (2006) Nucleic Acids Res , vol.34 , pp. 2864-2877
    • Gemmen, G.J.1    Millin, R.2    Smith, D.E.3
  • 41
    • 42749100161 scopus 로고    scopus 로고
    • Transverse fluctuations of single DNA molecules attached at both extremities to a surface
    • Crut,A., Lasne,D., Allemand,J.F., Dahan,M. and Desbiolles,P. (2003) Transverse fluctuations of single DNA molecules attached at both extremities to a surface. Phys. Rev. E, 67, 051910.
    • (2003) Phys. Rev. E , vol.67 , pp. 051910
    • Crut, A.1    Lasne, D.2    Allemand, J.F.3    Dahan, M.4    Desbiolles, P.5
  • 42
    • 30344473311 scopus 로고    scopus 로고
    • Organized arrays of individual DNA molecules tethered to supported lipid bilayers
    • Granéli,A., Yeykal,C.C., Prasad,T.K. and Greene,E.C. (2006) Organized arrays of individual DNA molecules tethered to supported lipid bilayers. Langmuir, 22, 292-299.
    • (2006) Langmuir , vol.22 , pp. 292-299
    • Granéli, A.1    Yeykal, C.C.2    Prasad, T.K.3    Greene, E.C.4
  • 43
    • 0033559928 scopus 로고    scopus 로고
    • Buffer effects on EcoRV kinetics as measured by fluorescent staining and digital imaging of plasmid cleavage
    • Wenner,JR. and Bloomfield,V.A. (1999) Buffer effects on EcoRV kinetics as measured by fluorescent staining and digital imaging of plasmid cleavage. Anal. Biochem., 268, 201-212.
    • (1999) Anal. Biochem , vol.268 , pp. 201-212
    • Wenner, J.R.1    Bloomfield, V.A.2
  • 44
    • 0022573212 scopus 로고    scopus 로고
    • Kinetics of protein-nucleic acid interactions: Use of salt effects to probe mechanisms of interaction
    • Lohman,T.M. (1996) Kinetics of protein-nucleic acid interactions: Use of salt effects to probe mechanisms of interaction. CRC Crit. Rev. Biochem., 19, 191-245.
    • (1996) CRC Crit. Rev. Biochem , vol.19 , pp. 191-245
    • Lohman, T.M.1
  • 45
    • 0036656143 scopus 로고    scopus 로고
    • How to get from A to B: Strategies for analysing protein motion on DNA
    • Halford,S.E. and Szczelkun,M.D. (2002) How to get from A to B: strategies for analysing protein motion on DNA. Eur. Biophys. J., 31, 257-267.
    • (2002) Eur. Biophys. J , vol.31 , pp. 257-267
    • Halford, S.E.1    Szczelkun, M.D.2
  • 46
    • 0018472170 scopus 로고
    • The one-dimensional diffusion coefficient of proteins absorbed on DNA hydrodynamic considerations
    • Schurr,J.M. (1975) The one-dimensional diffusion coefficient of proteins absorbed on DNA hydrodynamic considerations. Biophys. Chem., 9 413-414.
    • (1975) Biophys. Chem , vol.9 , pp. 413-414
    • Schurr, J.M.1
  • 47
    • 0030985132 scopus 로고    scopus 로고
    • Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease
    • Erskine,S.G., Baldwin,G.S. and Halford,S.E. (1997) Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease. Biochemistry, 36, 7567-7576.
    • (1997) Biochemistry , vol.36 , pp. 7567-7576
    • Erskine, S.G.1    Baldwin, G.S.2    Halford, S.E.3
  • 48
    • 0001973959 scopus 로고
    • On diffusion-controlled dissociation
    • Berg,O.G. (1978) On diffusion-controlled dissociation. Chem. Phys. 31, 47-57.
    • (1978) Chem. Phys , vol.31 , pp. 47-57
    • Berg, O.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.