메뉴 건너뛰기




Volumn 91, Issue 11, 2006, Pages 4154-4165

Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENDONUCLEASE; PROTEIN SAU3AI;

EID: 33845353937     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.088518     Document Type: Article
Times cited : (15)

References (46)
  • 2
    • 0021188333 scopus 로고
    • An operator at -280 base pairs that is required for repression of araBAD operon promoter: Addition of DNA helical turns between the operator and promoter cyclically hinders repression
    • Dunn, T. M., S. Hahn, S. Ogden, and R. F. Schleif. 1984. An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression. Proc. Natl. Acad. Sci. USA. 81:5017-5020.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 5017-5020
    • Dunn, T.M.1    Hahn, S.2    Ogden, S.3    Schleif, R.F.4
  • 3
    • 0024284848 scopus 로고
    • Enhancer origin interaction in plasmid-R6K involves a DNA loop mediated by initiator protein
    • Mukherjee, S., H. Erickson, and D. Bastia. 1988. Enhancer origin interaction in plasmid-R6K involves a DNA loop mediated by initiator protein. Cell. 52:375-383.
    • (1988) Cell , vol.52 , pp. 375-383
    • Mukherjee, S.1    Erickson, H.2    Bastia, D.3
  • 4
    • 0025721021 scopus 로고
    • DNA looping between the origin of replication of Epstein-Barr virus and its enhancer site: Stabilization of an origin complex with Epstein-Barr nuclear antigen 1
    • Su, W., T. Middleton, B. Sugden, and H. Echols. 1991. DNA looping between the origin of replication of Epstein-Barr virus and its enhancer site: stabilization of an origin complex with Epstein-Barr nuclear antigen 1. Proc. Natl. Acad. Sci. USA. 88:10870-10874.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 10870-10874
    • Su, W.1    Middleton, T.2    Sugden, B.3    Echols, H.4
  • 5
    • 0028365289 scopus 로고
    • Quality and position of the three lac operators of E. coli define efficiency of repression
    • Oehler, S., M. Amouyal, P. Kolkhof, B. von Wilcken-Bergmann, and B. Muller-Hill. 1994. Quality and position of the three lac operators of E. coli define efficiency of repression. EMBO J. 13:3348-3355.
    • (1994) EMBO J. , vol.13 , pp. 3348-3355
    • Oehler, S.1    Amouyal, M.2    Kolkhof, P.3    Von Wilcken-Bergmann, B.4    Muller-Hill, B.5
  • 6
    • 0028247038 scopus 로고
    • Chromosome pairing via multiple interstitial interactions before and during meiosis in yeast
    • Weiner, B. M., and N. Kleckner. 1994. Chromosome pairing via multiple interstitial interactions before and during meiosis in yeast. Cell. 77:977-991.
    • (1994) Cell , vol.77 , pp. 977-991
    • Weiner, B.M.1    Kleckner, N.2
  • 7
    • 0032479079 scopus 로고    scopus 로고
    • Going the distance: A current view of enhancer action
    • Blackwood, E. M., and J. T. Kadonaga. 1998. Going the distance: a current view of enhancer action. Science. 281:60-63.
    • (1998) Science , vol.281 , pp. 60-63
    • Blackwood, E.M.1    Kadonaga, J.T.2
  • 8
    • 0041375463 scopus 로고    scopus 로고
    • New insight into site-specific recombination from Flp recombinase-DNA structures
    • Chen, Y., and P. A. Rice. 2003. New insight into site-specific recombination from Flp recombinase-DNA structures. Annu. Rev. Biophys. Biomol. Struct. 32:135-159.
    • (2003) Annu. Rev. Biophys. Biomol. Struct. , vol.32 , pp. 135-159
    • Chen, Y.1    Rice, P.A.2
  • 9
    • 0042622638 scopus 로고    scopus 로고
    • DNA looping and physical constraints on transcription regulation
    • Vilar, J. M., and S. Leibler. 2003. DNA looping and physical constraints on transcription regulation. J. Mol. Biol. 331:981-989.
    • (2003) J. Mol. Biol. , vol.331 , pp. 981-989
    • Vilar, J.M.1    Leibler, S.2
  • 10
    • 0037965981 scopus 로고    scopus 로고
    • On schemes of combinatorial transcription logic
    • Buchler, N. E., U. Gerland, and T. Hwa. 2003. On schemes of combinatorial transcription logic. Proc. Natl. Acad. Sci. USA. 100:5136-5141.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 5136-5141
    • Buchler, N.E.1    Gerland, U.2    Hwa, T.3
  • 11
    • 0024284313 scopus 로고
    • EcoRII can be activated to cleave refractory DNA recognition sites
    • Kruger, D. H., G. J. Barcak, M. Reuter, and H. O. Smith. 1988. EcoRII can be activated to cleave refractory DNA recognition sites. Nucleic Acids Res. 16:3997-4008.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 3997-4008
    • Kruger, D.H.1    Barcak, G.J.2    Reuter, M.3    Smith, H.O.4
  • 12
    • 0035968257 scopus 로고    scopus 로고
    • Sau3AI, a monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops
    • Friedhoff, P., R. Lurz, G. Luder, and A. Pingoud. 2001. Sau3AI, a monomeric type II restriction endonuclease that dimerizes on the DNA and thereby induces DNA loops. J. Biol. Chem. 276:23581-23588.
    • (2001) J. Biol. Chem. , vol.276 , pp. 23581-23588
    • Friedhoff, P.1    Lurz, R.2    Luder, G.3    Pingoud, A.4
  • 13
    • 0344011130 scopus 로고    scopus 로고
    • Diversity of type II restriction endonucleases that require two DNA recognition sites
    • Mucke, M., D. H. Kruger, and M. Reuter. 2003. Diversity of type II restriction endonucleases that require two DNA recognition sites. Nucleic Acids Res. 31:6079-6084.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6079-6084
    • Mucke, M.1    Kruger, D.H.2    Reuter, M.3
  • 15
    • 37049024837 scopus 로고    scopus 로고
    • Near-field-magnetic-tweezer manipulation of single DNA molecules
    • Yan, J., D. Skoko, and J. F. Marko. 2004. Near-field-magnetic-tweezer manipulation of single DNA molecules. Phys. Rev. E. 70:011905.
    • (2004) Phys. Rev. E , vol.70 , pp. 011905
    • Yan, J.1    Skoko, D.2    Marko, J.F.3
  • 16
    • 31544452261 scopus 로고    scopus 로고
    • Real-time observation of DNA looping dynamics of type IIE restriction enzymes NaeI and NarI
    • van den Broek, B., F. Vanzi, D. Normanno, F. S. Pavone, and G. J. Wuite. 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
  • 17
    • 33746824311 scopus 로고    scopus 로고
    • Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are "switched off" at low force
    • Gemmen, G. J., R. Millin, and D. E. Smith. 2006. Tension-dependent DNA cleavage by restriction endonucleases: two-site enzymes are "switched off" at low force. Proc. Natl. Acad. Sci. USA. 103:11555-11560.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 11555-11560
    • Gemmen, G.J.1    Millin, R.2    Smith, D.E.3
  • 18
    • 33744546367 scopus 로고    scopus 로고
    • DNA looping by two-site restriction endonucleases: Heterogeneous probability distributions for loop size and unbinding force
    • Gemmen, G. J., R. Millin, and D. E. Smith. 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
  • 19
    • 37649031368 scopus 로고    scopus 로고
    • Formation of loops in DNA under tension
    • Sankararaman, S., and J. F. Marko. 2005. Formation of loops in DNA under tension. Phys. Rev. E. 71:021911.
    • (2005) Phys. Rev. E , vol.71 , pp. 021911
    • Sankararaman, S.1    Marko, J.F.2
  • 20
    • 21244440748 scopus 로고    scopus 로고
    • Disruption of protein-mediated DNA looping by tension in the substrate DNA
    • Blumberg, S., A. V. Tkachenko, and J. C. Meiners. 2005. Disruption of protein-mediated DNA looping by tension in the substrate DNA. Biophys. J. 88:1692-1701.
    • (2005) Biophys. J. , vol.88 , pp. 1692-1701
    • Blumberg, S.1    Tkachenko, A.V.2    Meiners, J.C.3
  • 21
    • 22044436367 scopus 로고    scopus 로고
    • Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF
    • Gemmen, G. J., R. Sim, K. A. Haushalter, P. C. Ke, J. T. Kadonaga, and D. E. Smith. 2005. Forced unraveling of nucleosomes assembled on heterogeneous DNA using core histones, NAP-1, and ACF. J. Mol. Biol. 351:89-99.
    • (2005) J. Mol. Biol. , vol.351 , pp. 89-99
    • Gemmen, G.J.1    Sim, R.2    Haushalter, K.A.3    Ke, P.C.4    Kadonaga, J.T.5    Smith, D.E.6
  • 23
    • 1542375742 scopus 로고    scopus 로고
    • Effects of intermediate bound states in dynamic force spectroscopy
    • Derenyi, I., D. Bartolo, and A. Ajdari. 2004. Effects of intermediate bound states in dynamic force spectroscopy. Biophys. J. 86:1263-1269.
    • (2004) Biophys. J. , vol.86 , pp. 1263-1269
    • Derenyi, I.1    Bartolo, D.2    Ajdari, A.3
  • 24
    • 19444384194 scopus 로고    scopus 로고
    • DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway
    • van den Broek, B., M. C. Noom, and G. J. Wuite. 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
  • 25
    • 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., K. Rippe, K. V. Klenin, and J. Langowski. 1998. Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. Biophys. J. 74:773-779.
    • (1998) Biophys. J. , vol.74 , pp. 773-779
    • Merlitz, H.1    Rippe, K.2    Klenin, K.V.3    Langowski, J.4
  • 26
    • 0028801067 scopus 로고
    • Action at a distance: DNA-looping and initiation of transcription
    • Rippe, K., P. H. von Hippel, and J. Langowski. 1995. Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci. 20:500-506.
    • (1995) Trends Biochem. Sci. , vol.20 , pp. 500-506
    • Rippe, K.1    Von Hippel, P.H.2    Langowski, J.3
  • 27
    • 0035668536 scopus 로고    scopus 로고
    • Making contacts on a nucleic acid polymer
    • Rippe, K. 2001. Making contacts on a nucleic acid polymer. Trends Biochem. Sci. 26:733-740.
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 733-740
    • Rippe, K.1
  • 28
    • 27944487890 scopus 로고    scopus 로고
    • Statistics of loop formation along double helix DNAs
    • Yan, J., R. Kawamura, and J. F. Marko. 2005. Statistics of loop formation along double helix DNAs. Phys Rev E. 71:061905.
    • (2005) Phys. Rev. E , vol.71 , pp. 061905
    • Yan, J.1    Kawamura, R.2    Marko, J.F.3
  • 29
    • 27144547507 scopus 로고    scopus 로고
    • Entropic compression of interacting DNA loops
    • Sankararaman, S., and J. F. Marko. 2005. Entropic compression of interacting DNA loops. Phys. Rev. Lett. 95:078104.
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 078104
    • Sankararaman, S.1    Marko, J.F.2
  • 31
    • 0009699824 scopus 로고
    • In vivo DNA loops in araCBAD: Size limits and helical repeat
    • Lee, D. H., and R. F. Schleif. 1989. In vivo DNA loops in araCBAD: size limits and helical repeat. Proc. Natl. Acad. Sci. USA. 86:476-480.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 476-480
    • Lee, D.H.1    Schleif, R.F.2
  • 32
    • 0029975889 scopus 로고    scopus 로고
    • Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
    • Muller, J., S. Oehler, and B. Muller-Hill. 1996. Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J. Mol. Biol. 257:21-29.
    • (1996) J. Mol. Biol. , vol.257 , pp. 21-29
    • Muller, J.1    Oehler, S.2    Muller-Hill, B.3
  • 33
    • 0032029574 scopus 로고    scopus 로고
    • DNA bending and expression of the divergent nagE-B operons
    • Plumbridge, J., and A. Kolb. 1998. DNA bending and expression of the divergent nagE-B operons. Nucleic Acids Res. 26:1254-1260.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1254-1260
    • Plumbridge, J.1    Kolb, A.2
  • 35
    • 0028956979 scopus 로고
    • Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules
    • Finzi, L., and J. Gelles. 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
  • 37
    • 0032478624 scopus 로고    scopus 로고
    • Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites
    • Reuter, M., D. Kupper, A. Meisel, C. Schroeder, and D. H. Kruger. 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
  • 38
    • 0038440584 scopus 로고    scopus 로고
    • Single molecule detection of DNA looping by NgoMIV restriction endonuclease
    • Katiliene, Z., E. Katilius, and N. W. Woodbury. 2003. Single molecule detection of DNA looping by NgoMIV restriction endonuclease. Biophys. J. 84:4053-4061.
    • (2003) Biophys. J. , vol.84 , pp. 4053-4061
    • Katiliene, Z.1    Katilius, E.2    Woodbury, N.W.3
  • 40
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded DNA
    • Cloutier, T. E., and J. Widom. 2004. Spontaneous sharp bending of double-stranded DNA. Mol. Cell. 14:355-362.
    • (2004) Mol. Cell. , vol.14 , pp. 355-362
    • Cloutier, T.E.1    Widom, J.2
  • 41
    • 19544379865 scopus 로고    scopus 로고
    • Localized single-stranded bubble mechanism for cyclization of short double helix DNA
    • Yan, J., and J. F. Marko. 2004. Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett. 93:108108.
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 108108
    • Yan, J.1    Marko, J.F.2
  • 42
    • 41349084347 scopus 로고    scopus 로고
    • Exact theory of kinkable elastic polymers
    • Wiggins, P. A., R. Phillips, and P. C. Nelson. 2005. Exact theory of kinkable elastic polymers. Phys Rev E. 71:021909.
    • (2005) Phys. Rev. E , vol.71 , pp. 021909
    • Wiggins, P.A.1    Phillips, R.2    Nelson, P.C.3
  • 45
    • 4644349809 scopus 로고    scopus 로고
    • DNA-looping by RXR tetramers permits transcriptional regulation "at a distance"
    • Yasmin, R., K. T. Yeung, R. H. Chung, M. E. Gaczynska, P. A. Osmulski, and N. Noy. 2004. DNA-looping by RXR tetramers permits transcriptional regulation "at a distance". J. Mol. Biol. 343:327-338.
    • (2004) J. Mol. Biol. , vol.343 , pp. 327-338
    • Yasmin, R.1    Yeung, K.T.2    Chung, R.H.3    Gaczynska, M.E.4    Osmulski, P.A.5    Noy, N.6
  • 46
    • 18744391399 scopus 로고    scopus 로고
    • Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
    • Villa, E., A. Balaeff, and K. Schulten. 2005. Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc. Natl. Acad. Sci. USA. 102:6783-6788.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6783-6788
    • Villa, E.1    Balaeff, A.2    Schulten, K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.