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Volumn 92, Issue 8, 2007, Pages 2674-2684

Breathing dynamics in heteropolymer DNA

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN;

EID: 34147109694     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.095935     Document Type: Article
Times cited : (52)

References (40)
  • 1
    • 0004350427 scopus 로고
    • W. H. Freeman, San Francisco, CA
    • Kornberg, A. 1974. DNA Synthesis. W. H. Freeman, San Francisco, CA.
    • (1974) DNA Synthesis
    • Kornberg, A.1
  • 3
    • 0002459355 scopus 로고
    • Thermal denaturation of DNA molecules: A comparison of theory with experiment
    • Wartell, R. M., and A. S. Benight. 1985. Thermal denaturation of DNA molecules: a comparison of theory with experiment. Phys. Rep. 126:67-107.
    • (1985) Phys. Rep , vol.126 , pp. 67-107
    • Wartell, R.M.1    Benight, A.S.2
  • 7
    • 2542485691 scopus 로고    scopus 로고
    • Reparametrizing loop entropy weights: Effect on DNA melting curves
    • Blossey, R., and E. Carlon. 2003. Reparametrizing loop entropy weights: effect on DNA melting curves. Phys. Rev. E. 68:061911.
    • (2003) Phys. Rev. E , vol.68 , pp. 061911
    • Blossey, R.1    Carlon, E.2
  • 8
    • 32644444430 scopus 로고    scopus 로고
    • Sequence-dependent basepair opening in DNA double helix
    • Krueger, A., E. Protozanova, and M. D. Frank-Kamenetskii. 2006. Sequence-dependent basepair opening in DNA double helix. Biophys. J. 90:3091-3099.
    • (2006) Biophys. J , vol.90 , pp. 3091-3099
    • Krueger, A.1    Protozanova, E.2    Frank-Kamenetskii, M.D.3
  • 10
    • 0142198827 scopus 로고    scopus 로고
    • Bubble dynamics in DNA
    • Hanke, A., and R. Metzler. 2003. Bubble dynamics in DNA. J. Phys. A. 36:L473-L480.
    • (2003) J. Phys. A , vol.36
    • Hanke, A.1    Metzler, R.2
  • 11
    • 24344507289 scopus 로고    scopus 로고
    • Stochastic approach to DNA breathing dynamics
    • Banik, S. K., T. Ambjörnsson, and R. Metzler. 2005. Stochastic approach to DNA breathing dynamics. Europhys. Lett. 71:852-858.
    • (2005) Europhys. Lett , vol.71 , pp. 852-858
    • Banik, S.K.1    Ambjörnsson, T.2    Metzler, R.3
  • 12
    • 28844460043 scopus 로고    scopus 로고
    • Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA
    • R
    • Ambjörnsson, T., and R. Metzler. 2005. Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA. Phys. Rev. E. 72:030901 (R).
    • (2005) Phys. Rev. E , vol.72 , pp. 030901
    • Ambjörnsson, T.1    Metzler, R.2
  • 13
    • 18744416836 scopus 로고    scopus 로고
    • Binding dynamics of singlestranded DNA binding proteins to fluctuating bubbles in breathing DNA
    • Ambjörnsson, T., and R. Metzler. 2005. Binding dynamics of singlestranded DNA binding proteins to fluctuating bubbles in breathing DNA. J. Phys. Cond.Mat. 17:S1841-S1869.
    • (2005) J. Phys. Cond.Mat , vol.17
    • Ambjörnsson, T.1    Metzler, R.2
  • 14
    • 42749108665 scopus 로고    scopus 로고
    • Bubble relaxation dynamics in double-stranded DNA
    • R
    • Bicout, D. J., and E. Kats. 2004. Bubble relaxation dynamics in double-stranded DNA. Phys. Rev. E. 70:010902 (R).
    • (2004) Phys. Rev. E , vol.70 , pp. 010902
    • Bicout, D.J.1    Kats, E.2
  • 15
    • 0037447270 scopus 로고    scopus 로고
    • Localization of denaturation bubbles in random DNA sequences
    • Hwa, T., E. Marinari, K. Sneppen, and L. H. Tang. 2003. Localization of denaturation bubbles in random DNA sequences. Proc. Natl. Acad. Sci. USA. 100:4411-4416.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 4411-4416
    • Hwa, T.1    Marinari, E.2    Sneppen, K.3    Tang, L.H.4
  • 16
    • 33847309773 scopus 로고    scopus 로고
    • Master equation approach to DNA-breathing in heteropolymer DNA
    • Ambjörnsson, T., S. K. Banik, M. A. Lomholt, and R. Metzler. 2007. Master equation approach to DNA-breathing in heteropolymer DNA. Phys. Rev. E. 75:021908.
    • (2007) Phys. Rev. E , vol.75 , pp. 021908
    • Ambjörnsson, T.1    Banik, S.K.2    Lomholt, M.A.3    Metzler, R.4
  • 17
    • 0017587485 scopus 로고    scopus 로고
    • Theory of DNA melting curves
    • Fixman, M., and J. J. Freire. 1997. Theory of DNA melting curves. Biopolymers. 16:2693-2704.
    • (1997) Biopolymers , vol.16 , pp. 2693-2704
    • Fixman, M.1    Freire, J.J.2
  • 18
    • 3543010234 scopus 로고    scopus 로고
    • Poland-Scheraga models and the DNA denaturation transition
    • Richard, C., and A. J. Guttmann. 2004. Poland-Scheraga models and the DNA denaturation transition. J. Stat. Phys. 115:925-947.
    • (2004) J. Stat. Phys , vol.115 , pp. 925-947
    • Richard, C.1    Guttmann, A.J.2
  • 19
    • 33847248708 scopus 로고
    • Is crystallization from the melt controlled by melt viscosity and entanglement effects?
    • Di Marzio, E. A., C. M. Guttman, and J. D. Hoffman. 1979. Is crystallization from the melt controlled by melt viscosity and entanglement effects? Faraday Discuss. 68:210-217.
    • (1979) Faraday Discuss , vol.68 , pp. 210-217
    • Di Marzio, E.A.1    Guttman, C.M.2    Hoffman, J.D.3
  • 20
  • 21
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • Gillespie, D. T. 1976. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22:403-434.
    • (1976) J. Comput. Phys , vol.22 , pp. 403-434
    • Gillespie, D.T.1
  • 22
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D. T. 1977. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81:2340-2361.
    • (1977) J. Phys. Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 23
    • 0004291893 scopus 로고
    • J. Wiley & Sons, New York, NY
    • Cox, D. R. 1962. Renewal Theory. J. Wiley & Sons, New York, NY.
    • (1962) Renewal Theory
    • Cox, D.R.1
  • 26
    • 0036175642 scopus 로고    scopus 로고
    • Fluorescence correlation spectroscopy: The technique and its applications
    • Krichevsky, O., and G. Bonnet. 2002. Fluorescence correlation spectroscopy: the technique and its applications. Rep. Prog. Phys. 65:251-297.
    • (2002) Rep. Prog. Phys , vol.65 , pp. 251-297
    • Krichevsky, O.1    Bonnet, G.2
  • 27
    • 16644365966 scopus 로고    scopus 로고
    • Sequence-dependence of the energetics of opening of AT base pairs in DNA
    • Chen, C., and I. M. Russu. 2004. Sequence-dependence of the energetics of opening of AT base pairs in DNA. Biophys. J. 87:2545-2551.
    • (2004) Biophys. J , vol.87 , pp. 2545-2551
    • Chen, C.1    Russu, I.M.2
  • 28
    • 5744255023 scopus 로고    scopus 로고
    • Sequence-specific thermal fluctuations identify start sites for DNA transcription
    • Kalosakas, G., K. Ø. Rasmussen, A. R. Bishop, C. H. Choi, and A. Usheva. 2004. Sequence-specific thermal fluctuations identify start sites for DNA transcription. Europhys. Lett. 68:127.
    • (2004) Europhys. Lett , vol.68 , pp. 127
    • Kalosakas, G.1    Rasmussen, K.2    Bishop, A.R.3    Choi, C.H.4    Usheva, A.5
  • 30
  • 31
    • 33746894748 scopus 로고    scopus 로고
    • Comment on "Can One Predict DNA Transcription Start Sites by Studying Bubbles?
    • Benham, C. J., and R. R. P. Sing. 2006. Comment on "Can One Predict DNA Transcription Start Sites by Studying Bubbles?". Phys. Rev. Lett. 97:059801.
    • (2006) Phys. Rev. Lett , vol.97 , pp. 059801
    • Benham, C.J.1    Sing, R.R.P.2
  • 33
    • 33745205353 scopus 로고    scopus 로고
    • Choi, C. H., A. Usheva, G. Kalosakas, K. 2006. K. O. Rasmussen, and A. R. Bishop, Comment on Can One Predict DNA Transcription Start Sites by Studying Bubbles?. Phys. Rev. Lett. 96:239801.
    • Choi, C. H., A. Usheva, G. Kalosakas, K. 2006. K. O. Rasmussen, and A. R. Bishop, Comment on "Can One Predict DNA Transcription Start Sites by Studying Bubbles?". Phys. Rev. Lett. 96:239801.
  • 35
    • 28544451982 scopus 로고    scopus 로고
    • Blinking statistics of a molecular beacon triggered by end-denaturation of DNA
    • Ambjörnsson, T., and R. Metzler. 2005. Blinking statistics of a molecular beacon triggered by end-denaturation of DNA. J. Phys. Cond. Mat. 17:S4305.
    • (2005) J. Phys. Cond. Mat , vol.17
    • Ambjörnsson, T.1    Metzler, R.2
  • 36
    • 27644509796 scopus 로고    scopus 로고
    • Sensing DNA-DNA as nanosensor: A perspective towards nanobiotechnology
    • Metzler, R., and T. Ambjörnsson. 2005. Sensing DNA-DNA as nanosensor: a perspective towards nanobiotechnology. J. Comput. Theor. Nanosci. 2:389-398.
    • (2005) J. Comput. Theor. Nanosci , vol.2 , pp. 389-398
    • Metzler, R.1    Ambjörnsson, T.2
  • 37
    • 0023256126 scopus 로고
    • A single mode of DNA basepair opening drives imino proton exchange
    • Guéron, M., M. Kochoyan, and J.-L. Leroy. 1987. A single mode of DNA basepair opening drives imino proton exchange. Nature. 328:89-92.
    • (1987) Nature , vol.328 , pp. 89-92
    • Guéron, M.1    Kochoyan, M.2    Leroy, J.-L.3
  • 38
    • 4243187319 scopus 로고
    • Statistical mechanics of a nonlinear model for DNA denaturation
    • Peyrard, M., and A. R. Bishop. 1989. Statistical mechanics of a nonlinear model for DNA denaturation. Phys. Rev. Lett. 62:2755-2758.
    • (1989) Phys. Rev. Lett , vol.62 , pp. 2755-2758
    • Peyrard, M.1    Bishop, A.R.2
  • 40
    • 0000104103 scopus 로고
    • Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains
    • Campa, A., and A. Giansanti. 1993. Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains. Phys. Rev. E. 58:3585-3588.
    • (1993) Phys. Rev. E , vol.58 , pp. 3585-3588
    • Campa, A.1    Giansanti, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.