메뉴 건너뛰기




Volumn 96, Issue 10, 2009, Pages 4024-4034

A new computational approach for mechanical folding kinetics of RNA hairpins

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 68049147448     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.02.044     Document Type: Article
Times cited : (10)

References (53)
  • 3
    • 41149155366 scopus 로고    scopus 로고
    • Following translation by single ribosomes one codon at a time
    • Wen, J.-D., L. Lancaster, C. Hodges, A.-C. Zeri, S. H. Yoshimura, et al. 2008. Following translation by single ribosomes one codon at a time. Nature. 452:598-603.
    • (2008) Nature , vol.452 , pp. 598-603
    • Wen, J.-D.1    Lancaster, L.2    Hodges, C.3    Zeri, A.-C.4    Yoshimura, S.H.5
  • 5
    • 31944441873 scopus 로고    scopus 로고
    • A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy
    • Jung, J. Y., and A. Van Orden. 2006. A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy. J. Am. Chem. Soc. 128:1240-1249.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 1240-1249
    • Jung, J.Y.1    Van Orden, A.2
  • 6
    • 38049160345 scopus 로고    scopus 로고
    • Fluorescence correlation spectroscopy for probing the kinetics and mechanisms of DNA hairpin formation
    • Van Orden, A., and J. Jung. 2008. Fluorescence correlation spectroscopy for probing the kinetics and mechanisms of DNA hairpin formation. Biopolymers. 89:1-16.
    • (2008) Biopolymers , vol.89 , pp. 1-16
    • Van Orden, A.1    Jung, J.2
  • 9
    • 0016257808 scopus 로고
    • Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix
    • Porschke, D. 1974. Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix. Biophys. Chem. 1:381-386.
    • (1974) Biophys. Chem , vol.1 , pp. 381-386
    • Porschke, D.1
  • 10
    • 0034934258 scopus 로고    scopus 로고
    • Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins
    • Ansari, A., S. V. Kunznetsov, and Y. Shen. 2001. Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins. Proc. Natl. Acad. Sci. USA. 98:7771-7776.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 7771-7776
    • Ansari, A.1    Kunznetsov, S.V.2    Shen, Y.3
  • 12
    • 0032555119 scopus 로고    scopus 로고
    • Kinetics of conformational fluctuations in DNA hairpin-loops
    • Bonnet, G., O. Krichevsky, and A. Libchaber. 1998. Kinetics of conformational fluctuations in DNA hairpin-loops. Proc. Natl. Acad. Sci. USA. 95:8602-8606.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 8602-8606
    • Bonnet, G.1    Krichevsky, O.2    Libchaber, A.3
  • 13
    • 33646587736 scopus 로고    scopus 로고
    • Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins
    • Woodside, M. T., W. M. Behnke-Parks, K. Larizadeh, K. Travers, D. Herschlag, et al. 2006. Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins. Proc. Natl. Acad. Sci. USA. 103:6190-6195.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 6190-6195
    • Woodside, M.T.1    Behnke-Parks, W.M.2    Larizadeh, K.3    Travers, K.4    Herschlag, D.5
  • 15
    • 33646191609 scopus 로고    scopus 로고
    • Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis
    • Zhang, W. B., and S.-J. Chen. 2006. Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis. Biophys. J. 90:765-777.
    • (2006) Biophys. J , vol.90 , pp. 765-777
    • Zhang, W.B.1    Chen, S.-J.2
  • 16
    • 2942592663 scopus 로고    scopus 로고
    • Forces as a useful variable in reactions: Unfolding RNA
    • Tinoco, Jr., I. 2004. Forces as a useful variable in reactions: unfolding RNA. Annu. Rev. Biophys. Biomol. Struct. 33:363-385.
    • (2004) Annu. Rev. Biophys. Biomol. Struct , vol.33 , pp. 363-385
    • Tinoco Jr., I.1
  • 17
    • 33845681159 scopus 로고    scopus 로고
    • Determination of thermodynamics and kinetics of RNA reactions by force
    • Tinoco, Jr., I., P. T. X. Li, and C. Bustamante. 2006. Determination of thermodynamics and kinetics of RNA reactions by force. Q. Rev. Biophys. 39:325-360.
    • (2006) Q. Rev. Biophys , vol.39 , pp. 325-360
    • Tinoco Jr., I.1    Li, P.T.X.2    Bustamante, C.3
  • 20
    • 34249855274 scopus 로고    scopus 로고
    • Real-time control of the energy landscape by force directs the folding of RNA molecules
    • Li, P. T. X., C. Bustamante, and I. Tinoco, Jr. 2007. Real-time control of the energy landscape by force directs the folding of RNA molecules. Proc. Natl. Acad. Sci. USA. 104:7039-7044.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 7039-7044
    • Li, P.T.X.1    Bustamante, C.2    Tinoco Jr., I.3
  • 22
    • 36248968677 scopus 로고    scopus 로고
    • Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA
    • Chen, G., J.-D. Wen, and I. Tinoco, Jr. 2007. Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA. RNA. 13:2175-2188.
    • (2007) RNA , vol.13 , pp. 2175-2188
    • Chen, G.1    Wen, J.-D.2    Tinoco Jr., I.3
  • 23
    • 36749056800 scopus 로고    scopus 로고
    • Characterization of the mechanical unfolding of RNA pseudoknots
    • Green, L., C.-H. Kim, C. Bustamante, and I. Tinoco, Jr. 2008. Characterization of the mechanical unfolding of RNA pseudoknots. J. Mol. Biol. 375:511-528.
    • (2008) J. Mol. Biol , vol.375 , pp. 511-528
    • Green, L.1    Kim, C.-H.2    Bustamante, C.3    Tinoco Jr., I.4
  • 24
    • 33646131832 scopus 로고    scopus 로고
    • Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods
    • Li, P. T. X., D. Collin, S. B. Smith, C. Bustamante, and I. Tinoco, Jr. 2006. Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys. J. 90:250-260.
    • (2006) Biophys. J , vol.90 , pp. 250-260
    • Li, P.T.X.1    Collin, D.2    Smith, S.B.3    Bustamante, C.4    Tinoco Jr., I.5
  • 25
    • 34247640029 scopus 로고    scopus 로고
    • Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results
    • Wen, J. D., M. Manosas, P. T. X. Li, S. B. Smith, C. Bustamante, et al. 2007. Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results. Biophys. J. 92:2996-3009.
    • (2007) Biophys. J , vol.92 , pp. 2996-3009
    • Wen, J.D.1    Manosas, M.2    Li, P.T.X.3    Smith, S.B.4    Bustamante, C.5
  • 26
    • 0035957720 scopus 로고    scopus 로고
    • Reversible unfolding of single RNA molecules by mechanical force
    • Liphardt, J., B. Onoa, S. B. Smith, I. Tinoco, Jr., and C. Bustamante. 2001. Reversible unfolding of single RNA molecules by mechanical force. Science. 292:733-737.
    • (2001) Science , vol.292 , pp. 733-737
    • Liphardt, J.1    Onoa, B.2    Smith, S.B.3    Tinoco Jr., I.4    Bustamante, C.5
  • 27
    • 0037036070 scopus 로고    scopus 로고
    • Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
    • Liphardt, J., S. Dumont, S. B. Smith, I. Tinoco, Jr., and C. Bustamante. 2002. Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science. 296:1832-1835.
    • (2002) Science , vol.296 , pp. 1832-1835
    • Liphardt, J.1    Dumont, S.2    Smith, S.B.3    Tinoco Jr., I.4    Bustamante, C.5
  • 28
    • 0242417558 scopus 로고    scopus 로고
    • Identifying kinetic barriers to mechanical unfolding of the T. thermophilia ribozyme
    • Onoa, B., S. Dumont, J. Liphardt, S. B. Smith, I. Tinoco, Jr., et al. 2003. Identifying kinetic barriers to mechanical unfolding of the T. thermophilia ribozyme. Science. 299:1892-1895.
    • (2003) Science , vol.299 , pp. 1892-1895
    • Onoa, B.1    Dumont, S.2    Liphardt, J.3    Smith, S.B.4    Tinoco Jr., I.5
  • 30
    • 0034844254 scopus 로고    scopus 로고
    • Force induced denaturation of RNA
    • Gerland, U., R. Bundschuh, and T. Hwa. 2001. Force induced denaturation of RNA. Biophys. J. 81:1324-1332.
    • (2001) Biophys. J , vol.81 , pp. 1324-1332
    • Gerland, U.1    Bundschuh, R.2    Hwa, T.3
  • 31
    • 0037623306 scopus 로고    scopus 로고
    • Mechanically probing the folding pathway of single RNA molecules
    • Gerland, U., R. Bundschuh, and T. Hwa. 2003. Mechanically probing the folding pathway of single RNA molecules. Biophys. J. 84:2831-2840.
    • (2003) Biophys. J , vol.84 , pp. 2831-2840
    • Gerland, U.1    Bundschuh, R.2    Hwa, T.3
  • 32
    • 0035902469 scopus 로고    scopus 로고
    • Force and kinetic barriers of unzipping of the DNA double helix
    • Cocco, S., R. Monasson, and J. F. Marko. 2001. Force and kinetic barriers of unzipping of the DNA double helix. Proc. Natl. Acad. Sci. USA. 98:8608-8613.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 8608-8613
    • Cocco, S.1    Monasson, R.2    Marko, J.F.3
  • 33
    • 33645996088 scopus 로고    scopus 로고
    • Force unfolding single RNAs
    • Liu, F., H. Tong, and Z. C. Ou-yang. 2006. Force unfolding single RNAs. Biophys. J. 90:1895-1902.
    • (2006) Biophys. J , vol.90 , pp. 1895-1902
    • Liu, F.1    Tong, H.2    Ou-yang, Z.C.3
  • 34
    • 34247609813 scopus 로고    scopus 로고
    • Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments
    • Manosas, M., J.-D. Wen, P. T. X. Li, S. B. Smith, C. Bustamante, et al. 2007. Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments. Biophys. J. 92:3010-3021.
    • (2007) Biophys. J , vol.92 , pp. 3010-3021
    • Manosas, M.1    Wen, J.-D.2    Li, P.T.X.3    Smith, S.B.4    Bustamante, C.5
  • 35
    • 33746675190 scopus 로고    scopus 로고
    • Single-molecule experiments in biological physics: Methods and applications
    • Ritort, F. 2006. Single-molecule experiments in biological physics: methods and applications. J. Phys. Condens. Matter. 18:R531-R583.
    • (2006) J. Phys. Condens. Matter , vol.18
    • Ritort, F.1
  • 36
    • 18744379775 scopus 로고    scopus 로고
    • Mechanical unfolding of RNA hairpins
    • Hyeon, C., and D. Thirumalai. 2005. Mechanical unfolding of RNA hairpins. Proc. Natl. Acad. Sci. USA. 102:6789-6794.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6789-6794
    • Hyeon, C.1    Thirumalai, D.2
  • 37
    • 33846820159 scopus 로고    scopus 로고
    • Mechanical unfolding of RNA: From hairpins to structures with internal multiloops
    • Hyeon, C., and D. Thirumalai. 2007. Mechanical unfolding of RNA: from hairpins to structures with internal multiloops. Biophys. J. 92:731-743.
    • (2007) Biophys. J , vol.92 , pp. 731-743
    • Hyeon, C.1    Thirumalai, D.2
  • 38
    • 47749150330 scopus 로고    scopus 로고
    • Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes
    • Hyeon, C., G. Morrison, and D. Thirumalai. 2008. Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes. Proc. Natl. Acad. Sci. USA. 105:9604-9609.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 9604-9609
    • Hyeon, C.1    Morrison, G.2    Thirumalai, D.3
  • 39
    • 1142310690 scopus 로고    scopus 로고
    • Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations
    • Yeh, I.-C., and G. Hummer. 2004. Diffusion and electrophoretic mobility of single-stranded RNA from molecular dynamics simulations. Biophys. J. 86:681-689.
    • (2004) Biophys. J , vol.86 , pp. 681-689
    • Yeh, I.-C.1    Hummer, G.2
  • 41
    • 2342470819 scopus 로고    scopus 로고
    • Slow nucleic acid unzipping kinetics from sequence-defined barriers
    • Cocco, S., J. F. Marko, and R. Monasson. 2003. Slow nucleic acid unzipping kinetics from sequence-defined barriers. Eur. Phys. J. E. 10:153-161.
    • (2003) Eur. Phys. J. E , vol.10 , pp. 153-161
    • Cocco, S.1    Marko, J.F.2    Monasson, R.3
  • 42
    • 42449095556 scopus 로고    scopus 로고
    • Predicting ribosomal frame-shifting efficiency
    • Cao, S., and S.-J. Chen. 2008. Predicting ribosomal frame-shifting efficiency. Phys. Biol. 5:016002.
    • (2008) Phys. Biol , vol.5 , pp. 016002
    • Cao, S.1    Chen, S.-J.2
  • 43
    • 42449155819 scopus 로고    scopus 로고
    • RNA folding: Conformational statistics, folding kinetics, and ion electrostatics
    • Chen, S.-J. 2008. RNA folding: conformational statistics, folding kinetics, and ion electrostatics. Annu. Rev. Biophys. 37:197-214.
    • (2008) Annu. Rev. Biophys , vol.37 , pp. 197-214
    • Chen, S.-J.1
  • 44
    • 0020482340 scopus 로고
    • Regeneration of ribonuclease A from the reduced protein. Rate-limiting steps
    • Konishi, Y., T. Ooi, and H. A. Scheraga. 1982. Regeneration of ribonuclease A from the reduced protein. Rate-limiting steps. Biochemistry. 21:4734-4740.
    • (1982) Biochemistry , vol.21 , pp. 4734-4740
    • Konishi, Y.1    Ooi, T.2    Scheraga, H.A.3
  • 45
    • 33847280837 scopus 로고    scopus 로고
    • Biphasic RNA folding kinetics and telomerase activity
    • Cao, S., and S.-J. Chen. 2007. Biphasic RNA folding kinetics and telomerase activity. J. Mol. Biol. 367:909-927.
    • (2007) J. Mol. Biol , vol.367 , pp. 909-927
    • Cao, S.1    Chen, S.-J.2
  • 47
    • 43749099405 scopus 로고    scopus 로고
    • Beyond energy minimization: Approaches to the kinetic folding of RNA
    • Flamm, C., and I. L. Hofacker. 2008. Beyond energy minimization: approaches to the kinetic folding of RNA. Monatsh. Chem. 139:447-457.
    • (2008) Monatsh. Chem , vol.139 , pp. 447-457
    • Flamm, C.1    Hofacker, I.L.2
  • 48
    • 48449084225 scopus 로고    scopus 로고
    • Simulating RNA folding kinetics on approximated energy landscapes
    • Tang, X., S. Thomas, L. Tapia, D. P. Giedroc, and N. M. Amato. 2008. Simulating RNA folding kinetics on approximated energy landscapes. J. Mol. Biol. 381:1055-1067.
    • (2008) J. Mol. Biol , vol.381 , pp. 1055-1067
    • Tang, X.1    Thomas, S.2    Tapia, L.3    Giedroc, D.P.4    Amato, N.M.5
  • 49
    • 0029100233 scopus 로고
    • Predicting thermodynamic properties of RNA
    • Serra, M. J., and D. H. Turner. 1995. Predicting thermodynamic properties of RNA. Methods Enzymol. 259:242-261.
    • (1995) Methods Enzymol , vol.259 , pp. 242-261
    • Serra, M.J.1    Turner, D.H.2
  • 50
    • 0032919143 scopus 로고    scopus 로고
    • Sequence-dependent mechanics of single DNA molecules
    • Rief, M., H. Clausen-Schaumann, and H. E. Gaub. 1999. Sequence-dependent mechanics of single DNA molecules. Nat. Struct. Biol. 6:346-349.
    • (1999) Nat. Struct. Biol , vol.6 , pp. 346-349
    • Rief, M.1    Clausen-Schaumann, H.2    Gaub, H.E.3
  • 51
    • 38949165395 scopus 로고    scopus 로고
    • Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins
    • Hyeon, C., and D. Thirumalai. 2008. Multiple probes are required to explore and control the rugged energy landscape of RNA hairpins. J. Am. Chem. Soc. 130:1538-1539.
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 1538-1539
    • Hyeon, C.1    Thirumalai, D.2
  • 52
    • 48149098589 scopus 로고    scopus 로고
    • Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA
    • Vrolijk, M. M., M. Ooms, A. Harwig, A. T. Das, and B. Berkhout. 2008. Destabilization of the TAR hairpin affects the structure and function of the HIV-1 leader RNA. Nucleic Acids Res. 36:4352-4363.
    • (2008) Nucleic Acids Res , vol.36 , pp. 4352-4363
    • Vrolijk, M.M.1    Ooms, M.2    Harwig, A.3    Das, A.T.4    Berkhout, B.5
  • 53
    • 24344435151 scopus 로고    scopus 로고
    • Structure and dynamics of an RNA tetraloop: A joint molecular dynamics and NMR study
    • Koplin, J., Y. Mu, C. Richter, H. Schwalbe, and G. Stock. 2006. Structure and dynamics of an RNA tetraloop: a joint molecular dynamics and NMR study. Structure. 13:1255-1267.
    • (2006) Structure , vol.13 , pp. 1255-1267
    • Koplin, J.1    Mu, Y.2    Richter, C.3    Schwalbe, H.4    Stock, G.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.