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Volumn 90, Issue 3, 2006, Pages 765-777

Exploring the complex folding kinetics of RNA hairpins: I. General folding kinetics analysis

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 33646191609     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.062935     Document Type: Article
Times cited : (60)

References (61)
  • 1
    • 0242500997 scopus 로고    scopus 로고
    • Exploration of the transition state for tertiary structure formation between an RNA helix and a large structure RNA
    • Bartley, L. E., X. Zhuang, R. Das, S. Chu, and D. Herschlag. 2003. Exploration of the transition state for tertiary structure formation between an RNA helix and a large structure RNA. J. Mol. Biol. 328:1011-1026.
    • (2003) J. Mol. Biol. , vol.328 , pp. 1011-1026
    • Bartley, L.E.1    Zhuang, X.2    Das, R.3    Chu, S.4    Herschlag, D.5
  • 3
    • 0034043484 scopus 로고    scopus 로고
    • Recent insights on RNA folding mechanisms from catalytic RNA
    • Woodson, S. A. 2000. Recent insights on RNA folding mechanisms from catalytic RNA. Cell. Mol. Life Sci. 57:796-808.
    • (2000) Cell. Mol. Life Sci. , vol.57 , pp. 796-808
    • Woodson, S.A.1
  • 4
    • 0036816641 scopus 로고    scopus 로고
    • Probing the structural dynamics of nucleic acids by quantitative timeresolved and equilibrium hydroxyl radical "footprinting"
    • Brenowitz, M., M. R. Chance, G. Dhavan, and K. Takamoto. 2002. Probing the structural dynamics of nucleic acids by quantitative timeresolved and equilibrium hydroxyl radical "footprinting". Curr. Opin. Struct. Biol. 12:648-653.
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 648-653
    • Brenowitz, M.1    Chance, M.R.2    Dhavan, G.3    Takamoto, K.4
  • 6
    • 0038508653 scopus 로고    scopus 로고
    • RNA folding: Models and perspectives
    • Sosnick, T. R., and T. Pan. 2003. RNA folding: models and perspectives. Curr. Opin. Struct. Biol. 13:309-316.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 309-316
    • Sosnick, T.R.1    Pan, T.2
  • 7
    • 0025061676 scopus 로고
    • Nucleic-acid structure-tetraloops and RNA folding
    • Uhlenbeck, O. C. 1990. Nucleic-acid structure-tetraloops and RNA folding. Nature. 346:613-614.
    • (1990) Nature , vol.346 , pp. 613-614
    • Uhlenbeck, O.C.1
  • 8
    • 0025085590 scopus 로고
    • Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. I. Kinetic description of the reaction of an RNA substrate complementary to the active site
    • Herschlag, D., and T. R. Cech. 1990. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. I. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry. 29:10159-10171.
    • (1990) Biochemistry , vol.29 , pp. 10159-10171
    • Herschlag, D.1    Cech, T.R.2
  • 9
    • 0025149015 scopus 로고
    • Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. II. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site
    • Herschlag, D., and T. R. Cech. 1990. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. II. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site. Biochemistry. 29:10172-10180.
    • (1990) Biochemistry , vol.29 , pp. 10172-10180
    • Herschlag, D.1    Cech, T.R.2
  • 10
    • 0000694197 scopus 로고
    • Single-stranded RNA bacteriophages
    • R. Calendar, editor. Plenum Press, New York
    • van Duin, J. 1988. Single-stranded RNA bacteriophages. In The Bacteriophages, Vol. 1. R. Calendar, editor. Plenum Press, New York. 117-167.
    • (1988) The Bacteriophages , vol.1 , pp. 117-167
    • Van Duin, J.1
  • 11
    • 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
  • 12
    • 0345731284 scopus 로고    scopus 로고
    • Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations
    • Hall, K. B., and J. Williams. 2004. Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations. RNA. 10:34-47.
    • (2004) RNA , vol.10 , pp. 34-47
    • Hall, K.B.1    Williams, J.2
  • 13
    • 0035793105 scopus 로고    scopus 로고
    • 2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking
    • Jean, J. M., and K. B. Hall. 2001. 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking. Proc. Natl. Acad. Sci. USA. 98:37-41.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 37-41
    • Jean, J.M.1    Hall, K.B.2
  • 14
    • 0032580790 scopus 로고    scopus 로고
    • C-13 relaxation and dynamics of the purine bases in the iron responsive element RNA hairpin
    • Hall, K. B., and C. G. Tang. 1998. C-13 relaxation and dynamics of the purine bases in the iron responsive element RNA hairpin. Biochemistry. 37:9323-9332.
    • (1998) Biochemistry , vol.37 , pp. 9323-9332
    • Hall, K.B.1    Tang, C.G.2
  • 15
    • 8344253719 scopus 로고    scopus 로고
    • Folding thermodynamics and kinetics of YNMG RNA hairpins: Specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate
    • Proctor, D. J., H. Ma, E. Kierzek, R. Kierzek, M. Gruebele, and P. C. Bevilacqua. 2004. Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate. Biochemistry. 43:14004-14014.
    • (2004) Biochemistry , vol.43 , pp. 14004-14014
    • Proctor, D.J.1    Ma, H.2    Kierzek, E.3    Kierzek, R.4    Gruebele, M.5    Bevilacqua, P.C.6
  • 16
    • 0035957720 scopus 로고    scopus 로고
    • Reversible unfolding of single RNA molecules by mechanical force
    • Liphardt, J., B. Onoa, S. B. Smith, I. J. Tinoco, 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, I.J.4    Bustamante, C.5
  • 17
    • 0038502170 scopus 로고    scopus 로고
    • Folding dynamics and mechanism of b-hairpin formation
    • Munoz, V., P. A. Thompson, J. Hofrichter, and W. A. Eaton. 1997. Folding dynamics and mechanism of b-hairpin formation. Nature. 390:196-199.
    • (1997) Nature , vol.390 , pp. 196-199
    • Munoz, V.1    Thompson, P.A.2    Hofrichter, J.3    Eaton, W.A.4
  • 18
    • 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
  • 19
    • 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
  • 20
    • 0034759469 scopus 로고    scopus 로고
    • A semiflexible polymer model applied to loop formation in DNA hairpins
    • Kuznetsov, S. V., Y. Shen, A. S. Benight, and A. Ansari. 2001. A semiflexible polymer model applied to loop formation in DNA hairpins. Biophys. J. 81:2864-2875.
    • (2001) Biophys. J. , vol.81 , pp. 2864-2875
    • Kuznetsov, S.V.1    Shen, Y.2    Benight, A.S.3    Ansari, A.4
  • 22
    • 0034505003 scopus 로고    scopus 로고
    • FRET fluctuation spectroscopy: Exploring the conformational dynamics of DNA hairpin loop
    • Wallace, M. I., L. Ying, S. Balasubramanian, and D. Klenerman. 2000. FRET fluctuation spectroscopy: exploring the conformational dynamics of DNA hairpin loop. J. Phys. Chem. B. 104:11551-11555.
    • (2000) J. Phys. Chem. B. , vol.104 , pp. 11551-11555
    • Wallace, M.I.1    Ying, L.2    Balasubramanian, S.3    Klenerman, D.4
  • 24
    • 0035819201 scopus 로고    scopus 로고
    • Loop dependence of the dynamics of DNA hairpins
    • Shen, Y., S. V. Kunznetsov, and A. Ansari. 2001. Loop dependence of the dynamics of DNA hairpins. J. Phys. Chem. B. 105:12202-12211.
    • (2001) J. Phys. Chem. B. , vol.105 , pp. 12202-12211
    • Shen, Y.1    Kunznetsov, S.V.2    Ansari, A.3
  • 26
    • 1842298212 scopus 로고    scopus 로고
    • From Levinthal to pathways to funnels
    • Dill, K. A., and H. S. Chan. 1997. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4:10-19.
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 10-19
    • Dill, K.A.1    Chan, H.S.2
  • 29
    • 0042845840 scopus 로고    scopus 로고
    • Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations
    • Sorin, E. J., Y. M. Rhee, B. J. Nakatani, and V. S. Pande. 2003. Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophys. J. 85:790-803.
    • (2003) Biophys. J. , vol.85 , pp. 790-803
    • Sorin, E.J.1    Rhee, Y.M.2    Nakatani, B.J.3    Pande, V.S.4
  • 30
    • 0036297661 scopus 로고    scopus 로고
    • RNA simulations: Probing hairpin unfolding and the dynamics of a GNRA tetraloop
    • Sorin, E. J., M. A. Engelhardt, D. Herschlag, and V. S. Pande. 2002. RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop. J. Mol. Biol. 317:493-506.
    • (2002) J. Mol. Biol. , vol.317 , pp. 493-506
    • Sorin, E.J.1    Engelhardt, M.A.2    Herschlag, D.3    Pande, V.S.4
  • 31
    • 0034021259 scopus 로고    scopus 로고
    • RNA folding at elementary step resolution
    • Flamm, C., W. Fontana, I. L. Hofacker, and P. Schuster. 2000. RNA folding at elementary step resolution. RNA. 6:325-338.
    • (2000) RNA , vol.6 , pp. 325-338
    • Flamm, C.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 32
    • 0034612331 scopus 로고    scopus 로고
    • Modeling RNA folding paths with pseudoknots: Application to hepatitis d-virus ribozyme
    • Isambert, H., and E. D. Siggia. 2000. Modeling RNA folding paths with pseudoknots: application to hepatitis d-virus ribozyme. Proc. Natl. Acad. Sci. USA. 97:6515-6520.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 6515-6520
    • Isambert, H.1    Siggia, E.D.2
  • 33
    • 0029061125 scopus 로고
    • The computer-simulation of RNA folding pathways using a genetic algorithm
    • Gultyaev, A. P., F. H. van Batenburg, and C. W. Pleij. 1995. The computer-simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:37-51.
    • (1995) J. Mol. Biol. , vol.250 , pp. 37-51
    • Gultyaev, A.P.1    Van Batenburg, F.H.2    Pleij, C.W.3
  • 34
    • 0008455050 scopus 로고    scopus 로고
    • Folding rate dependence on the chain length for RNA-like heteropolymers
    • Galzitskaya, O., and A. V. Finkelstein. 1998. Folding rate dependence on the chain length for RNA-like heteropolymers. Fold. Des. 3:69-78.
    • (1998) Fold. Des. , vol.3 , pp. 69-78
    • Galzitskaya, O.1    Finkelstein, A.V.2
  • 35
    • 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
  • 36
    • 0037440807 scopus 로고    scopus 로고
    • Master equation approach to finding the rate-limiting steps in biopolymer folding
    • Zhang, W. B., and S. J. Chen. 2003. Master equation approach to finding the rate-limiting steps in biopolymer folding. J. Chem. Phys. 118:3413-3420.
    • (2003) J. Chem. Phys. , vol.118 , pp. 3413-3420
    • Zhang, W.B.1    Chen, S.J.2
  • 37
    • 0242677752 scopus 로고    scopus 로고
    • Analyzing the biopolymer folding rates and pathways using kinetic cluster method
    • Zhang, W. B., and S. J. Chen. 2003. Analyzing the biopolymer folding rates and pathways using kinetic cluster method. J. Chem. Phys. 119:8716-8729.
    • (2003) J. Chem. Phys. , vol.119 , pp. 8716-8729
    • Zhang, W.B.1    Chen, S.J.2
  • 40
    • 0000789168 scopus 로고
    • Free energy increments for hydrogen-bonds in nucleic-acid basepairs
    • Turner, D. H., N. Sugimoto, R. Kierzek, and D. D. Dreiker. 1987. Free energy increments for hydrogen-bonds in nucleic-acid basepairs. J. Am. Chem. Soc. 109:3783-3785.
    • (1987) J. Am. Chem. Soc. , vol.109 , pp. 3783-3785
    • Turner, D.H.1    Sugimoto, N.2    Kierzek, R.3    Dreiker, D.D.4
  • 42
    • 0034581545 scopus 로고    scopus 로고
    • Enthalpy-entropy compensation in nucleic acids: Contribution of electrostriction and structure hydration
    • Marky, L. A., and D. W. Kupke. 2000. Enthalpy-entropy compensation in nucleic acids: contribution of electrostriction and structure hydration. Methods Enzymol. 323:419-441.
    • (2000) Methods Enzymol. , vol.323 , pp. 419-441
    • Marky, L.A.1    Kupke, D.W.2
  • 45
    • 0000191981 scopus 로고
    • Reaction-path study of conformational transitions in flexible systems-applications to peptides
    • Czerminski, R., and R. Elber. 1990. Reaction-path study of conformational transitions in flexible systems-applications to peptides. J. Chem. Phys. 92:5580-5601.
    • (1990) J. Chem. Phys. , vol.92 , pp. 5580-5601
    • Czerminski, R.1    Elber, R.2
  • 46
    • 0000370391 scopus 로고    scopus 로고
    • The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
    • Becker, O. M., and M. Karplus. 1997. The topology of multidimensional potential energy surfaces: theory and application to peptide structure and kinetics. J. Chem. Phys. 106:1495-1517.
    • (1997) J. Chem. Phys. , vol.106 , pp. 1495-1517
    • Becker, O.M.1    Karplus, M.2
  • 47
    • 0037115811 scopus 로고    scopus 로고
    • Free energy disconnectivity graphs: Application to peptide models
    • Krivov, S. V., and M. Karplus. 2002. Free energy disconnectivity graphs: application to peptide models. J. Chem. Phys. 117:10894-10903.
    • (2002) J. Chem. Phys. , vol.117 , pp. 10894-10903
    • Krivov, S.V.1    Karplus, M.2
  • 48
    • 0344236155 scopus 로고    scopus 로고
    • The free energy landscape and dynamics of Met-encephalin
    • Evans, D. A., and D. J. Wales. 2003. The free energy landscape and dynamics of Met-encephalin. J. Chem. Phys. 119:9947-9955.
    • (2003) J. Chem. Phys. , vol.119 , pp. 9947-9955
    • Evans, D.A.1    Wales, D.J.2
  • 49
    • 3242681886 scopus 로고    scopus 로고
    • Folding of the GB1 hairpin peptide from discrete path sampling
    • Evans, D. A., and D. J. Wales. 2004. Folding of the GB1 hairpin peptide from discrete path sampling. J. Chem. Phys. 121:1080-1090.
    • (2004) J. Chem. Phys. , vol.121 , pp. 1080-1090
    • Evans, D.A.1    Wales, D.J.2
  • 50
    • 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
  • 51
    • 0000239504 scopus 로고    scopus 로고
    • Master-equation approach to protein folding and kinetic traps
    • Cieplak, M., M. Henkel, J. Karbowski, and J. R. Banavar. 1998. Master-equation approach to protein folding and kinetic traps. Phys. Rev. Lett. 80:3654-3657.
    • (1998) Phys. Rev. Lett. , vol.80 , pp. 3654-3657
    • Cieplak, M.1    Henkel, M.2    Karbowski, J.3    Banavar, J.R.4
  • 52
    • 0034872511 scopus 로고    scopus 로고
    • Transition states and the meaning of F-values in protein folding kinetics
    • Ozkan, S. B., I. Bahar, and K. A. Dill. 2001. Transition states and the meaning of F-values in protein folding kinetics. Nat. Struct. Biol. 8:765-769.
    • (2001) Nat. Struct. Biol. , vol.8 , pp. 765-769
    • Ozkan, S.B.1    Bahar, I.2    Dill, K.A.3
  • 53
    • 36449000646 scopus 로고
    • Transition states and folding dynamics of proteins and heteropolymers
    • Chan, H. S., and K. A. Dill. 1994. Transition states and folding dynamics of proteins and heteropolymers. J. Chem. Phys. 100:9238-9257.
    • (1994) J. Chem. Phys. , vol.100 , pp. 9238-9257
    • Chan, H.S.1    Dill, K.A.2
  • 54
    • 0035366858 scopus 로고    scopus 로고
    • Kinetic Monte Carlo simulation off titin unfolding
    • Makarov, D. E., P. K. Hansma, and H. Metiu. 2001. Kinetic Monte Carlo simulation off titin unfolding. J. Chem. Phys. 114:9663-9673.
    • (2001) J. Chem. Phys. , vol.114 , pp. 9663-9673
    • Makarov, D.E.1    Hansma, P.K.2    Metiu, H.3
  • 55
    • 0242454276 scopus 로고    scopus 로고
    • Variational calculation of macrostate transition rates
    • Ulitsky, A., and D. Shalloway. 1998. Variational calculation of macrostate transition rates. J. Chem. Phys. 109:1670-1686.
    • (1998) J. Chem. Phys. , vol.109 , pp. 1670-1686
    • Ulitsky, A.1    Shalloway, D.2
  • 56
    • 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
  • 57
    • 0015223584 scopus 로고
    • Relaxation kinetics of dimer formation by self-complementary oligonucleotides
    • Craig, M. E., D. M. Crothers, and P. Doty. 1971. Relaxation kinetics of dimer formation by self-complementary oligonucleotides. J. Mol. Biol. 62:383-401.
    • (1971) J. Mol. Biol. , vol.62 , pp. 383-401
    • Craig, M.E.1    Crothers, D.M.2    Doty, P.3
  • 58
    • 0015846852 scopus 로고
    • Thermodynamics and kinetics of the helix-coil transitions of oligomers containing GC pairs
    • Porschke, D., O. C. Uhlenbeck, and F. H. Martin. 1973. Thermodynamics and kinetics of the helix-coil transitions of oligomers containing GC pairs. Biopolymers. 12:1313-1335.
    • (1973) Biopolymers , vol.12 , pp. 1313-1335
    • Porschke, D.1    Uhlenbeck, O.C.2    Martin, F.H.3
  • 59
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia, J. J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1460-1465.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 1460-1465
    • Santalucia, J.J.1
  • 61
    • 0038637695 scopus 로고    scopus 로고
    • Single-strand stacking free energy from DNA beacon kinetics
    • Aalberts, D. P., J. M. Parman, and N. L. Goddard. 2003. Single-strand stacking free energy from DNA beacon kinetics. Biophys. J. 84:3212-3217.
    • (2003) Biophys. J. , vol.84 , pp. 3212-3217
    • Aalberts, D.P.1    Parman, J.M.2    Goddard, N.L.3


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