메뉴 건너뛰기




Volumn 98, Issue 8, 2010, Pages 1617-1625

Predicting secondary structural folding kinetics for nucleic acids

Author keywords

[No Author keywords available]

Indexed keywords


EID: 77951637361     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.12.4319     Document Type: Article
Times cited : (40)

References (62)
  • 1
    • 33744996366 scopus 로고    scopus 로고
    • Structural parameters affecting the kinetics of RNA hairpin formation
    • Nagel, J. H., C. Flamm, C. W. Pleij. 2006. Structural parameters affecting the kinetics of RNA hairpin formation. Nucleic Acids Res. 34: 3568-3576.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 3568-3576
    • Nagel, J.H.1    Flamm, C.2    Pleij, C.W.3
  • 2
    • 17144441957 scopus 로고    scopus 로고
    • On secondary structure rearrangements and equilibria of small RNAs
    • DOI 10.1002/cbic.200300664
    • Micura, R., and C. Höbartner. 2003. On secondary structure rearrangements and equilibria of small RNAs. ChemBioChem. 4:984-990. (Pubitemid 37267586)
    • (2003) ChemBioChem , vol.4 , Issue.10 , pp. 984-990
    • Micura, R.1    Hobartner, C.2
  • 3
    • 34547812691 scopus 로고    scopus 로고
    • Time-resolved NMR studies of RNA folding
    • doi:10.1002/bip.2076l
    • Fürtig, B., J. Buck, H. Schwalbe. 2007. Time-resolved NMR studies of RNA folding. Biopolymers. 86: 360-383. doi:10.1002/bip.2076l.
    • (2007) Biopolymers , vol.86 , pp. 360-383
    • Fürtig, B.1    Buck, J.2    Schwalbe, H.3
  • 5
    • 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
  • 6
    • 0035957720 scopus 로고    scopus 로고
    • Reversible unfolding of single RNA molecules by mechanical force
    • Liphardt, J., B. Onoa, 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    Bustamante, C.3
  • 9
    • 0035826712 scopus 로고    scopus 로고
    • Non-Arrhenius kinetics for the loop closure of a DNA hairpin
    • Wallace, M. I., L. Ying, D. Klenerman. 2001. Non-Arrhenius kinetics for the loop closure of a DNA hairpin. Proc. Natl. Acad. Sci. USA. 98: 5584-5589.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 5584-5589
    • Wallace, M.I.1    Ying, L.2    Klenerman, D.3
  • 10
    • 0020475229 scopus 로고
    • Structural analysis of self-replicating RNA synthesized by Qβ replicase
    • Biebricher, C. K., S. Diekmann, and R. Luce. 1982. Structural analysis of self-replicating RNA synthesized by Qβ replicase. J. Mol. Biol. 154: 629-648.
    • (1982) J. Mol. Biol. , vol.154 , pp. 629-648
    • Biebricher, C.K.1    Diekmann, S.2    Luce, R.3
  • 11
    • 0027050568 scopus 로고
    • In vitro recombination and terminal elongation, of RNA by Qβ replicase
    • Biebricher, C. K., and R. Luce. 1992. In vitro recombination and terminal elongation, of RNA by Qβ replicase. EMBO J. 11: 5129-5135.
    • (1992) EMBO J. , vol.11 , pp. 5129-5135
    • Biebricher, C.K.1    Luce, R.2
  • 12
    • 0028943179 scopus 로고
    • Design of artificial short-chained RNA species that are replicated by Qβ replicase
    • Zamora, H., R. Luce, and C. K. Biebricher. 1995. Design of artificial short-chained RNA species that are replicated by Qβ replicase. Biochemistry. 34: 1261-1266.
    • (1995) Biochemistry , vol.34 , pp. 1261-1266
    • Zamora, H.1    Luce, R.2    Biebricher, C.K.3
  • 13
    • 19244375613 scopus 로고    scopus 로고
    • Viroid processing: Switch from cleavage to ligation is driven by a change from a tetraloop to a loop e conformation
    • DOI 10.1093/emboj/16.3.599
    • Baumstark, T., A. R. Schröder, and D. Riesner. 1997. Viroid processing: switch from, cleavage to ligation, is driven by a change from, a tetraloop to a loop E conformation. EMBO J. 16: 599-610. (Pubitemid 27067789)
    • (1997) EMBO Journal , vol.16 , Issue.3 , pp. 599-610
    • Baumstark, T.1    Schroder, A.R.2    Riesner, D.3
  • 14
    • 0032486091 scopus 로고    scopus 로고
    • A toggle duplex in hepatitis 5 virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation
    • Perrotta, A. T., and M. D. Been. 1998. A toggle duplex in hepatitis 5 virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation, J. Mol. Biol. 279: 361-373.
    • (1998) J. Mol. Biol. , vol.279 , pp. 361-373
    • Perrotta, A.T.1    Been, M.D.2
  • 15
    • 0034698298 scopus 로고    scopus 로고
    • One sequence, two ribozymes: Implications for the emergence of new ribozyme folds
    • Schultes, E. A., and D. P. Battel. 2000. One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science. 289: 448-452.
    • (2000) Science , vol.289 , pp. 448-452
    • Schultes, E.A.1    Battel, D.P.2
  • 16
    • 0020417286 scopus 로고
    • Self-splicing RNA: Autoexcision and autocyclization. of the ribosomal. RNA intervening sequence of
    • Kruger, K., P. J. Grabowski, T. R. Cech, 1982. Self-splicing RNA: autoexcision and autocyclization. of the ribosomal. RNA intervening sequence of Tetrahymena. Cell. 31: 147-157.
    • (1982) Tetrahymena. Cell , vol.31 , pp. 147-157
    • Kruger, K.1    Grabowski, P.J.2    Cech, T.R.3
  • 17
    • 0027488624 scopus 로고
    • Isolation of new ribozymes from a large pool of random sequences
    • Bartel, D. P., and J. W. Szostak. 1993. Isolation of new ribozymes from a large pool of random sequences. Science. 261: 1411-1418.
    • (1993) Science , vol.261 , pp. 1411-1418
    • Bartel, D.P.1    Szostak, J.W.2
  • 18
    • 0024443885 scopus 로고
    • Amplification, mutation, and selection of catalytic RNA
    • Joyce, G. F. 1989. Amplification, mutation, and selection of catalytic RNA. Gene. 82: 83-87.
    • (1989) Gene. , vol.82 , pp. 83-87
    • Joyce, G.F.1
  • 19
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington, A. D., and J. W. Szostak. 1990. In vitro selection of RNA molecules that bind specific ligands. Nature. 346: 818-822.
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 20
    • 0025194307 scopus 로고
    • Systemic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C., and L. Gold. 1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science. 249: 505-510. (Pubitemid 20248891)
    • (1990) Science , vol.249 , Issue.4968 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 21
    • 18744396047 scopus 로고    scopus 로고
    • Sensing small molecules by nascent RNA: A mechanism to control transcription in bacteria
    • Mironov, A. S., I. Gusarov, E. Nudler. 2002. Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria. Cell. 111: 747-756.
    • (2002) Cell , vol.111 , pp. 747-756
    • Mironov, A.S.1    Gusarov, I.2    Nudler, E.3
  • 22
    • 0036753365 scopus 로고    scopus 로고
    • Genetic control by a metabolite binding mRNA
    • Nahvi, A., N. Sudarsan, R. R. Breaker. 2002. Genetic control by a metabolite binding mRNA. Chem. Biol. 9:1043-1049.
    • (2002) Chem. Biol. , vol.9 , pp. 1043-1049
    • Nahvi, A.1    Sudarsan, N.2    Breaker, R.R.3
  • 23
    • 0142075327 scopus 로고    scopus 로고
    • Genetic control by metabolitebinding riboswitches
    • Winkler, W. C., and R. R. Breaker. 2003. Genetic control by metabolitebinding riboswitches. ChemBioChem. 4:1024-1032.
    • (2003) ChemBioChem. , vol.4 , pp. 1024-1032
    • Winkler, W.C.1    Breaker, R.R.2
  • 24
    • 0347444723 scopus 로고    scopus 로고
    • MicroRNAs: Genomics, biogenesis, mechanism, and function
    • Bartel, D. P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 116: 281-297.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.P.1
  • 25
    • 0346687595 scopus 로고    scopus 로고
    • The riboswitch control of bacterial metabolism
    • Nudler, E., and A. S. Mironov. 2004. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29: 11-17.
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 11-17
    • Nudler, E.1    Mironov, A.S.2
  • 26
    • 3042767202 scopus 로고    scopus 로고
    • MicroRNAs: Small RNAs with a big role in gene regulation
    • DOI 10.1038/nrg1379
    • He, L., and G. J. Hannon. 2004. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 5:522-531. (Pubitemid 38868508)
    • (2004) Nature Reviews Genetics , vol.5 , Issue.7 , pp. 522-531
    • He, L.1    Hannon, G.J.2
  • 27
    • 1642586299 scopus 로고    scopus 로고
    • Control of gene expression by a natural metabolite-responsive ribozyme
    • Winkler, W. C., A. Nahvi, R. R. Breaker. 2004. Control of gene expression by a natural metabolite-responsive ribozyme. Nature. 428: 281-286.
    • (2004) Nature , vol.428 , pp. 281-286
    • Winkler, W.C.1    Nahvi, A.2    Breaker, R.R.3
  • 29
    • 0032709143 scopus 로고    scopus 로고
    • Metastable structures and refolding kinetics in hok mRNA of plasmid RI
    • Nagel, J. H. A., A. P. Gultyaev, C. W. Pleij. 1999. Metastable structures and refolding kinetics in hok mRNA of plasmid RI. RNA. 5: 1408-1418.
    • (1999) RNA , vol.5 , pp. 1408-1418
    • Nagel, J.H.A.1    Gultyaev, A.P.2    Pleij, C.W.3
  • 30
    • 0000731155 scopus 로고    scopus 로고
    • Evidence for kinetic effects in the folding of large RNA molecules
    • Morgan, S. R., and P. G. Higgs. 1996. Evidence for kinetic effects in the folding of large RNA molecules. J. Chem. Phys. 105: 7152-7157.
    • (1996) J. Chem. Phys. , vol.105 , pp. 7152-7157
    • Morgan, S.R.1    Higgs, P.G.2
  • 31
    • 31544474375 scopus 로고    scopus 로고
    • DNA nanomechanical switches under folding kinetics control
    • DOI 10.1021/nl052161c
    • Viasnoff, V., A. Meiler, and H. Isambert. 2006. DNA nanomechanical switches under folding kinetics control. Nano Lett. 6:101-104. (Pubitemid 43166109)
    • (2006) Nano Letters , vol.6 , Issue.1 , pp. 101-104
    • Viasnoff, V.1    Meller, A.2    Isambert, H.3
  • 33
    • 0345281589 scopus 로고    scopus 로고
    • How RNA folds
    • Tinoco, Jr., I., and C. Bustamante. 1999. How RNA folds. J. Mol. Biol. 293: 271-281.
    • (1999) J. Mol. Biol. , vol.293 , pp. 271-281
    • Bustamante, C.1
  • 34
    • 0242500997 scopus 로고    scopus 로고
    • Exploration of the transition, state for tertiary structure formation, between an RNA helix and a large structured RNA
    • Bartley, L. E., X. Zhuang, D. Herschlag. 2003. Exploration of the transition, state for tertiary structure formation, between an RNA helix and a large structured RNA. J. Mol. Biol. 328: 1011-1026.
    • (2003) J. Mol. Biol. , vol.328 , pp. 1011-1026
    • Bartley, L.E.1    Zhuang, X.2    Herschlag, D.3
  • 36
    • 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
  • 37
    • 0036816641 scopus 로고    scopus 로고
    • Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical " footprinting"
    • Brenowitz, M., M. R. Chance, K. Takamoto. 2002. Probing the structural dynamics of nucleic acids by quantitative time-resolved 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    Takamoto, K.3
  • 39
    • 42449155819 scopus 로고    scopus 로고
    • RNA folding: Conformational statistics, folding kinetics, and ion.electrostaties
    • Chen, S. J. 2008. RNA folding: conformational statistics, folding kinetics, and ion.electrostaties. Annu. Rev. Biophys. 37: 197-214.
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 197-214
    • Chen, S.J.1
  • 40
    • 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
  • 41
    • 0029258928 scopus 로고
    • Keeping RNA happy
    • Uhlenbeck, O. C. 1995. Keeping RNA happy. RNA. 1:4-6.
    • (1995) RNA , vol.1 , pp. 4-6
    • Uhlenbeck, O.C.1
  • 42
    • 0042845840 scopus 로고    scopus 로고
    • Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations
    • Sorin, E. J., Y. M. Rhee, 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    Pande, V.S.3
  • 43
    • 0036297661 scopus 로고    scopus 로고
    • RNA simulations: Probing hairpin unfolding and the dynamics of a GNRA tetraloop
    • Sorin, E. J., M. A.Engelhardt, 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    Pande, V.S.3
  • 44
    • 0034021259 scopus 로고    scopus 로고
    • RNA folding at elementary step resolution
    • Flamm, C., W. Fontana, 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    Schuster, P.3
  • 46
    • 33745726561 scopus 로고    scopus 로고
    • RNAKinetics: A web server that models secondary structure kinetics of an elongating RNA
    • Danilova, L. V., D. D. Pervouchine, A. A. Mironov. 2006. RNAKinetics: a web server that models secondary structure kinetics of an elongating RNA, J. Bioinform, Comput. Biol. 4:589-596.
    • (2006) J. Bioinform, Comput. Biol. , vol.4 , pp. 589-596
    • Danilova, L.V.1    Pervouchine, D.D.2    Mironov, A.A.3
  • 47
    • 54849437727 scopus 로고    scopus 로고
    • Relative stability of helices determines the folding landscape of adenine riboswitch aptamers
    • Lin, J. C., and D. Thirumalai. 2008. Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J. Am. Chem. Soc. 130: 14080-14081.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 14080-14081
    • Lin, J.C.1    Thirumalai, D.2
  • 48
    • 44949181944 scopus 로고    scopus 로고
    • Effects of trimethylamine n-oxide (TMAO) and crowding agents on the stability of RNA hairpins
    • Pincus, D. L., C. Hyeon, and D. Thirumalai. 2008. Effects of trimethylamine n-oxide (TMAO) and crowding agents on the stability of RNA hairpins. J. Am. Chem. Soc. 130: 7364-7372.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 7364-7372
    • Pincus, D.L.1    Hyeon, C.2    Thirumalai, D.3
  • 49
    • 0029975949 scopus 로고    scopus 로고
    • Description of RNA folding by simulated annealing
    • Schmitz, M., and G. Steger. 1996. Description of RNA folding by " simulated annealing". J. Mol. Biol. 255: 254-266.
    • (1996) J. Mol. Biol. , vol.255 , pp. 254-266
    • Schmitz, M.1    Steger, G.2
  • 50
    • 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
  • 51
    • 0021760032 scopus 로고
    • An RNA folding rule
    • Martinez, H. M. 1984. An RNA folding rule. Nucleic Acids Res. 12: 323-334.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 323-334
    • Martinez, H.M.1
  • 54
    • 0347364655 scopus 로고    scopus 로고
    • Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
    • Xayaphoummine, A., T. Bucher, H. Isambert. 2003. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc. Natl. Acad. Sci. USA. 100: 15310-15315.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 15310-15315
    • Xayaphoummine, A.1    Bucher, T.2    Isambert, H.3
  • 55
    • 84855292917 scopus 로고    scopus 로고
    • Folding kinetics of large RNAs
    • Geis, M., C. Flamm, C. Thurner. 2008. Folding kinetics of large RNAs. J. Mol. Biol. 379: 242-261.
    • (2008) J. Mol. Biol. , vol.379 , pp. 242-261
    • Geis, M.1    Flamm, C.2    Thurner, C.3
  • 58
    • 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
  • 59
    • 0032502487 scopus 로고    scopus 로고
    • Barrier heights between ground states in a model of RNA secondary structure
    • DOI 10.1088/0305-4470/31/14/005
    • Morgan, S. R., and P. G. Higgs. 1998. Barrier heights between ground states in a model of RNA secondary structure. J. Phys. A. Math. Gen. 31: 3153-3170. (Pubitemid 128055228)
    • (1998) Journal of Physics A: Mathematical and General , vol.31 , Issue.14 , pp. 3153-3170
    • Morgan, S.R.1    Higgs, P.G.2
  • 60
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.