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Volumn 16, Issue 7, 2010, Pages 1308-1316

BarMap: RNA folding on dynamic energy landscapes

Author keywords

Barrier tree; Cotranscriptional folding; Dynamic energy landscape; RNA folding kinetics

Indexed keywords

RNA;

EID: 77953637928     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.2093310     Document Type: Article
Times cited : (51)

References (54)
  • 1
    • 0025315854 scopus 로고
    • Prediction of RNA secondary structure, including pseudoknotting, by computer simulation
    • Abrahams JP, van den Berg M, van Batenburg E, Pleij C. 1990. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Res 18: 3035-3044. (Pubitemid 20178150)
    • (1990) Nucleic Acids Research , vol.18 , Issue.10 , pp. 3035-3044
    • Abrahams, J.P.1    Van Den Berg, M.2    Van Batenburg, E.3    Pleij, C.4
  • 2
    • 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
    • Baumstark T, Schroder AR, Riesner D. 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.
    • (1997) EMBO J , vol.16 , pp. 599-610
    • Baumstark, T.1    Schroder, A.R.2    Riesner, D.3
  • 3
    • 0000370391 scopus 로고    scopus 로고
    • The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics
    • Becker OM, Karplus M. 1997. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics. J Chem Phys 106: 1495-1517. (Pubitemid 127627069)
    • (1997) Journal of Chemical Physics , vol.106 , Issue.4 , pp. 1495-1517
    • Becker, O.M.1    Karplus, M.2
  • 4
    • 28844503373 scopus 로고    scopus 로고
    • Coupled dynamics of RNA folding and nanopore translocation
    • doi: 10.1103/PhysRevLett.95.208104
    • Bundschuh R, Gerland U. 2005. Coupled dynamics of RNA folding and nanopore translocation. Phys Rev Lett 95: 208104/1-208104/4. doi: 10.1103/PhysRevLett.95.208104.
    • (2005) Phys Rev Lett , vol.95
    • Bundschuh, R.1    Gerland, U.2
  • 5
    • 13444292041 scopus 로고    scopus 로고
    • An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model
    • Clote P. 2005. An efficient algorithm to compute the landscape of locally optimal RNA secondary structures with respect to the Nussinov-Jacobson energy model. J Comput Biol 12: 83-101.
    • (2005) J Comput Biol , vol.12 , pp. 83-101
    • Clote, P.1
  • 6
    • 84867485251 scopus 로고    scopus 로고
    • Graphs, they are changing - Dynamic graph drawing for a sequence of graphs
    • ed. MT Goodrich, SG Kobourov Springer, Heidelberg, Germany
    • Diehl S, Görg C. 2002. Graphs, they are changing - dynamic graph drawing for a sequence of graphs. In Proceedings of 10th international symposium on graph drawing (ed. MT Goodrich, SG Kobourov), no. 2528, pages 23-31. Springer, Heidelberg, Germany.
    • (2002) Proceedings of 10th International Symposium on Graph Drawing , Issue.2528 , pp. 23-31
    • Diehl, S.1    Görg, C.2
  • 7
    • 0000672765 scopus 로고    scopus 로고
    • Evolution of the potential energy surface with size for Lennard-Jones clusters
    • Doye JP, Miller MA, Welsh DJ. 1999. Evolution of the potential energy surface with size for Lennard-Jones clusters. J Chem Phys 111: 8417-8429.
    • (1999) J Chem Phys , vol.111 , pp. 8417-8429
    • Doye, J.P.1    Miller, M.A.2    Welsh, D.J.3
  • 8
    • 34250356054 scopus 로고    scopus 로고
    • Extracting kinetics from single-molecule force spectroscopy: Nanopore unzipping of DNA hairpins
    • Dudko OK, Mathé J, Szabo A, Meller A, Hummer G. 2007. Extracting kinetics from single-molecule force spectroscopy: Nanopore unzipping of DNA hairpins. Biophys J 92: 4188-4195.
    • (2007) Biophys J , vol.92 , pp. 4188-4195
    • Dudko, O.K.1    Mathé, J.2    Szabo, A.3    Meller, A.4    Hummer, G.5
  • 9
    • 0021064616 scopus 로고
    • Escherichia coli phenylalanyl-tRNA synthetase operon region. Evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20
    • Fayat G, Mayaux JF, Sacerdot C, Fromant M, Springer M, Grunberg-Manago M, Blanquet S. 1983. Escherichia coli phenylalanyl-tRNA synthetase operon region. Evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20. J Mol Biol 171: 239-261. (Pubitemid 14224899)
    • (1983) Journal of Molecular Biology , vol.171 , Issue.3 , pp. 239-261
    • Fayat, G.1    Mayaux, J.F.2    Sacerdot, C.3
  • 10
    • 43749099405 scopus 로고    scopus 로고
    • Beyond energy minimization: Approaches to the kinetic folding of RNA
    • Flamm C, Hofacker IL. 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
  • 11
    • 0034021259 scopus 로고    scopus 로고
    • RNA folding kinetics at elementary step resolution
    • Flamm C, Fontana W, Hofacker I, Schuster P. 2000. RNA folding kinetics at elementary step resolution. RNA 6: 325-338.
    • (2000) RNA , vol.6 , pp. 325-338
    • Flamm, C.1    Fontana, W.2    Hofacker, I.3    Schuster, P.4
  • 17
    • 33748532490 scopus 로고    scopus 로고
    • Translocation of structured polynucleotides through nanopores
    • Gerland U, Bundschuh R, Hwa T. 2004. Translocation of structured polynucleotides through nanopores. Phys Biol 1: 19-26.
    • (2004) Phys Biol , vol.1 , pp. 19-26
    • Gerland, U.1    Bundschuh, R.2    Hwa, T.3
  • 18
    • 29144475324 scopus 로고    scopus 로고
    • Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis
    • Gollnick P, Babitzke P, Antson A, Yanofsky C. 2005. Complexity in regulation of tryptophan biosynthesis in Bacillus subtilis. Annu Rev Genet 39: 47-68.
    • (2005) Annu Rev Genet , vol.39 , pp. 47-68
    • Gollnick, P.1    Babitzke, P.2    Antson, A.3    Yanofsky, C.4
  • 19
    • 0025878210 scopus 로고
    • The computer simulation of RNA folding involving pseudoknot formation
    • Gultyaev AP. 1991. The computer simulation of RNA folding involving pseudoknot formation. Nucleic Acids Res 19: 2489-2493.
    • (1991) Nucleic Acids Res , vol.19 , pp. 2489-2493
    • Gultyaev, A.P.1
  • 20
    • 0003274263 scopus 로고
    • Properties of chemically interesting potential energy surfaces
    • Springer, Berlin, Germany
    • Heidrich D, Kliesch W, Quapp W. 1991. Properties of chemically interesting potential energy surfaces, In Lecture notes in chemistry, vol. 56. Springer, Berlin, Germany.
    • (1991) Lecture Notes in Chemistry , vol.56
    • Heidrich, D.1    Kliesch, W.2    Quapp, W.3
  • 22
    • 0035984639 scopus 로고    scopus 로고
    • Regulation by transcription attenuation in bacteria: How RNA provides instructions for transcription termination/antitermination decisions
    • Henkin TM, Yanofsky C. 2002. Regulation by transcription attenuation in bacteria: How RNA provides instructions for transcription termination/ antitermination decisions. Bioessays 24: 700-707.
    • (2002) Bioessays , vol.24 , pp. 700-707
    • Henkin, T.M.1    Yanofsky, C.2
  • 26
    • 0002631097 scopus 로고
    • 'Valley structures' in the phase space of a finite 3D Ising spin glass with 6i interactions
    • Klotz T, Kobe S. 1994. 'Valley structures' in the phase space of a finite 3D Ising spin glass with 6i interactions. J Phys Math Gen 27: L95-L100.
    • (1994) J Phys Math Gen , vol.27
    • Klotz, T.1    Kobe, S.2
  • 27
    • 0021760032 scopus 로고
    • An RNA folding rule
    • Martinez HM. 1984. An RNA folding rule. Nucleic Acids Res 12: 323-335.
    • (1984) Nucleic Acids Res , vol.12 , pp. 323-335
    • Martinez, H.M.1
  • 28
    • 14844318136 scopus 로고    scopus 로고
    • Nanopore unzipping of individual DNA hairpin molecules
    • Mathé J, Visram H, Viasnoff V, Rabin Y, Meller A. 2004. Nanopore unzipping of individual DNA hairpin molecules. Biophys J 87: 3205-3212.
    • (2004) Biophys J , vol.87 , pp. 3205-3212
    • Mathé, J.1    Visram, H.2    Viasnoff, V.3    Rabin, Y.4    Meller, A.5
  • 29
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure
    • Mathews D, Sabina J, Zuker M, Turner H. 1999. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J Mol Biol 288: 911-940.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.1    Sabina, J.2    Zuker, M.3    Turner, H.4
  • 30
    • 67649922893 scopus 로고    scopus 로고
    • Anomalous scaling in nanopore translocation of structured heteropolymers
    • doi: 10.1088/1478-3975/6/3/036006
    • McCauley M, Forties R, Gerland U, Bundschuh R. 2009. Anomalous scaling in nanopore translocation of structured heteropolymers. Phys Biol 6: 036006. doi: 10.1088/1478-3975/6/3/036006.
    • (2009) Phys Biol , vol.6 , pp. 036006
    • McCauley, M.1    Forties, R.2    Gerland, U.3    Bundschuh, R.4
  • 31
    • 42149126162 scopus 로고    scopus 로고
    • Evolution of bacterial trp operons and their regulation
    • Merino E, Jensen RA, Yanofsky C. 2008. Evolution of bacterial trp operons and their regulation. Curr Opin Microbiol 11: 78-86.
    • (2008) Curr Opin Microbiol , vol.11 , pp. 78-86
    • Merino, E.1    Jensen, R.A.2    Yanofsky, C.3
  • 33
    • 0021823907 scopus 로고
    • A kinetic approach to the prediction of RNA secondary structures
    • Mironov AA, Dyakonova LP, Kister AE. 1985. A kinetic approach to the prediction of RNA secondary structures. J Biomol Struct Dyn 2: 953-962.
    • (1985) J Biomol Struct Dyn , vol.2 , pp. 953-962
    • Mironov, A.A.1    Dyakonova, L.P.2    Kister, A.E.3
  • 35
    • 34347237191 scopus 로고    scopus 로고
    • Mechanism of DNA transport through pores
    • Muthukumar M. 2007. Mechanism of DNA transport through pores. Annu Rev Biophys Biomol Struct 36: 435-450.
    • (2007) Annu Rev Biophys Biomol Struct , vol.36 , pp. 435-450
    • Muthukumar, M.1
  • 37
    • 0000330158 scopus 로고
    • Metastable states of the SK spin glass model
    • Nemoto K. 1988. Metastable states of the SK spin glass model. J Phys A 21: L287-L294.
    • (1988) J Phys A , vol.21
    • Nemoto, K.1
  • 39
    • 0032486091 scopus 로고    scopus 로고
    • A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation
    • Perrotta AT, Been MD. 1998. A toggle duplex in hepatitis delta 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
  • 41
    • 0036494672 scopus 로고    scopus 로고
    • Combinatorial landscapes
    • Reidys CM, Stadler PF. 2002. Combinatorial landscapes. SIAM Rev 44: 3-54.
    • (2002) SIAM Rev , vol.44 , pp. 3-54
    • Reidys, C.M.1    Stadler, P.F.2
  • 42
    • 0043208178 scopus 로고    scopus 로고
    • Unzipping kinetics of double-stranded DNA in a nanopore
    • doi: 10.1103/PhysRevLett.90.238101
    • Sauer-Budge AF, Nyamwanda JA, Lubensky DK, Branton D. 2003. Unzipping kinetics of double-stranded DNA in a nanopore. Phys Rev Lett 90: doi: 10.1103/PhysRevLett.90.238101.
    • (2003) Phys Rev Lett , vol.90
    • Sauer-Budge, A.F.1    Nyamwanda, J.A.2    Lubensky, D.K.3    Branton, D.4
  • 43
    • 0034698298 scopus 로고    scopus 로고
    • One sequence, two ribozymes: Implications for the emergence of new ribozyme folds
    • Schultes EA, Bartel DP. 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    Bartel, D.P.2
  • 45
    • 48449084225 scopus 로고    scopus 로고
    • Simulating RNA folding kinetics on approximated energy landscapes
    • Tang X, Thomas S, Tapia L, Giedroc DP, Amato NM. 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
  • 47
    • 0035107270 scopus 로고    scopus 로고
    • Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel
    • Vercoutere W, Winters-Hilt S, Olsen H, Deamer D, Haussler D, Mar Akeson M. 2001. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol 19: 248-252.
    • (2001) Nat Biotechnol , vol.19 , pp. 248-252
    • Vercoutere, W.1    Winters-Hilt, S.2    Olsen, H.3    Deamer, D.4    Haussler, D.5    Mar Akeson, M.6
  • 50
  • 52
    • 33646878794 scopus 로고    scopus 로고
    • Exploring the lower part of discrete polymer model energy landscapes
    • DOI 10.1209/epl/i2005-10577-0
    • Wolfinger MT, Will S, Hofacker IL, Backofen R, Stadler PF. 2006. Exploring the lower part of discrete polymer model energy landscapes. Europhys Lett 74: 726-732. (Pubitemid 43781229)
    • (2006) Europhysics Letters , vol.74 , Issue.4 , pp. 726-732
    • Wolfinger, M.T.1    Will, S.2    Hofacker, I.L.3    Backofen, R.4    Stadler, P.F.5
  • 53
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structure
    • Wuchty S, Fontana W, Hofacker IL, Schuster P. 1998. Complete suboptimal folding of RNA and the stability of secondary structure. Biopolymers 49: 145-165.
    • (1998) Biopolymers , vol.49 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 54
    • 0033986936 scopus 로고    scopus 로고
    • Transcription attenuation: Once viewed as a novel regulatory strategy
    • Yanofsky C. 2000. Transcription attenuation: Once viewed as a novel regulatory strategy. J Bacteriol 182: 1-8. (Pubitemid 30004550)
    • (2000) Journal of Bacteriology , vol.182 , Issue.1 , pp. 1-8
    • Yanofsky, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.