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Volumn 13, Issue SUPPL.3, 2012, Pages

Predicting folding pathways between RNA conformational structures guided by RNA stacks

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATE APPROACHES; COARSE-GRAINED; CONFORMATIONAL STRUCTURES; CONFORMATIONAL SWITCHES; FOLDING PATHWAY; INTERMEDIATE STRUCTURES; LOCAL OPTIMA; LOWER ENERGY BARRIERS; REGULATORY FUNCTIONS; RNA ENERGY LANDSCAPES; RNA MOLECULES; SEARCH SPACES; SECONDARY STRUCTURES; SOURCE CODES; TEST DATA;

EID: 84874534014     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S3-S5     Document Type: Article
Times cited : (14)

References (41)
  • 1
    • 0020475229 scopus 로고
    • Structural analysis of self-replicating RNA synthesized by Qbeta replicase
    • 10.1016/S0022-2836(82)80019-3, 7086897
    • Biebricher CK, Diekmann S, Luce R. Structural analysis of self-replicating RNA synthesized by Qbeta replicase. J Mol Biol 1982, 154:629-648. 10.1016/S0022-2836(82)80019-3, 7086897.
    • (1982) J Mol Biol , vol.154 , pp. 629-648
    • Biebricher, C.K.1    Diekmann, S.2    Luce, R.3
  • 2
    • 0027050568 scopus 로고
    • In vitro recombination and terminal elongation of RNA by Q beta replicase
    • 556991, 1281452
    • Biebricher CK, Luce R. In vitro recombination and terminal elongation of RNA by Q beta replicase. EMBO J 1992, 11:5129-5135. 556991, 1281452.
    • (1992) EMBO J , vol.11 , pp. 5129-5135
    • Biebricher, C.K.1    Luce, R.2
  • 3
    • 0027319272 scopus 로고
    • Regulation of the Escherichia coli heat-shock response
    • 10.1111/j.1365-2958.1993.tb01727.x, 7901731
    • Bukau B. Regulation of the Escherichia coli heat-shock response. Mol Microbiol 1993, 9:671-680. 10.1111/j.1365-2958.1993.tb01727.x, 7901731.
    • (1993) Mol Microbiol , vol.9 , pp. 671-680
    • Bukau, B.1
  • 4
    • 0035957720 scopus 로고    scopus 로고
    • Reversible unfolding of single RNA molecules by mechanical force
    • 10.1126/science.1058498, 11326101
    • Liphardt J, Onoa B, Smith SB, Tinoco I, Bustamante C. Reversible unfolding of single RNA molecules by mechanical force. Science 2001, 292:733-737. 10.1126/science.1058498, 11326101.
    • (2001) Science , vol.292 , pp. 733-737
    • Liphardt, J.1    Onoa, B.2    Smith, S.B.3    Tinoco, I.4    Bustamante, C.5
  • 5
    • 0036428766 scopus 로고    scopus 로고
    • MRNA-mediated detection of environmental conditions
    • 10.1007/s00203-002-0481-8, 12420159
    • Narberhaus F. mRNA-mediated detection of environmental conditions. Arch Microbiol 2002, 178:404-410. 10.1007/s00203-002-0481-8, 12420159.
    • (2002) Arch Microbiol , vol.178 , pp. 404-410
    • Narberhaus, F.1
  • 7
    • 48249104039 scopus 로고    scopus 로고
    • Riboswitches: emerging themes in RNA structure and function
    • 10.1146/annurev.biophys.37.032807.130000, 18573075
    • Montange RK, Batey RT. Riboswitches: emerging themes in RNA structure and function. Annu Rev Biophys 2008, 37:117-133. 10.1146/annurev.biophys.37.032807.130000, 18573075.
    • (2008) Annu Rev Biophys , vol.37 , pp. 117-133
    • Montange, R.K.1    Batey, R.T.2
  • 8
    • 67650713931 scopus 로고    scopus 로고
    • The structural and functional diversity of metabolite-binding riboswitches
    • 10.1146/annurev.biochem.78.070507.135656, 19298181
    • Roth A, Breaker RR. The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 2009, 78:305-334. 10.1146/annurev.biochem.78.070507.135656, 19298181.
    • (2009) Annu Rev Biochem , vol.78 , pp. 305-334
    • Roth, A.1    Breaker, R.R.2
  • 9
    • 34548454557 scopus 로고    scopus 로고
    • Structural features of metabolite-sensing riboswitches
    • 10.1016/j.tibs.2007.08.005, 2933830, 17764952
    • Wakeman CA, Winkler WC, Dann CE. Structural features of metabolite-sensing riboswitches. Trends Biochem Sci 2007, 32:415-424. 10.1016/j.tibs.2007.08.005, 2933830, 17764952.
    • (2007) Trends Biochem Sci , vol.32 , pp. 415-424
    • Wakeman, C.A.1    Winkler, W.C.2    Dann, C.E.3
  • 10
    • 44949246374 scopus 로고    scopus 로고
    • Nought may endure but mutability: spliceosome dynamics and the regulation of splicing
    • 10.1016/j.molcel.2008.04.013, 2610350, 18570869
    • Smith DJ, Query CC, Konarska MM. Nought may endure but mutability: spliceosome dynamics and the regulation of splicing. Mol Cell 2008, 30:657-666. 10.1016/j.molcel.2008.04.013, 2610350, 18570869.
    • (2008) Mol Cell , vol.30 , pp. 657-666
    • Smith, D.J.1    Query, C.C.2    Konarska, M.M.3
  • 11
    • 71849084955 scopus 로고    scopus 로고
    • RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs
    • 2784224, 19501200
    • Simon AE, Gehrke L. RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs. Biochim Biophys Acta 2009, 1789:571-583. 2784224, 19501200.
    • (2009) Biochim Biophys Acta , vol.1789 , pp. 571-583
    • Simon, A.E.1    Gehrke, L.2
  • 12
    • 77649169870 scopus 로고    scopus 로고
    • MRNA secondary structures fold sequentially but exchange rapidly in vivo
    • 10.1371/journal.pbio.1000307, 2817708, 20161716
    • Mahen EM, Watson PY, Cottrell JW, Fedor MJ. mRNA secondary structures fold sequentially but exchange rapidly in vivo. PLoS Biol 2010, 8:e1000307. 10.1371/journal.pbio.1000307, 2817708, 20161716.
    • (2010) PLoS Biol , vol.8
    • Mahen, E.M.1    Watson, P.Y.2    Cottrell, J.W.3    Fedor, M.J.4
  • 13
    • 0031455172 scopus 로고    scopus 로고
    • Antisense RNA-regulated programmed cell death
    • 10.1146/annurev.genet.31.1.1, 9442888
    • Gerdes K, Gultyaev AP, Franch T, Pedersen K, Mikkelsen ND. Antisense RNA-regulated programmed cell death. Annu Rev Genet 1997, 31:1-31. 10.1146/annurev.genet.31.1.1, 9442888.
    • (1997) Annu Rev Genet , vol.31 , pp. 1-31
    • Gerdes, K.1    Gultyaev, A.P.2    Franch, T.3    Pedersen, K.4    Mikkelsen, N.D.5
  • 14
    • 0019082587 scopus 로고
    • Fast algorithm for predicting the secondary structure of single-stranded RNA
    • 10.1073/pnas.77.11.6309, 350273, 6161375
    • Nussinov R, Jacobson AB. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci USA 1980, 77:6309-6313. 10.1073/pnas.77.11.6309, 350273, 6161375.
    • (1980) Proc Natl Acad Sci USA , vol.77 , pp. 6309-6313
    • Nussinov, R.1    Jacobson, A.B.2
  • 16
    • 0032502487 scopus 로고    scopus 로고
    • Barrier heights between ground states in a model of RNA secondary structure
    • Morgan S, Higgs P. Barrier heights between ground states in a model of RNA secondary structure. J Phys A 1998, 31(14):3153.
    • (1998) J Phys A , vol.31 , Issue.14 , pp. 3153
    • Morgan, S.1    Higgs, P.2
  • 18
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • 10.1006/jmbi.1999.2700, 10329189
    • Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999, 288:911-940. 10.1006/jmbi.1999.2700, 10329189.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 19
    • 0023785594 scopus 로고
    • RNA structure prediction
    • 10.1146/annurev.bb.17.060188.001123, 2456074
    • Turner DH, Sugimoto N, Freier SM. RNA structure prediction. Annu Rev Biophys Biophys Chem 1988, 17:167-192. 10.1146/annurev.bb.17.060188.001123, 2456074.
    • (1988) Annu Rev Biophys Biophys Chem , vol.17 , pp. 167-192
    • Turner, D.H.1    Sugimoto, N.2    Freier, S.M.3
  • 20
    • 0034021259 scopus 로고    scopus 로고
    • RNA folding at elementary step resolution
    • 10.1017/S1355838200992161, 1369916, 10744018
    • Flamm C, Fontana W, Hofacker IL, Schuster P. RNA folding at elementary step resolution. RNA 2000, 6:325-338. 10.1017/S1355838200992161, 1369916, 10744018.
    • (2000) RNA , vol.6 , pp. 325-338
    • Flamm, C.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 22
    • 0033080745 scopus 로고    scopus 로고
    • Complete suboptimal folding of RNA and the stability of secondary structures
    • Wuchty S, Fontana W, Hofacker IL, Schuster P. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 1999, 49:145-165.
    • (1999) Biopolymers , vol.49 , pp. 145-165
    • Wuchty, S.1    Fontana, W.2    Hofacker, I.L.3    Schuster, P.4
  • 23
    • 71549170506 scopus 로고    scopus 로고
    • NP completeness of the direct energy barrier problem without pseudoknots
    • Berlin, Heidelberg: Springer-Verlag, Deaton R, Suyama A
    • Manuch J, Thachuk C, Stacho L, Condon A. NP completeness of the direct energy barrier problem without pseudoknots. 15th International Conference DNA Computing and Molecular Programming 2009, 106-115. Berlin, Heidelberg: Springer-Verlag, Deaton R, Suyama A., http://dx.doi.org/10.1007/978-3-642-10604-0_11
    • (2009) 15th International Conference DNA Computing and Molecular Programming , pp. 106-115
    • Manuch, J.1    Thachuk, C.2    Stacho, L.3    Condon, A.4
  • 24
    • 0035257394 scopus 로고    scopus 로고
    • Design of multistable RNA molecules
    • 10.1017/S1355838201000863, 1370083, 11233982
    • Flamm C, Hofacker IL, Maurer-Stroh S, Stadler PF, Zehl M. Design of multistable RNA molecules. RNA 2001, 7:254-265. 10.1017/S1355838201000863, 1370083, 11233982.
    • (2001) RNA , vol.7 , pp. 254-265
    • Flamm, C.1    Hofacker, I.L.2    Maurer-Stroh, S.3    Stadler, P.F.4    Zehl, M.5
  • 25
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • 10.1093/nar/gkg599, 169005, 12824340
    • Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31:3429-3431. 10.1093/nar/gkg599, 169005, 12824340.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 26
    • 3543128223 scopus 로고    scopus 로고
    • Evaluating the predictability of conformational switching in RNA
    • 10.1093/bioinformatics/bth129, 14962925
    • Voss B, Meyer C, Giegerich R. Evaluating the predictability of conformational switching in RNA. Bioinformatics 2004, 20:1573-1582. 10.1093/bioinformatics/bth129, 14962925.
    • (2004) Bioinformatics , vol.20 , pp. 1573-1582
    • Voss, B.1    Meyer, C.2    Giegerich, R.3
  • 28
    • 77950494855 scopus 로고    scopus 로고
    • Computing folding pathways between RNA secondary structures
    • 10.1093/nar/gkp1054, 2836545, 20044352
    • Dotu I, Lorenz WA, Van Hentenryck P, Clote P. Computing folding pathways between RNA secondary structures. Nucleic Acids Res 2010, 38:1711-1722. 10.1093/nar/gkp1054, 2836545, 20044352.
    • (2010) Nucleic Acids Res , vol.38 , pp. 1711-1722
    • Dotu, I.1    Lorenz, W.A.2    Van Hentenryck, P.3    Clote, P.4
  • 31
    • 43749099405 scopus 로고    scopus 로고
    • Beyond energy minimization: Approaches to the kinetic folding of RNA
    • Flamm C, Hofacker IL. Beyond energy minimization: Approaches to the kinetic folding of RNA. Monatsh Chem 2008, 139:447-457.
    • (2008) Monatsh Chem , vol.139 , pp. 447-457
    • Flamm, C.1    Hofacker, I.L.2
  • 32
    • 57549096731 scopus 로고    scopus 로고
    • Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs
    • 10.1016/j.cbpa.2008.09.017, 2739931, 18926923
    • Shcherbakova I, Mitra S, Laederach A, Brenowitz M. Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol 2008, 12:655-666. 10.1016/j.cbpa.2008.09.017, 2739931, 18926923.
    • (2008) Curr Opin Chem Biol , vol.12 , pp. 655-666
    • Shcherbakova, I.1    Mitra, S.2    Laederach, A.3    Brenowitz, M.4
  • 33
    • 27844604240 scopus 로고    scopus 로고
    • A complex adaptive systems approach to the kinetic folding of RNA
    • 10.1016/j.biosystems.2005.08.004, 16171941
    • Ndifon W. A complex adaptive systems approach to the kinetic folding of RNA. Biosystems 2005, 82:257-265. 10.1016/j.biosystems.2005.08.004, 16171941.
    • (2005) Biosystems , vol.82 , pp. 257-265
    • Ndifon, W.1
  • 34
    • 33748621478 scopus 로고    scopus 로고
    • Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterizaion of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs
    • Sponer J, Leszczynski J, Hobza P. Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterizaion of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs. J Phys Chem 1996, 100(13):5590-5596.
    • (1996) J Phys Chem , vol.100 , Issue.13 , pp. 5590-5596
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 35
    • 32644434270 scopus 로고    scopus 로고
    • Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
    • 10.1093/nar/gkj454, 1360284, 16449200
    • Yakovchuk P, Protozanova E, Frank-Kamenetskii MD. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 2006, 34:564-574. 10.1093/nar/gkj454, 1360284, 16449200.
    • (2006) Nucleic Acids Res , vol.34 , pp. 564-574
    • Yakovchuk, P.1    Protozanova, E.2    Frank-Kamenetskii, M.D.3
  • 36
    • 77951637361 scopus 로고    scopus 로고
    • Predicting secondary structural folding kinetics for nucleic acids
    • 10.1016/j.bpj.2009.12.4319, 2856163, 20409482
    • Zhao P, Zhang WB, Chen SJ. Predicting secondary structural folding kinetics for nucleic acids. Biophys J 2010, 98:1617-1625. 10.1016/j.bpj.2009.12.4319, 2856163, 20409482.
    • (2010) Biophys J , vol.98 , pp. 1617-1625
    • Zhao, P.1    Zhang, W.B.2    Chen, S.J.3
  • 37
    • 27844448362 scopus 로고    scopus 로고
    • Evolutionary computing: the most powerful problem solver in the universe?
    • Eiben A. Evolutionary computing: the most powerful problem solver in the universe?. Dutch Mathematical Archive 2002, 5:126-131.
    • (2002) Dutch Mathematical Archive , vol.5 , pp. 126-131
    • Eiben, A.1
  • 38
    • 33645984848 scopus 로고    scopus 로고
    • Consensus folding of unaligned RNA sequences revisited
    • 10.1089/cmb.2006.13.283, 16597240
    • Bafna V, Tang H, Zhang S. Consensus folding of unaligned RNA sequences revisited. J Comput Biol 2006, 13:283-295. 10.1089/cmb.2006.13.283, 16597240.
    • (2006) J Comput Biol , vol.13 , pp. 283-295
    • Bafna, V.1    Tang, H.2    Zhang, S.3
  • 39
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • 10.1016/S0092-8674(03)00391-X, 12787499
    • Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell 2003, 113:577-586. 10.1016/S0092-8674(03)00391-X, 12787499.
    • (2003) Cell , vol.113 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 40
    • 84874518862 scopus 로고    scopus 로고
    • PaRNAss
    • paRNAss. , http://bibiserv.techfak.uni-bielefeld.de/parnass/examples.html
  • 41
    • 34548604264 scopus 로고    scopus 로고
    • Boltzmann probability of RNA structural neighbors and riboswitch detection
    • 10.1093/bioinformatics/btm314, 17573364
    • Freyhult E, Moulton V, Clote P. Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics 2007, 23:2054-2062. 10.1093/bioinformatics/btm314, 17573364.
    • (2007) Bioinformatics , vol.23 , pp. 2054-2062
    • Freyhult, E.1    Moulton, V.2    Clote, P.3


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