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Volumn 42, Issue 21, 2014, Pages 13306-13314

The role of nucleobase interactions in RNA structure and dynamics

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

EID: 84941094198     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku972     Document Type: Article
Times cited : (117)

References (48)
  • 1
    • 0020417286 scopus 로고
    • Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena
    • Kruger, K., Grabowski, P. J., Zaug, A. J., Sands, J., Gottschling, D. E. And Cech, T. R. (1982) Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence of tetrahymena. Cell, 31, 147-157.
    • (1982) Cell , vol.31 , pp. 147-157
    • Kruger, K.1    Grabowski, P.J.2    Zaug, A.J.3    Sands, J.4    Gottschling, D.E.5    Cech, T.R.6
  • 2
    • 2942615089 scopus 로고    scopus 로고
    • The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit
    • Klein, D., Moore, P. And Steitz, T. (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol., 340, 141-177.
    • (2004) J. Mol. Biol. , vol.340 , pp. 141-177
    • Klein, D.1    Moore, P.2    Steitz, T.3
  • 3
    • 84872543206 scopus 로고    scopus 로고
    • A decade of riboswitches
    • Serganov, A. And Nudler, E. (2013) A decade of riboswitches. Cell, 152, 17-24.
    • (2013) Cell , vol.152 , pp. 17-24
    • Serganov, A.1    Nudler, E.2
  • 5
    • 0030219249 scopus 로고    scopus 로고
    • Nucleic acid structures, energetics, and dynamics
    • Tinoco, I. (1996) Nucleic acid structures, energetics, and dynamics. J. Phys. Chem., 100, 13311-13322.
    • (1996) J. Phys. Chem. , vol.100 , pp. 13311-13322
    • Tinoco, I.1
  • 8
    • 84885818229 scopus 로고    scopus 로고
    • High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations
    • Chen, A. A. And Garcia, A. E. (2013) High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations. Proc. Natl Acad. Sci. U. S. A., 110, 16820-16825.
    • (2013) Proc. Natl Acad. Sci. U. S. A. , vol.110 , pp. 16820-16825
    • Chen, A.A.1    Garcia, A.E.2
  • 9
    • 44149101971 scopus 로고    scopus 로고
    • Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
    • Ding, F., Sharma, S., Chalasani, P., Demidov, V. V., Broude, N. E. And Dokholyan, N. V. (2008) Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA, 14, 1164-1173.
    • (2008) RNA , vol.14 , pp. 1164-1173
    • Ding, F.1    Sharma, S.2    Chalasani, P.3    Demidov, V.V.4    Broude, N.E.5    Dokholyan, N.V.6
  • 10
    • 84877022321 scopus 로고    scopus 로고
    • Coarse-grained model for predicting RNA folding thermodynamics
    • Denesyuk, N. A. And Thirumalai, D. (2013) Coarse-grained model for predicting RNA folding thermodynamics. J. Phys. Chem. B, 117, 4901-4911.
    • (2013) J. Phys. Chem. B , vol.117 , pp. 4901-4911
    • Denesyuk, N.A.1    Thirumalai, D.2
  • 11
    • 40449139010 scopus 로고    scopus 로고
    • The MC-fold and MC-sym pipeline infers RNA structure from sequence data
    • Parisien, M. And Major, F. (2008) The MC-fold and MC-sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55.
    • (2008) Nature , vol.452 , pp. 51-55
    • Parisien, M.1    Major, F.2
  • 12
    • 79953795893 scopus 로고    scopus 로고
    • Physics-based de novo prediction of RNA 3D structures
    • Cao, S. And Chen, S.-J. (2011) Physics-based de novo prediction of RNA 3D structures. J. Phys. Chem. B, 115, 4216-4226.
    • (2011) J. Phys. Chem. B , vol.115 , pp. 4216-4226
    • Cao, S.1    Chen, S.-J.2
  • 13
    • 35548950310 scopus 로고    scopus 로고
    • Automated de novo prediction of native-like RNA tertiary structures
    • Das, R. And Baker, D. (2007) Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl Acad. Sci. U. S. A., 104, 14664-14669.
    • (2007) Proc. Natl Acad. Sci. U. S. A. , vol.104 , pp. 14664-14669
    • Das, R.1    Baker, D.2
  • 15
    • 77951643739 scopus 로고    scopus 로고
    • Atomic accuracy in predicting and designing noncanonical RNA structure
    • Das, R., Karanicolas, J. And Baker, D. (2010) Atomic accuracy in predicting and designing noncanonical RNA structure. Nat. Methods, 7, 291-294.
    • (2010) Nat. Methods , vol.7 , pp. 291-294
    • Das, R.1    Karanicolas, J.2    Baker, D.3
  • 16
    • 79956189724 scopus 로고    scopus 로고
    • Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation
    • Bernauer, J., Huang, X., Sim, A. Y. And Levitt, M. (2011) Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation. RNA, 17, 1066-1075.
    • (2011) RNA , vol.17 , pp. 1066-1075
    • Bernauer, J.1    Huang, X.2    Sim, A.Y.3    Levitt, M.4
  • 17
    • 79954460627 scopus 로고    scopus 로고
    • All-atom knowledge-based potential for RNA structure prediction and assessment
    • Capriotti, E., Norambuena, T., Marti-Renom, M. A. And Melo, F. (2011) All-atom knowledge-based potential for RNA structure prediction and assessment. Bioinformatics, 27, 1086-1093.
    • (2011) Bioinformatics , vol.27 , pp. 1086-1093
    • Capriotti, E.1    Norambuena, T.2    Marti-Renom, M.A.3    Melo, F.4
  • 18
    • 0017021957 scopus 로고
    • Medium-and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins
    • Tanaka, S. And Scheraga, H. A. (1976) Medium-and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins. Macromolecules, 9, 945-950.
    • (1976) Macromolecules , vol.9 , pp. 945-950
    • Tanaka, S.1    Scheraga, H.A.2
  • 22
    • 0032545158 scopus 로고    scopus 로고
    • Stepping through an RNA structure: A novel approach to conformational analysis
    • Duarte, C. M. And Pyle, A. M. (1998) Stepping through an RNA structure: A novel approach to conformational analysis. J. Mol. Biol., 284, 1465-1478.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1465-1478
    • Duarte, C.M.1    Pyle, A.M.2
  • 24
    • 0035010211 scopus 로고    scopus 로고
    • Geometric nomenclature and classification of RNA base pairs
    • Leontis, N. B. And Westhof, E. (2001) Geometric nomenclature and classification of RNA base pairs. RNA, 7, 499-512.
    • (2001) RNA , vol.7 , pp. 499-512
    • Leontis, N.B.1    Westhof, E.2
  • 25
    • 0035906639 scopus 로고    scopus 로고
    • Quantitative analysis of nucleic acid three-dimensional structures
    • Gendron, P., Lemieux, S. And Major, F. (2001) Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol., 308, 919-936.
    • (2001) J. Mol. Biol. , vol.308 , pp. 919-936
    • Gendron, P.1    Lemieux, S.2    Major, F.3
  • 26
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch, W. (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A, 32, 922-923.
    • (1976) Acta Crystallogr. A , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 27
    • 70349149051 scopus 로고    scopus 로고
    • New metrics for comparing and assessing discrepancies between RNA 3D structures and models
    • Parisien, M., Cruz, J. A., Westhof, E. And Major, F. (2009) New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA, 15, 1875-1885.
    • (2009) RNA , vol.15 , pp. 1875-1885
    • Parisien, M.1    Cruz, J.A.2    Westhof, E.3    Major, F.4
  • 29
    • 36448954303 scopus 로고    scopus 로고
    • FR3D: Finding local and composite recurrent structural motifs in RNA 3D structures
    • Sarver, M., Zirbel, C. L., Stombaugh, J., Mokdad, A. And Leontis, N. B. (2008) FR3D: finding local and composite recurrent structural motifs in RNA 3D structures. J. Math. Biol., 56, 215-252.
    • (2008) J. Math. Biol. , vol.56 , pp. 215-252
    • Sarver, M.1    Zirbel, C.L.2    Stombaugh, J.3    Mokdad, A.4    Leontis, N.B.5
  • 31
    • 78649347324 scopus 로고    scopus 로고
    • Rnamotifscan: Automatic identification of RNA structural motifs using secondary structural alignment
    • Zhong, C., Tang, H. And Zhang, S. (2010) Rnamotifscan: Automatic identification of RNA structural motifs using secondary structural alignment. Nucleic Acids Res., 38, e176.
    • (2010) Nucleic Acids Res. , vol.38 , pp. e176
    • Zhong, C.1    Tang, H.2    Zhang, S.3
  • 33
    • 0002594455 scopus 로고    scopus 로고
    • Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases
    • Sponer, J., Leszczynski, J. And Hobza, P. (2001) Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers, 61, 3-31.
    • (2001) Biopolymers , vol.61 , pp. 3-31
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 34
    • 0014980698 scopus 로고
    • Stereochemistry of nucleic acids and their constituents. X. Solid-slate base-slacking patterns in nucleic acid constituents and polynucleotides
    • Bugg, C., Thomas, J., Sundaralingam, M. T. And Rao, S. (1971) Stereochemistry of nucleic acids and their constituents. X. Solid-slate base-slacking patterns in nucleic acid constituents and polynucleotides. Biopolymers, 10, 175-219.
    • (1971) Biopolymers , vol.10 , pp. 175-219
    • Bugg, C.1    Thomas, J.2    Sundaralingam, M.T.3    Rao, S.4
  • 35
    • 43449137856 scopus 로고    scopus 로고
    • Nature and magnitude of aromatic stacking of nucleic acid bases
    • Sponer, J., Riley, K. E. And Hobza, P. (2013) Nature and magnitude of aromatic stacking of nucleic acid bases. Phys. Chem. Chem. Phys., 10, 2595-2610.
    • (2013) Phys. Chem. Chem. Phys. , vol.10 , pp. 2595-2610
    • Sponer, J.1    Riley, K.E.2    Hobza, P.3
  • 37
    • 54249091171 scopus 로고    scopus 로고
    • The unfolded ensemble and folding mechanism of the C-terminal GB1-hairpin
    • Bonomi, M., Branduardi, D., Gervasio, F. L. And Parrinello, M. (2008) The unfolded ensemble and folding mechanism of the C-terminal GB1-hairpin. J. Am. Chem. Soc., 130, 13938-13944.
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 13938-13944
    • Bonomi, M.1    Branduardi, D.2    Gervasio, F.L.3    Parrinello, M.4
  • 38
    • 79959761281 scopus 로고    scopus 로고
    • Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory
    • Cossio, P., Laio, A. And Pietrucci, F. (2011)Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory? Phys. Chem. Chem. Phys., 13, 10421-10425.
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 10421-10425
    • Cossio, P.1    Laio, A.2    Pietrucci, F.3
  • 39
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons, K. T., Kooperberg, C., Huang, E. And Baker, D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 268, 209-225.
    • (1997) J. Mol. Biol. , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 40
    • 84859738455 scopus 로고    scopus 로고
    • A simple and efficient statistical potential for scoring ensembles of protein structures
    • Cossio, P., Granata, D., Laio, A., Seno, F. And Trovato, A. (2012) A simple and efficient statistical potential for scoring ensembles of protein structures. Sci. Rep., 2, 351.
    • (2012) Sci. Rep. , vol.2 , pp. 351
    • Cossio, P.1    Granata, D.2    Laio, A.3    Seno, F.4    Trovato, A.5
  • 41
    • 84865064420 scopus 로고    scopus 로고
    • Distribution of reciprocal of interatomic distances: A fast structural metric
    • Zhou, T. And Caflisch, A. (2012) Distribution of reciprocal of interatomic distances: A fast structural metric. J. Chem. Theory Comput., 8, 2930-2937.
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 2930-2937
    • Zhou, T.1    Caflisch, A.2
  • 43
    • 84885985615 scopus 로고    scopus 로고
    • Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch
    • Di Palma, F., Colizzi, F. And Bussi, G. (2013) Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch. RNA, 19, 1517-1524.
    • (2013) RNA , vol.19 , pp. 1517-1524
    • Di Palma, F.1    Colizzi, F.2    Bussi, G.3
  • 44
    • 0032870204 scopus 로고    scopus 로고
    • Structural motifs in RNA
    • Moore, P. B. (1999) Structural motifs in RNA. Annu. Rev. Biochem., 68, 287-300.
    • (1999) Annu. Rev. Biochem. , vol.68 , pp. 287-300
    • Moore, P.B.1
  • 45
    • 84884679567 scopus 로고    scopus 로고
    • Automated classification of RNA 3D motifs and the RNA 3D motif atlas
    • Petrov, A. I., Zirbel, C. L. And Leontis, N. B. (2013) Automated classification of RNA 3D motifs and the RNA 3D motif atlas. RNA, 19, 1327-1340.
    • (2013) RNA , vol.19 , pp. 1327-1340
    • Petrov, A.I.1    Zirbel, C.L.2    Leontis, N.B.3
  • 46
    • 33646845815 scopus 로고    scopus 로고
    • Automated extraction and classification of RNA tertiary structure cyclic motifs
    • Lemieux, S. And Major, F. (2006) Automated extraction and classification of rna tertiary structure cyclic motifs. Nucleic Acids Res., 34, 2340-2346.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2340-2346
    • Lemieux, S.1    Major, F.2
  • 47
    • 0030045924 scopus 로고    scopus 로고
    • Modeling of polypeptide chains as C-chains, C-chains with C-, and C-chains with ellipsoidal lateral chains
    • Fogolari, F., Esposito, G., Viglino, P. And Cattarinussi, S. (1996) Modeling of polypeptide chains as C-chains, C-chains with C-, and C-chains with ellipsoidal lateral chains. Biophys. J., 70, 1183-1197.
    • (1996) Biophys. J. , vol.70 , pp. 1183-1197
    • Fogolari, F.1    Esposito, G.2    Viglino, P.3    Cattarinussi, S.4
  • 48
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty, K., Denise, A. And Ponty, Y. (2009) VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics, 25, 1974.
    • (2009) Bioinformatics , vol.25 , pp. 1974
    • Darty, K.1    Denise, A.2    Ponty, Y.3


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