메뉴 건너뛰기




Volumn 40, Issue 2, 2012, Pages 487-498

Predicting coaxial helical stacking in RNA junctions

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; PREDICTION; PRIORITY JOURNAL; PROTEIN LOCALIZATION; PROTEIN RNA BINDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; RANDOM FOREST; RNA ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION;

EID: 84862969708     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr629     Document Type: Article
Times cited : (48)

References (69)
  • 1
    • 78049392640 scopus 로고    scopus 로고
    • Identification of regulatory RNAs in Bacillus subtilis
    • Irnov, I., Sharma, C. M., Vogel, J. and Winkler, W. C. (2010) Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res., 38, 6637-6651.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 6637-6651
    • Irnov, I.1    Sharma, C.M.2    Vogel, J.3    Winkler, W.C.4
  • 3
    • 77951606278 scopus 로고    scopus 로고
    • Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
    • Weinberg, Z., Wang, J. X., Bogue, J., Yang, J., Corbino, K., Moy, R. H. and Breaker, R. R. (2010) Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes. Genome Biol., 11, R31.
    • (2010) Genome Biol. , vol.11
    • Weinberg, Z.1    Wang, J.X.2    Bogue, J.3    Yang, J.4    Corbino, K.5    Moy, R.H.6    Breaker, R.R.7
  • 4
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel, D. P. (2009) MicroRNAs: target recognition and regulatory functions. Cell, 136, 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 5
    • 0034637111 scopus 로고    scopus 로고
    • The complete atomic structure of the large ribosomal subunit at 2.4 A resolution
    • Ban, N., Nissen, P., Hansen, J., Moore, P. B. and Steitz, T. A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science, 289, 905-920.
    • (2000) Science , vol.289 , pp. 905-920
    • Ban, N.1    Nissen, P.2    Hansen, J.3    Moore, P.B.4    Steitz, T.A.5
  • 8
    • 77953784130 scopus 로고    scopus 로고
    • Computational approaches to 3D modeling of RNA
    • Laing, C. and Schlick, T. (2010) Computational approaches to 3D modeling of RNA. J. Phys. Condens. Matter, 22, 283101.
    • (2010) J. Phys. Condens. Matter , vol.22 , pp. 283101
    • Laing, C.1    Schlick, T.2
  • 9
    • 77955405123 scopus 로고    scopus 로고
    • Assemble: An interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels
    • Jossinet, F., Ludwig, T. E. and Westhof, E. (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics, 26, 2057-2059.
    • (2010) Bioinformatics , vol.26 , pp. 2057-2059
    • Jossinet, F.1    Ludwig, T.E.2    Westhof, E.3
  • 10
    • 43749124906 scopus 로고    scopus 로고
    • RNA2D3D: A program for generating, viewing, and comparing 3-dimensional models of RNA
    • Martinez, H. M., Maizel, J. V. Jr. and Shapiro, B. A. (2008) RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA. J. Biomol. Struct. Dyn., 25, 669-683.
    • (2008) J. Biomol. Struct. Dyn. , vol.25 , pp. 669-683
    • Martinez, H.M.1    Maizel Jr., J.V.2    Shapiro, B.A.3
  • 12
    • 0030476765 scopus 로고    scopus 로고
    • Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme
    • Scott, W. G., Murray, J. B., Arnold, J. R., Stoddard, B. L. and Klug, A. (1996) Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science, 274, 2065-2069.
    • (1996) Science , vol.274 , pp. 2065-2069
    • Scott, W.G.1    Murray, J.B.2    Arnold, J.R.3    Stoddard, B.L.4    Klug, A.5
  • 13
    • 9244225713 scopus 로고    scopus 로고
    • Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
    • Batey, R. T., Gilbert, S. D. and Montange, R. K. (2004) Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature, 432, 411-415.
    • (2004) Nature , vol.432 , pp. 411-415
    • Batey, R.T.1    Gilbert, S.D.2    Montange, R.K.3
  • 14
    • 0036237981 scopus 로고    scopus 로고
    • Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation
    • Kieft, J. S., Zhou, K., Grech, A., Jubin, R. and Doudna, J. A. (2002) Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat. Struct. Biol., 9, 370-374.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 370-374
    • Kieft, J.S.1    Zhou, K.2    Grech, A.3    Jubin, R.4    Doudna, J.A.5
  • 16
    • 17844378705 scopus 로고    scopus 로고
    • Asymmetry in RNA pseudoknots: Observation and theory
    • Aalberts, D. P. and Hodas, N. O. (2005) Asymmetry in RNA pseudoknots: observation and theory. Nucleic Acids Res., 33, 2210-2214.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2210-2214
    • Aalberts, D.P.1    Hodas, N.O.2
  • 17
    • 41749109563 scopus 로고    scopus 로고
    • Crystal structure of a self-spliced group II intron
    • Toor, N., Keating, K. S., Taylor, S. D. and Pyle, A. M. (2008) Crystal structure of a self-spliced group II intron. Science, 320, 77-82.
    • (2008) Science , vol.320 , pp. 77-82
    • Toor, N.1    Keating, K.S.2    Taylor, S.D.3    Pyle, A.M.4
  • 18
    • 0029855518 scopus 로고    scopus 로고
    • Thermodynamics of coaxially stacked helixes with GA and CC mismatches
    • Kim, J., Walter, A. E. and Turner, D. H. (1996) Thermodynamics of coaxially stacked helixes with GA and CC mismatches. Biochemistry, 35, 13753-13761.
    • (1996) Biochemistry , vol.35 , pp. 13753-13761
    • Kim, J.1    Walter, A.E.2    Turner, D.H.3
  • 19
    • 0028000994 scopus 로고
    • Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
    • Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Muller, P., Mathews, D. H. and Zuker, M. (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl Acad. Sci. USA, 91, 9218-9222.
    • (1994) Proc. Natl Acad. Sci. USA , vol.91 , pp. 9218-9222
    • Walter, A.E.1    Turner, D.H.2    Kim, J.3    Lyttle, M.H.4    Muller, P.5    Mathews, D.H.6    Zuker, M.7
  • 20
    • 77953630339 scopus 로고    scopus 로고
    • A two-length-scale polymer theory for RNA loop free energies and helix stacking
    • Aalberts, D. P. and Nandagopal, N. (2010) A two-length-scale polymer theory for RNA loop free energies and helix stacking. RNA, 16, 1350-1355.
    • (2010) RNA , vol.16 , pp. 1350-1355
    • Aalberts, D.P.1    Nandagopal, N.2
  • 21
    • 57049151833 scopus 로고    scopus 로고
    • Annotation of tertiary interactions in RNA structures reveals variations and correlations
    • Xin, Y., Laing, C., Leontis, N. B. and Schlick, T. (2008) Annotation of tertiary interactions in RNA structures reveals variations and correlations. RNA, 14, 2465-2477.
    • (2008) RNA , vol.14 , pp. 2465-2477
    • Xin, Y.1    Laing, C.2    Leontis, N.B.3    Schlick, T.4
  • 22
    • 29844453234 scopus 로고    scopus 로고
    • Topology of three-way junctions in folded RNAs
    • Lescoute, A. and Westhof, E. (2006) Topology of three-way junctions in folded RNAs. RNA, 12, 83-93.
    • (2006) RNA , vol.12 , pp. 83-93
    • Lescoute, A.1    Westhof, E.2
  • 23
    • 67449103067 scopus 로고    scopus 로고
    • Analysis of four-way junctions in RNA structures
    • Laing, C. and Schlick, T. (2009) Analysis of four-way junctions in RNA structures. J. Mol. Biol., 390, 547-559.
    • (2009) J. Mol. Biol. , vol.390 , pp. 547-559
    • Laing, C.1    Schlick, T.2
  • 24
    • 0028143014 scopus 로고
    • Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces
    • Walter, A. E. and Turner, D. H. (1994) Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry, 33, 12715-12719.
    • (1994) Biochemistry , vol.33 , pp. 12715-12719
    • Walter, A.E.1    Turner, D.H.2
  • 25
    • 0035919726 scopus 로고    scopus 로고
    • AA. AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices
    • Elgavish, T., Cannone, J. J., Lee, J. C., Harvey, S. C. and Gutell, R. R. (2001) AA. AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices. J. Mol. Biol., 310, 735-753.
    • (2001) J. Mol. Biol. , vol.310 , pp. 735-753
    • Elgavish, T.1    Cannone, J.J.2    Lee, J.C.3    Harvey, S.C.4    Gutell, R.R.5
  • 26
    • 0032559410 scopus 로고    scopus 로고
    • Protein and Mg (2+)-induced conformational changes in the S15 binding site of 16 S ribosomal RNA
    • Orr, J. W., Hagerman, P. J. and Williamson, J. R. (1998) Protein and Mg (2+)-induced conformational changes in the S15 binding site of 16 S ribosomal RNA. J. Mol. Biol., 275, 453-464.
    • (1998) J. Mol. Biol. , vol.275 , pp. 453-464
    • Orr, J.W.1    Hagerman, P.J.2    Williamson, J.R.3
  • 27
    • 70349238567 scopus 로고    scopus 로고
    • Tertiary motifs revealed in analyses of higher-order RNA junctions
    • Laing, C., Jung, S., Iqbal, A. and Schlick, T. (2009) Tertiary motifs revealed in analyses of higher-order RNA junctions. J. Mol. Biol., 393, 67-82.
    • (2009) J. Mol. Biol. , vol.393 , pp. 67-82
    • Laing, C.1    Jung, S.2    Iqbal, A.3    Schlick, T.4
  • 28
    • 60149112933 scopus 로고    scopus 로고
    • The dynamic landscapes of RNA architecture
    • Cruz, J. A. and Westhof, E. (2009) The dynamic landscapes of RNA architecture. Cell, 136, 604-609.
    • (2009) Cell , vol.136 , pp. 604-609
    • Cruz, J.A.1    Westhof, E.2
  • 29
    • 48249125095 scopus 로고    scopus 로고
    • Structural principles from large RNAs
    • Holbrook, S. R. (2008) Structural principles from large RNAs. Annu. Rev. Biophys., 37, 445-464.
    • (2008) Annu. Rev. Biophys. , vol.37 , pp. 445-464
    • Holbrook, S.R.1
  • 31
    • 0032439514 scopus 로고    scopus 로고
    • Folding of branched RNA species
    • Lilley, D. M. (1998) Folding of branched RNA species. Biopolymers, 48, 101-112.
    • (1998) Biopolymers , vol.48 , pp. 101-112
    • Lilley, D.M.1
  • 32
    • 0033636685 scopus 로고    scopus 로고
    • Structures of helical junctions in nucleic acids
    • Lilley, D. M. (2000) Structures of helical junctions in nucleic acids. Q. Rev. Biophys., 33, 109-159.
    • (2000) Q. Rev. Biophys. , vol.33 , pp. 109-159
    • Lilley, D.M.1
  • 33
    • 2942615089 scopus 로고    scopus 로고
    • The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit
    • Klein, D. J., Moore, P. B. and Steitz, T. A. (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.J.1    Moore, P.B.2    Steitz, T.A.3
  • 34
    • 34250804011 scopus 로고    scopus 로고
    • Predicting helical coaxial stacking in RNA multibranch loops
    • Tyagi, R. and Mathews, D. H. (2007) Predicting helical coaxial stacking in RNA multibranch loops. RNA, 13, 939-951.
    • (2007) RNA , vol.13 , pp. 939-951
    • Tyagi, R.1    Mathews, D.H.2
  • 35
    • 78049420557 scopus 로고    scopus 로고
    • Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome
    • Besseova, I., Reblova, K., Leontis, N. B. and Šponer, J. (2010) Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Res., 38, 6247-6264.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 6247-6264
    • Besseova, I.1    Reblova, K.2    Leontis, N.B.3    Šponer, J.4
  • 36
    • 38549083634 scopus 로고    scopus 로고
    • RNAJunction: A database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
    • Bindewald, E., Hayes, R., Yingling, Y. G., Kasprzak, W. and Shapiro, B. A. (2008) RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. Nucleic Acids Res., 36, D392-D397.
    • (2008) Nucleic Acids Res. , vol.36
    • Bindewald, E.1    Hayes, R.2    Yingling, Y.G.3    Kasprzak, W.4    Shapiro, B.A.5
  • 37
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman, L. (2001) Random Forests. Mach. Learn., 45, 5-32.
    • (2001) Mach. Learn. , vol.45 , pp. 5-32
    • Breiman, L.1
  • 38
    • 0035869008 scopus 로고    scopus 로고
    • Structure, folding and activity of the VS ribozyme: Importance of the 2-3-6 helical junction
    • Lafontaine, D.A., Norman, D. G. and Lilley, D. M. (2001) Structure, folding and activity of the VS ribozyme: importance of the 2-3-6 helical junction. EMBO J., 20, 1415-1424.
    • (2001) EMBO J. , vol.20 , pp. 1415-1424
    • Lafontaine, D.A.1    Norman, D.G.2    Lilley, D.M.3
  • 39
    • 1642580826 scopus 로고    scopus 로고
    • The Varkud satellite ribozyme
    • Lilley, D. M. (2004) The Varkud satellite ribozyme. RNA, 10, 151-158.
    • (2004) RNA , vol.10 , pp. 151-158
    • Lilley, D.M.1
  • 40
    • 77955121660 scopus 로고    scopus 로고
    • Structure of the three-way helical junction of the hepatitis C virus IRES element
    • Ouellet, J., Melcher, S., Iqbal, A., Ding, Y. and Lilley, D. M. (2010) Structure of the three-way helical junction of the hepatitis C virus IRES element. RNA, 16, 1597-1609.
    • (2010) RNA , vol.16 , pp. 1597-1609
    • Ouellet, J.1    Melcher, S.2    Iqbal, A.3    Ding, Y.4    Lilley, D.M.5
  • 41
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
    • Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M. and Turner, D. H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.L.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 42
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D. H., Sabina, J., Zuker, M. and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
    • (1999) J. Mol. Biol. , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 43
  • 44
    • 67449156722 scopus 로고    scopus 로고
    • RNA secondary structure analysis using RNAstructure
    • Chapter 12, Unit 12 16
    • Mathews, D. H. (2006) RNA secondary structure analysis using RNAstructure. Curr. Protoc. Bioinformatics, Chapter 12, Unit 12 16.
    • (2006) Curr. Protoc. Bioinformatics
    • Mathews, D.H.1
  • 46
    • 0345040873 scopus 로고    scopus 로고
    • Classification and regression by randomForest
    • Liaw, A. and Wiener, M. (2002) Classification and regression by randomForest. R. News, 2, 18-22.
    • (2002) R. News , vol.2 , pp. 18-22
    • Liaw, A.1    Wiener, M.2
  • 47
    • 0031800080 scopus 로고    scopus 로고
    • Global structure of four-way RNA junctions studied using fluorescence resonance energy transfer
    • Walter, F., Murchie, A. I., Duckett, D. R. and Lilley, D. M. (1998) Global structure of four-way RNA junctions studied using fluorescence resonance energy transfer. RNA, 4, 719-728.
    • (1998) RNA , vol.4 , pp. 719-728
    • Walter, F.1    Murchie, A.I.2    Duckett, D.R.3    Lilley, D.M.4
  • 48
    • 50649108803 scopus 로고    scopus 로고
    • The complete VS ribozyme in solution studied by small-angle X-ray scattering
    • Lipfert, J., Ouellet, J., Norman, D. G., Doniach, S. and Lilley, D. M. (2008) The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure, 16, 1357-1367.
    • (2008) Structure , vol.16 , pp. 1357-1367
    • Lipfert, J.1    Ouellet, J.2    Norman, D.G.3    Doniach, S.4    Lilley, D.M.5
  • 49
    • 4644247805 scopus 로고    scopus 로고
    • Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: The IRES functions as an RNA-based translation factor
    • Spahn, C. M., Jan, E., Mulder, A., Grassucci, R.A., Sarnow, P. and Frank, J. (2004) Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor. Cell, 118, 465-475.
    • (2004) Cell , vol.118 , pp. 465-475
    • Spahn, C.M.1    Jan, E.2    Mulder, A.3    Grassucci, R.A.4    Sarnow, P.5    Frank, J.6
  • 50
    • 0014024193 scopus 로고
    • The importance of London dispersion forces in the maintenance of the deoxyribonucleic acid helix
    • Hanlon, S. (1966) The importance of London dispersion forces in the maintenance of the deoxyribonucleic acid helix. Biochem. Biophys. Res. Commun., 23, 861-867.
    • (1966) Biochem. Biophys. Res. Commun. , vol.23 , pp. 861-867
    • Hanlon, S.1
  • 51
    • 0019048028 scopus 로고
    • Stacking properties of a highly hydrophobic dinucleotide sequence, N6, N6-dimethyladenylyl (3′ leads to 5′) N6, N6-dimethyladenosine, occurring in 16-18-S ribosomal RNA
    • Tazawa, I., Koike, T. and Inoue, Y. (1980) Stacking properties of a highly hydrophobic dinucleotide sequence, N6, N6-dimethyladenylyl (3′ leads to 5′) N6, N6-dimethyladenosine, occurring in 16-18-S ribosomal RNA. Eur. J. Biochem., 109, 33-38.
    • (1980) Eur. J. Biochem. , vol.109 , pp. 33-38
    • Tazawa, I.1    Koike, T.2    Inoue, Y.3
  • 52
    • 0023732135 scopus 로고
    • Origin of DNA helical structure and its sequence dependence
    • Sarai, A., Mazur, J., Nussinov, R. and Jernigan, R. L. (1988) Origin of DNA helical structure and its sequence dependence. Biochemistry, 27, 8498-8502.
    • (1988) Biochemistry , vol.27 , pp. 8498-8502
    • Sarai, A.1    Mazur, J.2    Nussinov, R.3    Jernigan, R.L.4
  • 53
    • 15944379585 scopus 로고    scopus 로고
    • Influence of the π-π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases
    • Mignon, P., Loverix, S., Steyaert, J. and Geerlings, P. (2005) Influence of the π-π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases. Nucleic Acids Res., 33, 1779-1789.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 1779-1789
    • Mignon, P.1    Loverix, S.2    Steyaert, J.3    Geerlings, P.4
  • 55
    • 33748621478 scopus 로고    scopus 로고
    • Nature of nucleic acid-base stacking: Nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs
    • Sponer, J., Leszczynski, J. and Hobza, P. (1996) Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs. J. Phys. Chem., 100, 5590-5596.
    • (1996) J. Phys. Chem. , vol.100 , pp. 5590-5596
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 56
    • 0029011972 scopus 로고
    • A secondary-structure model for the self-cleaving region of Neurospora VS RNA
    • Beattie, T. L., Olive, J. E. and Collins, R. A. (1995) A secondary-structure model for the self-cleaving region of Neurospora VS RNA. Proc. Natl Acad. Sci. USA, 92, 4686-4690.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 4686-4690
    • Beattie, T.L.1    Olive, J.E.2    Collins, R.A.3
  • 57
    • 0031978817 scopus 로고    scopus 로고
    • Group I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites
    • Einvik, C., Nielsen, H., Westhof, E., Michel, F. and Johansen, S. (1998) Group I-like ribozymes with a novel core organization perform obligate sequential hydrolytic cleavages at two processing sites. RNA, 4, 530-541.
    • (1998) RNA , vol.4 , pp. 530-541
    • Einvik, C.1    Nielsen, H.2    Westhof, E.3    Michel, F.4    Johansen, S.5
  • 58
    • 0037107418 scopus 로고    scopus 로고
    • Hierarchical, clustered protein interactions with U4/U6 snRNA: A biochemical role for U4/U6 proteins
    • Nottrott, S., Urlaub, H. and Luhrmann, R. (2002) Hierarchical, clustered protein interactions with U4/U6 snRNA: a biochemical role for U4/U6 proteins. EMBO J., 21, 5527-5538.
    • (2002) EMBO J. , vol.21 , pp. 5527-5538
    • Nottrott, S.1    Urlaub, H.2    Luhrmann, R.3
  • 59
    • 0032903304 scopus 로고    scopus 로고
    • A phylogenetically conserved stem-loop structure at the 5′ border of the internal ribosome entry site of hepatitis C virus is required for cap-independent viral translation
    • Honda, M., Beard, M. R., Ping, L. H. and Lemon, S. M. (1999) A phylogenetically conserved stem-loop structure at the 5′ border of the internal ribosome entry site of hepatitis C virus is required for cap-independent viral translation. J. Virol., 73, 1165-1174.
    • (1999) J. Virol. , vol.73 , pp. 1165-1174
    • Honda, M.1    Beard, M.R.2    Ping, L.H.3    Lemon, S.M.4
  • 61
    • 0036761518 scopus 로고    scopus 로고
    • DiGIR1 and NaGIR1: Naturally occurring group I-like ribozymes with unique core organization and evolved biological role
    • Johansen, S., Einvik, C. and Nielsen, H. (2002) DiGIR1 and NaGIR1: naturally occurring group I-like ribozymes with unique core organization and evolved biological role. Biochimie, 84, 905-912.
    • (2002) Biochimie , vol.84 , pp. 905-912
    • Johansen, S.1    Einvik, C.2    Nielsen, H.3
  • 62
    • 0036301332 scopus 로고    scopus 로고
    • Secondary structure prediction for aligned RNA sequences
    • Hofacker, I. L., Fekete, M. and Stadler, P. F. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol., 319, 1059-1066.
    • (2002) J. Mol. Biol. , vol.319 , pp. 1059-1066
    • Hofacker, I.L.1    Fekete, M.2    Stadler, P.F.3
  • 63
    • 70349145411 scopus 로고    scopus 로고
    • Time-resolved RNA SHAPE chemistry: Quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution
    • Mortimer, S. A. and Weeks, K. M. (2009) Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution. Nat. Protoc., 4, 1413-1421.
    • (2009) Nat. Protoc. , vol.4 , pp. 1413-1421
    • Mortimer, S.A.1    Weeks, K.M.2
  • 64
    • 52049083257 scopus 로고    scopus 로고
    • RNA STRAND: The RNA secondary structure and statistical analysis database
    • Andronescu, M., Bereg, V., Hoos, H. H. and Condon, A. (2008) RNA STRAND: the RNA secondary structure and statistical analysis database. BMC Bioinformatics, 9, 340.
    • (2008) BMC Bioinformatics , vol.9 , pp. 340
    • Andronescu, M.1    Bereg, V.2    Hoos, H.H.3    Condon, A.4
  • 65
    • 0014688034 scopus 로고
    • Detailed molecular model for transfer ribonucleic acid
    • Levitt, M. (1969) Detailed molecular model for transfer ribonucleic acid. Nature, 224, 759-763.
    • (1969) Nature , vol.224 , pp. 759-763
    • Levitt, M.1
  • 66
    • 77956021842 scopus 로고    scopus 로고
    • Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch
    • Smith, K. D., Lipchock, S. V., Livingston, A. L., Shanahan, C. A. and Strobel, S. A. Structural and biochemical determinants of ligand binding by the c-di-GMP riboswitch. Biochemistry, 49, 7351-7359.
    • Biochemistry , vol.49 , pp. 7351-7359
    • Smith, K.D.1    Lipchock, S.V.2    Livingston, A.L.3    Shanahan, C.A.4    Strobel, S.A.5
  • 67
    • 0029283999 scopus 로고
    • GNRA tetraloops make a U-turn
    • Jucker, F. M. and Pardi, A. (1995) GNRA tetraloops make a U-turn. RNA, 1, 219-222.
    • (1995) RNA , vol.1 , pp. 219-222
    • Jucker, F.M.1    Pardi, A.2
  • 68
    • 70350107533 scopus 로고    scopus 로고
    • Three-way RNA junctions with remote tertiary contacts: A recurrent and highly versatile fold
    • De La Pena, M., Dufour, D. and Gallego, J. (2009) Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold. RNA, 15, 1949-1964.
    • (2009) RNA , vol.15 , pp. 1949-1964
    • De La Pena, M.1    Dufour, D.2    Gallego, J.3
  • 69
    • 58249111738 scopus 로고    scopus 로고
    • Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters
    • Jonikas, M. A., Radmer, R. J., Laederach, A., Das, R., Pearlman, S., Herschlag, D. and Altman, R. B. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA, 15, 189-199.
    • (2009) RNA , vol.15 , pp. 189-199
    • Jonikas, M.A.1    Radmer, R.J.2    Laederach, A.3    Das, R.4    Pearlman, S.5    Herschlag, D.6    Altman, R.B.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.