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Volumn 49, Issue 42, 2010, Pages 9058-9062

Thermodynamic characterization of RNA triloops

Author keywords

[No Author keywords available]

Indexed keywords

FREE ENERGY; RNA;

EID: 77958103511     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101164s     Document Type: Article
Times cited : (18)

References (39)
  • 1
    • 0025047647 scopus 로고
    • Architecture of ribosomal RNA: Constraints on the sequence of tetra-loops
    • Woese, C. R., Winker, S., and Gutell, R. R. (1990) Architecture of ribosomal RNA: Constraints on the sequence of tetra-loops Proc. Natl. Acad. Sci. U.S.A. 87, 8467-8471
    • (1990) Proc. Natl. Acad. Sci. U.S.A. , vol.87 , pp. 8467-8471
    • Woese, C.R.1    Winker, S.2    Gutell, R.R.3
  • 2
    • 0026548897 scopus 로고
    • The nature of preferred hairpin structures in 16S-like rRNA variable regions
    • Wolters, J. (1992) The nature of preferred hairpin structures in 16S-like rRNA variable regions Nucleic Acids Res. 20, 1843-1850
    • (1992) Nucleic Acids Res. , vol.20 , pp. 1843-1850
    • Wolters, J.1
  • 3
    • 0027225783 scopus 로고
    • A compilation of large subunit (23s and 23s-like) ribosomal-RNA structures - 1993
    • Gutell, R. R., Gray, M. W., and Schnare, M. N. (1993) A compilation of large subunit (23s and 23s-like) ribosomal-RNA structures - 1993 Nucleic Acids Res. 21, 3055-3074
    • (1993) Nucleic Acids Res. , vol.21 , pp. 3055-3074
    • Gutell, R.R.1    Gray, M.W.2    Schnare, M.N.3
  • 4
    • 0029877001 scopus 로고    scopus 로고
    • Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA
    • Schnare, M. N., Damberger, S. H., Gray, M. W., and Gutell, R. R. (1996) Comprehensive comparison of structural characteristics in eukaryotic cytoplasmic large subunit (23 S-like) ribosomal RNA J. Mol. Biol. 256, 701-719
    • (1996) J. Mol. Biol. , vol.256 , pp. 701-719
    • Schnare, M.N.1    Damberger, S.H.2    Gray, M.W.3    Gutell, R.R.4
  • 6
    • 0031866668 scopus 로고    scopus 로고
    • The signal recognition particle database (SRPDB)
    • Larsen, N., Samuelsson, T., and Zwieb, C. (1998) The signal recognition particle database (SRPDB) Nucleic Acids Res. 26, 177-178
    • (1998) Nucleic Acids Res. , vol.26 , pp. 177-178
    • Larsen, N.1    Samuelsson, T.2    Zwieb, C.3
  • 7
    • 0031841911 scopus 로고    scopus 로고
    • The ribonuclease P database
    • Brown, J. W. (1998) The ribonuclease P database Nucleic Acids Res. 26, 351-352
    • (1998) Nucleic Acids Res. , vol.26 , pp. 351-352
    • Brown, J.W.1
  • 8
    • 0021256581 scopus 로고
    • Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing - A review
    • Waring, R. B. and Davies, R. W. (1984) Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing - A review Gene 28, 277-291
    • (1984) Gene , vol.28 , pp. 277-291
    • Waring, R.B.1    Davies, R.W.2
  • 9
    • 0028146967 scopus 로고
    • A comparative database of group i intron structures
    • Damberger, S. H. and Gutell, R. R. (1994) A comparative database of group I intron structures Nucleic Acids Res. 22, 3508-3510
    • (1994) Nucleic Acids Res. , vol.22 , pp. 3508-3510
    • Damberger, S.H.1    Gutell, R.R.2
  • 10
    • 0034023892 scopus 로고    scopus 로고
    • RNA motifs that determine specificity between an viral replicase and its promoter
    • Kim, C. H., Kao, C. C., and Tinoco, I. (2000) RNA motifs that determine specificity between an viral replicase and its promoter Nat. Struct. Biol. 7, 415-423
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 415-423
    • Kim, C.H.1    Kao, C.C.2    Tinoco, I.3
  • 12
    • 0037470595 scopus 로고    scopus 로고
    • Refined solution structure of the iron-responsive element RNA using residual dipolar couplings
    • McCallum, S. A. and Pardi, A. (2003) Refined solution structure of the iron-responsive element RNA using residual dipolar couplings J. Mol. Biol. 326, 1037-1050
    • (2003) J. Mol. Biol. , vol.326 , pp. 1037-1050
    • McCallum, S.A.1    Pardi, A.2
  • 14
    • 0036340611 scopus 로고    scopus 로고
    • Role of an essential triloop hairpin and flanking structures in the 3′-untranslated region of alfalfa mosaic virus RNA in in vitro transcription
    • Olsthoorn, R. C. L. and Bol, J. F. (2002) Role of an essential triloop hairpin and flanking structures in the 3′-untranslated region of alfalfa mosaic virus RNA in in vitro transcription J. Virol. 76, 8747-8756
    • (2002) J. Virol. , vol.76 , pp. 8747-8756
    • Olsthoorn, R.C.L.1    Bol, J.F.2
  • 15
    • 0242363180 scopus 로고    scopus 로고
    • A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA-protein interactions
    • Haasnoot, P. C. J., Bol, J. F., and Olsthoorn, R. C. L. (2003) A plant virus replication system to assay the formation of RNA pseudotriloop motifs in RNA-protein interactions Proc. Natl. Acad. Sci. U.S.A. 100, 12596-12600
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 12596-12600
    • Haasnoot, P.C.J.1    Bol, J.F.2    Olsthoorn, R.C.L.3
  • 17
    • 0024295554 scopus 로고
    • Characterization of RNA hairpin loop stability
    • Groebe, D. R. and Uhlenbeck, O. C. (1988) Characterization of RNA hairpin loop stability Nucleic Acids Res. 16, 11725-11735
    • (1988) Nucleic Acids Res. , vol.16 , pp. 11725-11735
    • Groebe, D.R.1    Uhlenbeck, O.C.2
  • 19
    • 0033576289 scopus 로고    scopus 로고
    • Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloops combinatorial library
    • Shu, Z. and Bevilacqua, P. C. (1999) Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloops combinatorial library Biochemistry 38, 15369-15379
    • (1999) Biochemistry , vol.38 , pp. 15369-15379
    • Shu, Z.1    Bevilacqua, P.C.2
  • 21
    • 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. C., 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. U.S.A. 101, 7287-7292
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.C.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 22
    • 0028071557 scopus 로고
    • Collection of small-subunit (16s- and 16s-like) ribosomal-RNA structures: 1994
    • Gutell, R. R. (1994) Collection of small-subunit (16s- and 16s-like) ribosomal-RNA structures: 1994 Nucleic Acids Res. 22, 3502-3507
    • (1994) Nucleic Acids Res. , vol.22 , pp. 3502-3507
    • Gutell, R.R.1
  • 24
    • 0024428420 scopus 로고
    • Comparative and functional-anatomy of group-Ii catalytic introns - A review
    • Michel, F., Umesono, K., and Ozeki, H. (1989) Comparative and functional-anatomy of group-Ii catalytic introns - A review Gene 82, 5-30
    • (1989) Gene , vol.82 , pp. 5-30
    • Michel, F.1    Umesono, K.2    Ozeki, H.3
  • 25
    • 43949091791 scopus 로고    scopus 로고
    • Structures, kinetics, thermodynamics, and biological functions of RNA hairpins
    • Bevilacqua, P. C. and Blose, J. M. (2008) Structures, kinetics, thermodynamics, and biological functions of RNA hairpins Annu. Rev. Phys. Chem. 59, 79-103
    • (2008) Annu. Rev. Phys. Chem. , vol.59 , pp. 79-103
    • Bevilacqua, P.C.1    Blose, J.M.2
  • 26
    • 33750214512 scopus 로고    scopus 로고
    • A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
    • Lu, Z. J., Turner, D. H., and Mathews, D. H. (2006) A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation Nucleic Acids Res. 34, 4912-4924
    • (2006) Nucleic Acids Res. , vol.34 , pp. 4912-4924
    • Lu, Z.J.1    Turner, D.H.2    Mathews, D.H.3
  • 27
    • 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
  • 28
    • 34247526026 scopus 로고    scopus 로고
    • Nearest neighbor parameters for inosine-uridine pairs in RNA duplexes
    • Wright, D. J., Rice, J. L., Yanker, D. M., and Znosko, B. M. (2007) Nearest neighbor parameters for inosine-uridine pairs in RNA duplexes Biochemistry 46, 4625-4634
    • (2007) Biochemistry , vol.46 , pp. 4625-4634
    • Wright, D.J.1    Rice, J.L.2    Yanker, D.M.3    Znosko, B.M.4
  • 29
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • Xia, T., SantaLucia, J., Jr., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., and Turner, D. H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs Biochemistry 37, 14719-14735
    • (1998) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    Santalucia Jr., J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6    Cox, C.7    Turner, D.H.8
  • 32
    • 0025942059 scopus 로고
    • A thermodynamic study of unusually stable RNA and DNA hairpins
    • Antao, V. P., Lai, S. Y., and Tinoco, I. (1991) A thermodynamic study of unusually stable RNA and DNA hairpins Nucleic Acids Res. 19, 5901-5905
    • (1991) Nucleic Acids Res. , vol.19 , pp. 5901-5905
    • Antao, V.P.1    Lai, S.Y.2    Tinoco, I.3
  • 33
    • 0025811124 scopus 로고
    • Structure of an unusually stable RNA hairpin
    • Varani, G., Cheong, C., and Tinoco, I., Jr. (1991) Structure of an unusually stable RNA hairpin Biochemistry 30, 3280-3289
    • (1991) Biochemistry , vol.30 , pp. 3280-3289
    • Varani, G.1    Cheong, C.2    Tinoco Jr., I.3
  • 34
    • 0026423027 scopus 로고
    • Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops
    • Heus, H. A. and Pardi, A. (1991) Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops Science 253, 191-194
    • (1991) Science , vol.253 , pp. 191-194
    • Heus, H.A.1    Pardi, A.2
  • 35
    • 0026593806 scopus 로고
    • Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
    • Antao, V. P. and Tinoco, I. (1992) Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops Nucleic Acids Res. 20, 819-824
    • (1992) Nucleic Acids Res. , vol.20 , pp. 819-824
    • Antao, V.P.1    Tinoco, I.2
  • 36
    • 0034646572 scopus 로고    scopus 로고
    • Experimental and computational studies of the G[UUCG]C RNA tetraloop
    • Williams, D. J. and Hall, K. B. (2000) Experimental and computational studies of the G[UUCG]C RNA tetraloop J. Mol. Biol. 297, 10445-11061
    • (2000) J. Mol. Biol. , vol.297 , pp. 10445-11061
    • Williams, D.J.1    Hall, K.B.2
  • 37
    • 0034002687 scopus 로고    scopus 로고
    • A test of the model to predict unusually stable RNA hairpin loop stability
    • Dale, T., Smith, R., and Serra, M. J. (2000) A test of the model to predict unusually stable RNA hairpin loop stability RNA 6, 608-615
    • (2000) RNA , vol.6 , pp. 608-615
    • Dale, T.1    Smith, R.2    Serra, M.J.3
  • 38
    • 0037044315 scopus 로고    scopus 로고
    • Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions
    • Proctor, D. J., Schaak, J. E., Bevilacqua, J. M., Falzone, C. J., and Bevilacqua, P. C. (2002) Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions Biochemistry 41, 12062-12075
    • (2002) Biochemistry , vol.41 , pp. 12062-12075
    • Proctor, D.J.1    Schaak, J.E.2    Bevilacqua, J.M.3    Falzone, C.J.4    Bevilacqua, P.C.5
  • 39
    • 75149139054 scopus 로고    scopus 로고
    • Thermodynamic characterization of naturally occurrring RNA tetraloops
    • Sheehy, J. P., Davis, A. R., and Znosko, B. M. (2010) Thermodynamic characterization of naturally occurrring RNA tetraloops RNA 16, 417-429
    • (2010) RNA , vol.16 , pp. 417-429
    • Sheehy, J.P.1    Davis, A.R.2    Znosko, B.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.