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Volumn 6, Issue 4, 2000, Pages 608-615

A test of the model to predict unusually stable RNA hairpin loop stability

Author keywords

Nearest neighbor parameters; RNA secondary structure

Indexed keywords

RNA;

EID: 0034002687     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1017/S1355838200992495     Document Type: Article
Times cited : (45)

References (41)
  • 1
    • 0025942059 scopus 로고
    • A thermodynamic study of unusually stable RNA and DNA hairpins
    • Antao VP, Lai SY, Tinoco I Jr. 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., Jr.3
  • 2
    • 0026593806 scopus 로고
    • Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
    • Antao VP, Tinoco I Jr. 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., Jr.2
  • 6
    • 0025863844 scopus 로고
    • Ribosomal RNA identity element for A-chain recognition and catalysis
    • Endo Y, Gluck A, Wool IG. 1991. Ribosomal RNA identity element for A-chain recognition and catalysis. J Mol Biol 221:193-207.
    • (1991) J Mol Biol , vol.221 , pp. 193-207
    • Endo, Y.1    Gluck, A.2    Wool, I.G.3
  • 7
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferré D'Amaré AR, Zhou K, Doudna JA. 1998. Crystal structure of a hepatitis delta virus ribozyme. Nature 395:567-574.
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferré D'Amaré, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 9
    • 0026704534 scopus 로고
    • Ribosomal RNA identity element for ricin α-chain recognition and catalysis
    • Gluck A, Endo Y, Wool IG. 1992. Ribosomal RNA identity element for ricin α-chain recognition and catalysis. J Mol Biol 226:411-424.
    • (1992) J Mol Biol , vol.226 , pp. 411-424
    • Gluck, A.1    Endo, Y.2    Wool, I.G.3
  • 10
    • 0032500731 scopus 로고    scopus 로고
    • A preorganized active site in the crystal structure of the Tetrahymena ribozyme
    • Golden BL, Gooding AR, Podell TR, Cech TR. 1998. A preorganized active site in the crystal structure of the Tetrahymena ribozyme. Science 282:259-264.
    • (1998) Science , vol.282 , pp. 259-264
    • Golden, B.L.1    Gooding, A.R.2    Podell, T.R.3    Cech, T.R.4
  • 11
    • 0024579255 scopus 로고
    • Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide
    • Grobe DR, Uhlenbeck OC. 1989. Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide. Biochemistry 28:742-747.
    • (1989) Biochemistry , vol.28 , pp. 742-747
    • Grobe, D.R.1    Uhlenbeck, O.C.2
  • 12
    • 0028071557 scopus 로고
    • Collection of small subunit (16S and 16S-like) ribosomal RNA structures
    • Gutell RR. 1994. Collection of small subunit (16S and 16S-like) ribosomal RNA structures. Nucleic Acids Res 22:3502-3507.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3502-3507
    • Gutell, R.R.1
  • 13
    • 0027225783 scopus 로고
    • A compilation of large subunit (23S and 23S-like) ribosomal RNA structures
    • Gutell RR, Gray MW, Schnare MN. 1993. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures. 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
  • 14
    • 0025305796 scopus 로고
    • DNA cleavage catalyzed by the ribozyme from Tetrahymena
    • Herschlag D, Cech TR. 1990. DNA cleavage catalyzed by the ribozyme from Tetrahymena. Nature 344:405-409.
    • (1990) Nature , vol.344 , pp. 405-409
    • Herschlag, D.1    Cech, T.R.2
  • 15
    • 0026423027 scopus 로고
    • Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops
    • Heus HA, 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
  • 16
    • 0027444622 scopus 로고
    • An NMR study of the HIV-1 TAR element hairpin
    • Jaeger J, Tinoco I Jr. 1993. An NMR study of the HIV-1 TAR element hairpin. Biochemistry 32:12522-12530.
    • (1993) Biochemistry , vol.32 , pp. 12522-12530
    • Jaeger, J.1    Tinoco I., Jr.2
  • 17
    • 0028294458 scopus 로고
    • Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
    • Jaeger L, Michel F, Westhof E. 1994. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J Mol Biol 236:1271-1276.
    • (1994) J Mol Biol , vol.236 , pp. 1271-1276
    • Jaeger, L.1    Michel, F.2    Westhof, E.3
  • 18
    • 0029283999 scopus 로고
    • GNRA tetraloops make a U-turn
    • Jucker FM, 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
  • 19
    • 0031570344 scopus 로고    scopus 로고
    • Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III)
    • Kieft JS, Tinoco I Jr. 1997. Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III). Structure 5:713-721.
    • (1997) Structure , vol.5 , pp. 713-721
    • Kieft, J.S.1    Tinoco I., Jr.2
  • 21
    • 0029861968 scopus 로고    scopus 로고
    • A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data
    • Laing LG, Hall KB. 1996. A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data. Biochemistry 35:13586-13596.
    • (1996) Biochemistry , vol.35 , pp. 13586-13596
    • Laing, L.G.1    Hall, K.B.2
  • 22
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews DH, Sabina J, Zuker M, Turner DH. 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
  • 23
    • 0029805937 scopus 로고    scopus 로고
    • Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: Solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing
    • McDowell JA, Turner DH. 1996. Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: Solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing. Biochemistry 35:14077-14089.
    • (1996) Biochemistry , vol.35 , pp. 14077-14089
    • McDowell, J.A.1    Turner, D.H.2
  • 24
    • 0028301674 scopus 로고
    • GAAA tetraloop and conserved bulge stabilize tertiary structure of group I intron domain
    • Murphy FL, Cech TR. 1994. GAAA tetraloop and conserved bulge stabilize tertiary structure of group I intron domain. J Mol Biol 236:49-63.
    • (1994) J Mol Biol , vol.236 , pp. 49-63
    • Murphy, F.L.1    Cech, T.R.2
  • 25
    • 0024829458 scopus 로고
    • Genetic methods for identification and characterization of RNA-RNA and RNA-protein interactions
    • Parker R. 1989. Genetic methods for identification and characterization of RNA-RNA and RNA-protein interactions. Methods Enzymol 180:510-517.
    • (1989) Methods Enzymol , vol.180 , pp. 510-517
    • Parker, R.1
  • 26
    • 0028063567 scopus 로고
    • Three-dimensional structure of a hammerhead ribozyme
    • Pley HW, Flaherty KM, McKay DB. 1994. Three-dimensional structure of a hammerhead ribozyme. Nature 372:68-74.
    • (1994) Nature , vol.372 , pp. 68-74
    • Pley, H.W.1    Flaherty, K.M.2    McKay, D.B.3
  • 28
    • 0026562625 scopus 로고
    • Context dependence of hydrogen bonding free energy revealed by substitutions in an RNA hairpin
    • SantaLucia J Jr, Kierzek R, Turner DH. 1992. Context dependence of hydrogen bonding free energy revealed by substitutions in an RNA hairpin. Science 256:217-219.
    • (1992) Science , vol.256 , pp. 217-219
    • SantaLucia J., Jr.1    Kierzek, R.2    Turner, D.H.3
  • 29
    • 0029073091 scopus 로고
    • The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
    • Scott WG, Finch JT, Klug A. 1995. The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage. Cell 81:991-1002.
    • (1995) Cell , vol.81 , pp. 991-1002
    • Scott, W.G.1    Finch, J.T.2    Klug, A.3
  • 30
    • 0027992843 scopus 로고
    • A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides
    • Serra MJ, Axenson TJ, Turner DH. 1994. A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry 33:14289-14296.
    • (1994) Biochemistry , vol.33 , pp. 14289-14296
    • Serra, M.J.1    Axenson, T.J.2    Turner, D.H.3
  • 35
    • 0025061676 scopus 로고
    • Tetraloops and RNA folding
    • Uhlenbeck OC. 1990. Tetraloops and RNA folding. Nature 346:613-614.
    • (1990) Nature , vol.346 , pp. 613-614
    • Uhlenbeck, O.C.1
  • 36
    • 0032500734 scopus 로고    scopus 로고
    • Ribosome architectural diversity made visible
    • Westhof E, Michel F. 1999. Ribosome architectural diversity made visible. Science 282:251-252.
    • (1999) Science , vol.282 , pp. 251-252
    • Westhof, E.1    Michel, F.2
  • 37
    • 0002277269 scopus 로고
    • Probing RNA structure, function, and history by comparative analysis
    • Gesteland RF, Atkins JF, eds. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press
    • Woese CR, Pace HR. 1993. Probing RNA structure, function, and history by comparative analysis. In: Gesteland RF, Atkins JF, eds. The RNA world. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, pp 91-117.
    • (1993) The RNA World , pp. 91-117
    • Woese, C.R.1    Pace, H.R.2
  • 38
    • 0025047647 scopus 로고
    • Architecture of ribosomal RNA: Constraints on the sequence of tetraloops
    • Woese CR, Winker S, Gutell RR. 1990. Architecture of ribosomal RNA: Constraints on the sequence of tetraloops. Proc Natl Acad Sd USA 87:8467-8471.
    • (1990) Proc Natl Acad Sd USA , vol.87 , pp. 8467-8471
    • Woese, C.R.1    Winker, S.2    Gutell, R.R.3
  • 39
    • 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, Burkhard ME, Kierek R, Schroeder SJ, Jiao X, Cox C, Turner DH. 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 J., Jr.2    Burkhard, M.E.3    Kierek, R.4    Schroeder, S.J.5    Jiao, X.6    Cox, C.7    Turner, D.H.8
  • 40
    • 0022649937 scopus 로고
    • The intervening sequence RNA on Tetrahymena is an enzyme
    • Zaug B, Cech T. 1986. The intervening sequence RNA on Tetrahymena is an enzyme. Science 231:470-475.
    • (1986) Science , vol.231 , pp. 470-475
    • Zaug, B.1    Cech, T.2
  • 41
    • 0026775308 scopus 로고
    • Conformity of RNAs that interact with tetranucleotide loop binding proteins
    • Zweib C. 1992. Conformity of RNAs that interact with tetranucleotide loop binding proteins. Nucleic Acids Res 20:4397-4400.
    • (1992) Nucleic Acids Res , vol.20 , pp. 4397-4400
    • Zweib, C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.