메뉴 건너뛰기




Volumn 288, Issue 5, 1999, Pages 911-940

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

Author keywords

Enzymatic cleavage; Flavin mononucleotide cleavage; Free energy minimization; Nearest neighbor parameters; RNA secondary structure

Indexed keywords

RNA;

EID: 0033591465     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2700     Document Type: Article
Times cited : (3365)

References (101)
  • 1
    • 0026593806 scopus 로고
    • Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
    • Antao V. P., Tinoco I. Jr. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucl. Acids Res. 20:1992;819-824.
    • (1992) Nucl. Acids Res. , vol.20 , pp. 819-824
    • Antao, V.P.1    Tinoco I., Jr.2
  • 2
    • 0025942059 scopus 로고
    • A thermodynamic study of unusually stable RNA and DNA hairpins
    • Antao V. P., Lai S. Y., Tinoco I. Jr. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucl. Acids Res. 19:1991;5901-5905.
    • (1991) Nucl. Acids Res. , vol.19 , pp. 5901-5905
    • Antao, V.P.1    Lai, S.Y.2    Tinoco I., Jr.3
  • 3
    • 0027434244 scopus 로고
    • Thermal unfolding of a group I ribozyme: The low temperature transition is primarily a disruption of tertiary structure
    • Banerjee A. R., Jaeger J. A., Turner D. H. Thermal unfolding of a group I ribozyme: the low temperature transition is primarily a disruption of tertiary structure. Biochemistry. 32:1993;153-163.
    • (1993) Biochemistry , vol.32 , pp. 153-163
    • Banerjee, A.R.1    Jaeger, J.A.2    Turner, D.H.3
  • 4
    • 0032506045 scopus 로고    scopus 로고
    • Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin
    • Bevilacqua J. M., Bevilacqua P. C. Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin. Biochemistry. 37:1998;15877-15884.
    • (1998) Biochemistry , vol.37 , pp. 15877-15884
    • Bevilacqua, J.M.1    Bevilacqua, P.C.2
  • 6
    • 0031841911 scopus 로고    scopus 로고
    • The ribonuclease P database
    • Brown J. W. The ribonuclease P database. Nucl. Acids Res. 26:1998;351-352.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 351-352
    • Brown, J.W.1
  • 7
    • 0031029398 scopus 로고    scopus 로고
    • Flavin-dependent photocleavage of RNA at G·U base pairs
    • Burgstaller P., Famulok M. Flavin-dependent photocleavage of RNA at G·U base pairs. J. Am. Chem. Soc. 119:1997;1137-1138.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 1137-1138
    • Burgstaller, P.1    Famulok, M.2
  • 8
    • 0030873521 scopus 로고    scopus 로고
    • Isoalloxazine derivatives promote photocleavage of natural RNAs at G·U base pairs embedded within helices
    • Burgstaller P., Hermann T., Huber C., Westhof E., Famulok M. Isoalloxazine derivatives promote photocleavage of natural RNAs at G·U base pairs embedded within helices. Nucl. Acids Res. 25:1997;4018-4027.
    • (1997) Nucl. Acids Res. , vol.25 , pp. 4018-4027
    • Burgstaller, P.1    Hermann, T.2    Huber, C.3    Westhof, E.4    Famulok, M.5
  • 9
    • 0031463994 scopus 로고    scopus 로고
    • Solution structure of a GAAA tetraloop receptor RNA
    • Butcher S. E., Dieckmann T., Feigon J. Solution structure of a GAAA tetraloop receptor RNA. EMBO J. 16:1997;7490-7499.
    • (1997) EMBO J. , vol.16 , pp. 7490-7499
    • Butcher, S.E.1    Dieckmann, T.2    Feigon, J.3
  • 11
    • 0030856333 scopus 로고    scopus 로고
    • Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain
    • Correl C. C., Freeborn B., Moore P. B., Steitz T. A. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell. 91:1997;705-712.
    • (1997) Cell , vol.91 , pp. 705-712
    • Correl, C.C.1    Freeborn, B.2    Moore, P.B.3    Steitz, T.A.4
  • 12
    • 0028921811 scopus 로고
    • Frequent use of the same tertiary motif by self-folding RNAs
    • Costa M., Michel F. Frequent use of the same tertiary motif by self-folding RNAs. EMBO J. 14:1995;1276-1285.
    • (1995) EMBO J. , vol.14 , pp. 1276-1285
    • Costa, M.1    Michel, F.2
  • 13
    • 0016169138 scopus 로고
    • The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA
    • Crothers D. M., Cole P. E., Hilbers C. W., Schulman R. G. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J. Mol. Biol. 87:1974;63-88.
    • (1974) J. Mol. Biol , vol.87 , pp. 63-88
    • Crothers, D.M.1    Cole, P.E.2    Hilbers, C.W.3    Schulman, R.G.4
  • 14
    • 0028146967 scopus 로고
    • A comparative database of group I intron structures
    • Damberger S. H., Gutell R. R. A comparative database of group I intron structures. Nucl. Acids Res. 22:1994;3508-3510.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 3508-3510
    • Damberger, S.H.1    Gutell, R.R.2
  • 17
    • 0015526994 scopus 로고
    • Free energy of imperfect nucleic acid helices. I. The bulge defect
    • Fink T. R., Crothers D. M. Free energy of imperfect nucleic acid helices. I. The bulge defect. J. Mol. Biol. 66:1972;1-12.
    • (1972) J. Mol. Biol. , vol.66 , pp. 1-12
    • Fink, T.R.1    Crothers, D.M.2
  • 18
  • 19
    • 0027640931 scopus 로고
    • Genetic algorithms: Principles of natural selection applied to computation
    • Forrest S. Genetic algorithms: principles of natural selection applied to computation. Science. 261:1993;872-878.
    • (1993) Science , vol.261 , pp. 872-878
    • Forrest, S.1
  • 21
    • 0001613489 scopus 로고
    • Effects of 3′ dangling end stacking on the stability of GGCC and CCGG double helices
    • Freier S. M., Burger B. J., Alkema D., Neilson T., Turner D. H. Effects of 3′ dangling end stacking on the stability of GGCC and CCGG double helices. Biochemistry. 22:1983;6198-6206.
    • (1983) Biochemistry , vol.22 , pp. 6198-6206
    • Freier, S.M.1    Burger, B.J.2    Alkema, D.3    Neilson, T.4    Turner, D.H.5
  • 23
    • 0023040892 scopus 로고
    • Free energy contributions of G·U and other terminal mismatches to helix stability
    • Freier S. M., Kierzek R., Caruthers M. H., Neilson T., Turner D. H. Free energy contributions of G·U and other terminal mismatches to helix stability. Biochemistry. 25:1986a;3209-3213.
    • (1986) Biochemistry , vol.25 , pp. 3209-3213
    • Freier, S.M.1    Kierzek, R.2    Caruthers, M.H.3    Neilson, T.4    Turner, D.H.5
  • 25
    • 0023040885 scopus 로고
    • Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: An empirical estimate of the energetics of hydrogen bonds in nucleic acids
    • Freier S. M., Sugimoto N., Sinclair A., Alkema D., Neilson T., Kierzek R., Caruthers M. H., Turner D. H. Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids. Biochemistry. 25:1986c;3214-3219.
    • (1986) Biochemistry , vol.25 , pp. 3214-3219
    • Freier, S.M.1    Sugimoto, N.2    Sinclair, A.3    Alkema, D.4    Neilson, T.5    Kierzek, R.6    Caruthers, M.H.7    Turner, D.H.8
  • 26
    • 0028823370 scopus 로고
    • An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints
    • Gaspin C., Westhof E. An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints. J. Mol. Biol. 254:1995;163-174.
    • (1995) J. Mol. Biol. , vol.254 , pp. 163-174
    • Gaspin, C.1    Westhof, E.2
  • 28
    • 0024295554 scopus 로고
    • Characterization of RNA hairpin loop stability
    • Groebe D. R., Uhlenbeck O. C. Characterization of RNA hairpin loop stability. Nucl. Acids Res. 16:1988;11725-11735.
    • (1988) Nucl. Acids Res. , vol.16 , pp. 11725-11735
    • Groebe, D.R.1    Uhlenbeck, O.C.2
  • 29
    • 0024579255 scopus 로고
    • Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide
    • Groebe D. R., Uhlenbeck O. C. Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide. Biochemistry. 28:1989;742-747.
    • (1989) Biochemistry , vol.28 , pp. 742-747
    • Groebe, D.R.1    Uhlenbeck, O.C.2
  • 30
    • 0029061125 scopus 로고
    • The computer simulation of RNA folding pathways using a genetic algorithm
    • Gultyaev A. P., van Batenburg F. H. D., Pleij C. W. A. The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol. 250:1995;37-51.
    • (1995) J. Mol. Biol. , vol.250 , pp. 37-51
    • Gultyaev, A.P.1    Van Batenburg, F.H.D.2    Pleij, C.W.A.3
  • 31
    • 0028071557 scopus 로고
    • Collection of small subunit (16 S- And 16 S-like) ribosomal RNA structures
    • Gutell R. R. Collection of small subunit (16 S- and 16 S-like) ribosomal RNA structures. Nucl. Acids Res. 22:1994;3502-3507.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 3502-3507
    • Gutell, R.R.1
  • 32
    • 0027225783 scopus 로고
    • A compilation of large subunit (23 S- And 23 S-like) ribosomal RNA structures
    • Gutell R. R., Gray M. W., Schnare M. N. A compilation of large subunit (23 S- and 23 S-like) ribosomal RNA structures. Nucl. Acids Res. 21:1993;3055-3074.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 3055-3074
    • Gutell, R.R.1    Gray, M.W.2    Schnare, M.N.3
  • 33
    • 0031010235 scopus 로고    scopus 로고
    • Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by photoaffinity crosslinking
    • Harris M. E., Kazantchev A. V., Chen J. L., Pace N. R. Analysis of the tertiary structure of the ribonuclease P ribozyme-substrate complex by photoaffinity crosslinking. RNA. 3:1997;561-574.
    • (1997) RNA , vol.3 , pp. 561-574
    • Harris, M.E.1    Kazantchev, A.V.2    Chen, J.L.3    Pace, N.R.4
  • 38
    • 0031576996 scopus 로고    scopus 로고
    • Assessing the reliability of RNA folding using statistical mechanics
    • Huynen M., Gutell R., Konings D. Assessing the reliability of RNA folding using statistical mechanics. J. Mol. Biol. 267:1997;1104-1112.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1104-1112
    • Huynen, M.1    Gutell, R.2    Konings, D.3
  • 39
    • 0031414413 scopus 로고    scopus 로고
    • Kinetic and secondary structure analysis of Naegleria anderson: GIR1, a group I ribozyme whose putative biological function is site-specific hydrolysis
    • Jabri E., Aigner S., Cech T. R. Kinetic and secondary structure analysis of Naegleria anderson: GIR1, a group I ribozyme whose putative biological function is site-specific hydrolysis. Biochemistry. 36:1997;16345-16354.
    • (1997) Biochemistry , vol.36 , pp. 16345-16354
    • Jabri, E.1    Aigner, S.2    Cech, T.R.3
  • 40
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations. I. The theory of linear systems
    • Jacobson H., Stockmayer W. H. Intramolecular reaction in polycondensations. I. The theory of linear systems. J. Chem. Phys. 18:1950;1600-1606.
    • (1950) J. Chem. Phys. , vol.18 , pp. 1600-1606
    • Jacobson, H.1    Stockmayer, W.H.2
  • 41
  • 42
    • 0027433710 scopus 로고
    • Monitoring of cooperative unfolding of the sunY group I intron of bacteriophage T4
    • Jaeger L., Westhof E., Michel F. Monitoring of cooperative unfolding of the sunY group I intron of bacteriophage T4. J. Mol. Biol. 234:1993;331-346.
    • (1993) J. Mol. Biol , vol.234 , pp. 331-346
    • Jaeger, L.1    Westhof, E.2    Michel, F.3
  • 43
    • 0028294458 scopus 로고
    • Involvement of a GNRA tetraloop in long-range RNA tertiary interactions
    • Jaeger L., Michel F., Westhof E. Involvement of a GNRA tetraloop in long-range RNA tertiary interactions. J. Mol. Biol. 236:1994;1271-1276.
    • (1994) J. Mol. Biol. , vol.236 , pp. 1271-1276
    • Jaeger, L.1    Michel, F.2    Westhof, E.3
  • 44
    • 0024827733 scopus 로고
    • Phylogenetic comparative analysis of RNA secondary structure
    • James B. D., Olsen G. J., Pace N. R. Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol. 180:1989;227-239.
    • (1989) Methods Enzymol. , vol.180 , pp. 227-239
    • James, B.D.1    Olsen, G.J.2    Pace, N.R.3
  • 45
    • 0028866812 scopus 로고
    • Solution structure of the CUUG hairpin loop - A novel RNA tetraloop motif
    • Jucker F. M., Pardi A. Solution structure of the CUUG hairpin loop - a novel RNA tetraloop motif. Biochemistry. 34:1995;14416-14427.
    • (1995) Biochemistry , vol.34 , pp. 14416-14427
    • Jucker, F.M.1    Pardi, A.2
  • 46
    • 0021970326 scopus 로고
    • Secondary structure of a 345-base RNA fragment covering the S8/S15 protein binding domain of Escherichia coli 16 S ribosomal RNA
    • Kean J. M., Draper D. E. Secondary structure of a 345-base RNA fragment covering the S8/S15 protein binding domain of Escherichia coli 16 S ribosomal RNA. Biochemistry. 24:1985;5052-5061.
    • (1985) Biochemistry , vol.24 , pp. 5052-5061
    • Kean, J.M.1    Draper, D.E.2
  • 47
    • 0029855518 scopus 로고    scopus 로고
    • Thermodynamics of coaxially stacked helices with GA and CC mismatches
    • Kim J., Walter A. E., Turner D. H. Thermodynamics of coaxially stacked helices with GA and CC mismatches. Biochemistry. 35:1996;13753-13761.
    • (1996) Biochemistry , vol.35 , pp. 13753-13761
    • Kim, J.1    Walter, A.E.2    Turner, D.H.3
  • 48
    • 0024841809 scopus 로고
    • Enzymatic approaches to probing RNA secondary and tertiary structure
    • Knapp G. Enzymatic approaches to probing RNA secondary and tertiary structure. Methods Enzymol. 180:1989;192-212.
    • (1989) Methods Enzymol. , vol.180 , pp. 192-212
    • Knapp, G.1
  • 49
    • 0028234517 scopus 로고
    • Thermodynamics of RNA folding in a conserved ribosomal RNA domain
    • Laing L. G., Draper D. E. Thermodynamics of RNA folding in a conserved ribosomal RNA domain. J. Mol. Biol. 237:1994;560-576.
    • (1994) J. Mol. Biol. , vol.237 , pp. 560-576
    • Laing, L.G.1    Draper, D.E.2
  • 50
    • 0031866668 scopus 로고    scopus 로고
    • The signal recognition particle database (SRPDB)
    • Larsen N., Samuelsson T., Zwieb C. The signal recognition particle database (SRPDB). Nucl. Acids Res. 26:1998;177-178.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 177-178
    • Larsen, N.1    Samuelsson, T.2    Zwieb, C.3
  • 51
    • 0030452773 scopus 로고    scopus 로고
    • New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: A complete 3D model of theTetrahymena thermophila ribozyme
    • Lehnert V., Jaeger L., Michel F., Westhof E. New loop-loop tertiary interactions in self-splicing introns of subgroup IC and ID: a complete 3D model of theTetrahymena thermophila ribozyme. Chem. Biol. 3:1996;993-1009.
    • (1996) Chem. Biol. , vol.3 , pp. 993-1009
    • Lehnert, V.1    Jaeger, L.2    Michel, F.3    Westhof, E.4
  • 52
    • 0025186882 scopus 로고
    • Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides
    • Longfellow C. E., Kierzek R., Turner D. H. Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry. 29:1990;278-285.
    • (1990) Biochemistry , vol.29 , pp. 278-285
    • Longfellow, C.E.1    Kierzek, R.2    Turner, D.H.3
  • 53
    • 0039161225 scopus 로고    scopus 로고
    • Thermodynamic prediction of conserved secondary structure: Application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein
    • Lück R., Steger G., Riesner D. Thermodynamic prediction of conserved secondary structure: application to the RRE element of HIV, the tRNA-like element of CMV and the mRNA of prion protein. J. Mol. Biol. 258:1996;813-826.
    • (1996) J. Mol. Biol. , vol.258 , pp. 813-826
    • Lück, R.1    Steger, G.2    Riesner, D.3
  • 54
    • 0032546728 scopus 로고    scopus 로고
    • Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis
    • Massire C., Jaeger L., Westhof E. Derivation of the three-dimensional architecture of bacterial ribonuclease P RNAs from comparative sequence analysis. J. Mol. Biol. 279:1998;773-793.
    • (1998) J. Mol. Biol. , vol.279 , pp. 773-793
    • Massire, C.1    Jaeger, L.2    Westhof, E.3
  • 55
    • 0031014702 scopus 로고    scopus 로고
    • Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element
    • Mathews D. H., Banerjee A. R., Luan D. D., Eickbush T. H., Turner D. H. Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. RNA. 3:1997;1-16.
    • (1997) RNA , vol.3 , pp. 1-16
    • Mathews, D.H.1    Banerjee, A.R.2    Luan, D.D.3    Eickbush, T.H.4    Turner, D.H.5
  • 56
    • 0004286966 scopus 로고    scopus 로고
    • An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters
    • N. B. Leontis, & J. Jr. SantaLucia. New York: American Chemical Society
    • Mathews D. H., Andre T. C., Kim J., Turner D. H., Zuker M. An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters. Leontis N. B., SantaLucia J. Jr. Molecular Modeling of Nucleic Acids. 1998;246-257 American Chemical Society, New York.
    • (1998) Molecular Modeling of Nucleic Acids , pp. 246-257
    • Mathews, D.H.1    Andre, T.C.2    Kim, J.3    Turner, D.H.4    Zuker, M.5
  • 57
    • 0025264854 scopus 로고
    • The equilibrium partition function and base-pair probabilities for RNA secondary structure
    • McCaskill J. S. The equilibrium partition function and base-pair probabilities for RNA secondary structure. Biopolymers. 29:1990;1105-1119.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 58
    • 0029805937 scopus 로고    scopus 로고
    • 2by two-dimensional NMR and simulated annealing
    • 2by two-dimensional NMR and simulated annealing. Biochemistry. 35:1996;14077-14089.
    • (1996) Biochemistry , vol.35 , pp. 14077-14089
    • McDowell, J.A.1    Turner, D.H.2
  • 60
    • 0033557138 scopus 로고    scopus 로고
    • Thermodynamics of RNA hairpins containing single internal mismatches
    • Meroueh M., Chow C. S. Thermodynamics of RNA hairpins containing single internal mismatches. Nucl. Acids Res. 27:1999;1118-1125.
    • (1999) Nucl. Acids Res. , vol.27 , pp. 1118-1125
    • Meroueh, M.1    Chow, C.S.2
  • 61
    • 0025678737 scopus 로고
    • Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis
    • Michel F., Westhof E. Modeling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216:1990;585-610.
    • (1990) J. Mol. Biol. , vol.216 , pp. 585-610
    • Michel, F.1    Westhof, E.2
  • 62
    • 0024428420 scopus 로고
    • Comparative and functional anatomy of group II catalytic introns - A review
    • Michel F., Umesono K., Ozeki H. Comparative and functional anatomy of group II catalytic introns - a review. Gene. 82:1989;5-30.
    • (1989) Gene , vol.82 , pp. 5-30
    • Michel, F.1    Umesono, K.2    Ozeki, H.3
  • 63
    • 0028897382 scopus 로고
    • Purine-purine mismatches in RNA helixes: Evidence for protonated G·A pairs and next-nearest neighbor effects
    • Morse S. E., Draper D. E. Purine-purine mismatches in RNA helixes: evidence for protonated G·A pairs and next-nearest neighbor effects. Nucl. Acids Res. 23:1995;302-306.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 302-306
    • Morse, S.E.1    Draper, D.E.2
  • 64
    • 0028301674 scopus 로고
    • GAAA tetra loop and conserved bulge stabilize tertiary structure of a group I intron domain
    • Murphy F. L., Cech T. R. GAAA tetra loop and conserved bulge stabilize tertiary structure of a group I intron domain. J. Mol. Biol. 236:1994;49-63.
    • (1994) J. Mol. Biol. , vol.236 , pp. 49-63
    • Murphy, F.L.1    Cech, T.R.2
  • 65
    • 0030271495 scopus 로고    scopus 로고
    • The development of microfabricated arrays for DNA sequencing and analysis
    • O'Donnell-Maloney M. J., Smith C. L., Cantor C. R. The development of microfabricated arrays for DNA sequencing and analysis. Trends Biotechnol. 14:1996;401-407.
    • (1996) Trends Biotechnol. , vol.14 , pp. 401-407
    • O'Donnell-Maloney, M.J.1    Smith, C.L.2    Cantor, C.R.3
  • 66
    • 0001899745 scopus 로고    scopus 로고
    • Probing RNA structure, function, and history by comparative analysis
    • R. F. Gesteland, T. R. Cech, & J. F. Atkins. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
    • Pace N. R., Thomas B. C., Woese C. R. Probing RNA structure, function, and history by comparative analysis. Gesteland R. F., Cech T. R., Atkins J. F. The RNA World. 1999;113-141 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
    • (1999) The RNA World , pp. 113-141
    • Pace, N.R.1    Thomas, B.C.2    Woese, C.R.3
  • 67
    • 0025900996 scopus 로고
    • Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops
    • Peritz A. E., Kierzek R., Sugimoto N., Turner D. H. Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops. Biochemistry. 30:1991;6428-6436.
    • (1991) Biochemistry , vol.30 , pp. 6428-6436
    • Peritz, A.E.1    Kierzek, R.2    Sugimoto, N.3    Turner, D.H.4
  • 68
    • 0028037302 scopus 로고
    • Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix
    • Pley H. W., Flaherty K. M., McKay D. B. Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature. 372:1994;111-114.
    • (1994) Nature , vol.372 , pp. 111-114
    • Pley, H.W.1    Flaherty, K.M.2    McKay, D.B.3
  • 69
    • 12044257509 scopus 로고
    • Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops
    • SantaLucia J. Jr, Kierzek R., Turner D. H. Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops. J. Am. Chem. Soc. 113:1991a;4313-4322.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 4313-4322
    • Santalucia J., Jr.1    Kierzek, R.2    Turner, D.H.3
  • 70
    • 0025925206 scopus 로고
    • Stabilities of consecutive A·C, C·C, G·G, U·C, and U·U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U·U and C·C+ pairs
    • SantaLucia J. Jr, Kierzek R., Turner D. H. Stabilities of consecutive A·C, C·C, G·G, U·C, and U·U mismatches in RNA internal loops: evidence for stable hydrogen-bonded U·U and C·C+ pairs. Biochemistry. 30:1991b;8242-8251.
    • (1991) Biochemistry , vol.30 , pp. 8242-8251
    • Santalucia J., Jr.1    Kierzek, R.2    Turner, D.H.3
  • 71
    • 0029877001 scopus 로고    scopus 로고
    • Comprehensive comparison of structural characteristics in Eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA
    • Schnare M. N., Damberger S. H., Gray M. W., Gutell R. R. Comprehensive comparison of structural characteristics in Eukaryotic cytoplasmic large subunit (23S-like) ribosomal RNA. J. Mol. Biol. 256:1996;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
  • 72
    • 0030299990 scopus 로고    scopus 로고
    • G·A and U·U mismatches can stabilize RNA internal loops of three nucleotides
    • Schroeder S., Kim J., Turner D. H. G·A and U·U mismatches can stabilize RNA internal loops of three nucleotides. Biochemistry. 35:1996;16105-16109.
    • (1996) Biochemistry , vol.35 , pp. 16105-16109
    • Schroeder, S.1    Kim, J.2    Turner, D.H.3
  • 73
    • 0029100233 scopus 로고
    • Predicting thermodynamic properties of RNA
    • Serra M. J., Turner D. H. Predicting thermodynamic properties of RNA. Methods Enzymol. 259:1995;242-261.
    • (1995) Methods Enzymol. , vol.259 , pp. 242-261
    • Serra, M.J.1    Turner, D.H.2
  • 75
    • 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 M. J., Axenson T. J., Turner D. H. A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry. 33:1994;14289-14296.
    • (1994) Biochemistry , vol.33 , pp. 14289-14296
    • Serra, M.J.1    Axenson, T.J.2    Turner, D.H.3
  • 77
    • 0020480145 scopus 로고
    • Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25
    • Speek M., Lind A. Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25. Nucl. Acids Res. 10:1982;947-965.
    • (1982) Nucl. Acids Res. , vol.10 , pp. 947-965
    • Speek, M.1    Lind, A.2
  • 79
    • 0023055766 scopus 로고
    • Energetics of internal GU mismatches in ribooligonucleotide helixes
    • Sugimoto N., Kierzek R., Freier S. M., Turner D. H. Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry. 25:1986;5755-5759.
    • (1986) Biochemistry , vol.25 , pp. 5755-5759
    • Sugimoto, N.1    Kierzek, R.2    Freier, S.M.3    Turner, D.H.4
  • 81
    • 0027295076 scopus 로고
    • Comparative structural-analysis of nuclear RNase-P RNAs from yeast
    • Tranguch A. J., Engelke D. R. Comparative structural-analysis of nuclear RNase-P RNAs from yeast. J. Biol. Chem. 268:1993;14045-14055.
    • (1993) J. Biol. Chem. , vol.268 , pp. 14045-14055
    • Tranguch, A.J.1    Engelke, D.R.2
  • 84
    • 0029025720 scopus 로고
    • An APL-programmed genetic algorithm for the prediction of RNA secondary structure
    • Van Batenburg F. H. D., Gultyaev A. P., Pleij C. W. A. An APL-programmed genetic algorithm for the prediction of RNA secondary structure. J. Theor. Biol. 174:1995;269-280.
    • (1995) J. Theor. Biol. , vol.174 , pp. 269-280
    • Van Batenburg, F.H.D.1    Gultyaev, A.P.2    Pleij, C.W.A.3
  • 85
    • 0025811124 scopus 로고
    • Structure of an unusually stable RNA hairpin
    • Varani G., Cheong C., Tinoco I. Jr. Structure of an unusually stable RNA hairpin. Biochemistry. 30:1991;3280-3289.
    • (1991) Biochemistry , vol.30 , pp. 3280-3289
    • Varani, G.1    Cheong, C.2    Tinoco I., Jr.3
  • 86
  • 87
    • 0028143014 scopus 로고
    • Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces
    • Walter A. E., Turner D. H. Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces. Biochemistry. 33:1994b;12715-12719.
    • (1994) Biochemistry , vol.33 , pp. 12715-12719
    • Walter, A.E.1    Turner, D.H.2
  • 88
    • 0028085964 scopus 로고
    • The stability and structure of tandem GA mismatches in RNA depend on closing base-pairs
    • Walter A. E., Wu M., Turner D. H. The stability and structure of tandem GA mismatches in RNA depend on closing base-pairs. Biochemistry. 33:1994c;11349-11354.
    • (1994) Biochemistry , vol.33 , pp. 11349-11354
    • Walter, A.E.1    Wu, M.2    Turner, D.H.3
  • 89
    • 0021256581 scopus 로고
    • Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing - A review
    • Waring R. B., Davies R. W. Assessment of a model for intron RNA secondary structure relevant to RNA self-splicing - a review. Gene. 28:1984;277-291.
    • (1984) Gene. , vol.28 , pp. 277-291
    • Waring, R.B.1    Davies, R.W.2
  • 90
    • 0027370486 scopus 로고
    • Major groove accessibility of RNA
    • Weeks K. M., Crothers D. M. Major groove accessibility of RNA. Science. 261:1993;1574-1577.
    • (1993) Science , vol.261 , pp. 1574-1577
    • Weeks, K.M.1    Crothers, D.M.2
  • 91
    • 0029907105 scopus 로고    scopus 로고
    • Phylogenetic analysis of tmRNA secondary structure
    • Williams K. P., Bartel D. P. Phylogenetic analysis of tmRNA secondary structure. RNA. 2:1996;1306-1310.
    • (1996) RNA , vol.2 , pp. 1306-1310
    • Williams, K.P.1    Bartel, D.P.2
  • 92
    • 0021012648 scopus 로고
    • Detailed analysis of the higher order structure of 16S-like ribosomal ribonucleic acids
    • Woese C. R., Gutell R. R., Gupta R., Noller H. F. Detailed analysis of the higher order structure of 16S-like ribosomal ribonucleic acids. Microbiol. Rev. 47:1983;621-669.
    • (1983) Microbiol. Rev. , vol.47 , pp. 621-669
    • Woese, C.R.1    Gutell, R.R.2    Gupta, R.3    Noller, H.F.4
  • 93
    • 0025047647 scopus 로고
    • Architecture of ribosomal RNA: Constraints on the sequence of "tetra-loops."
    • Woese C. R., Winker S., Gutell R. R. Architecture of ribosomal RNA: constraints on the sequence of "tetra-loops." Proc. Natl Acad. Sci. USA. 87:1990;8467-8471.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 8467-8471
    • Woese, C.R.1    Winker, S.2    Gutell, R.R.3
  • 94
    • 0028917227 scopus 로고
    • A periodic table of symmetric tandem mismatches in RNA
    • Wu M., McDowell J. A., Turner D. H. A periodic table of symmetric tandem mismatches in RNA. Biochemistry. 34:1995;3204-3211.
    • (1995) Biochemistry , vol.34 , pp. 3204-3211
    • Wu, M.1    McDowell, J.A.2    Turner, D.H.3
  • 95
    • 0030815643 scopus 로고    scopus 로고
    • Thermodynamics of nonsymmetric tandem mismatches adjacent to G·C base pairs in RNA
    • Xia T., McDowell J. A., Turner D. H. Thermodynamics of nonsymmetric tandem mismatches adjacent to G·C base pairs in RNA. Biochemistry. 36:1997;12486-12487.
    • (1997) Biochemistry , vol.36 , pp. 12486-12487
    • Xia, T.1    McDowell, J.A.2    Turner, D.H.3
  • 97
    • 0030700595 scopus 로고    scopus 로고
    • The relative stabilities of base-pair stacking interactions and single mismatches in long RNA measured by temperature gradient gel electrophoresis
    • Zhu J., Wartell R. M. The relative stabilities of base-pair stacking interactions and single mismatches in long RNA measured by temperature gradient gel electrophoresis. Biochemistry. 36:1997;15326-15335.
    • (1997) Biochemistry , vol.36 , pp. 15326-15335
    • Zhu, J.1    Wartell, R.M.2
  • 98
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 244:1989;48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 99
    • 0029131459 scopus 로고
    • "well-determined" regions in RNA secondary structure predictions. Applications to small and large subunit rRNA
    • Zuker M., Jacobson A. B. "Well-determined" regions in RNA secondary structure predictions. Applications to small and large subunit rRNA. Nucl. Acids Res. 23:1995;2791-2798.
    • (1995) Nucl. Acids Res. , vol.23 , pp. 2791-2798
    • Zuker, M.1    Jacobson, A.B.2
  • 100
    • 0031745782 scopus 로고    scopus 로고
    • Using reliability information to annotate RNA secondary structures
    • Zuker M., Jacobson A. B. Using reliability information to annotate RNA secondary structures. RNA. 4:1998;669-679.
    • (1998) RNA , vol.4 , pp. 669-679
    • Zuker, M.1    Jacobson, A.B.2
  • 101
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • Zuker M., Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl. Acids Res. 9:1981;133-148.
    • (1981) Nucl. Acids Res. , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.