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Volumn 290, Issue 5, 1999, Pages 967-982

Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs

Author keywords

2 Pyrimidinone; Dangling end; Electrostatics; Inosine; RNA folding

Indexed keywords

ADENINE; CYTOSINE; GUANINE; NUCLEOTIDE; URACIL;

EID: 0033618268     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.2906     Document Type: Article
Times cited : (80)

References (84)
  • 1
    • 0028864394 scopus 로고
    • The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein
    • Aboul-ela F., Karn J., Varani G. The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J. Mol. Biol. 253:1995;313-332.
    • (1995) J. Mol. Biol. , vol.253 , pp. 313-332
    • Aboul-Ela, F.1    Karn, J.2    Varani, G.3
  • 2
    • 0030660482 scopus 로고    scopus 로고
    • Structure and dynamics of the iron responsive element RNA: Implications for binding of the RNA by iron regulatory binding proteins
    • Addess K. J., Basilion J. P., Klausner R. D., Rouault T. A., Pardi A. Structure and dynamics of the iron responsive element RNA: implications for binding of the RNA by iron regulatory binding proteins. J. Mol. Biol. 274:1997;72-83.
    • (1997) J. Mol. Biol. , vol.274 , pp. 72-83
    • Addess, K.J.1    Basilion, J.P.2    Klausner, R.D.3    Rouault, T.A.4    Pardi, A.5
  • 3
    • 0002587695 scopus 로고
    • Ionization constants of heterocyclic substances. II. Hydroxy-derivatives of nitrogenous six-membered ring-compounds
    • Albert A., Phillips J. N. Ionization constants of heterocyclic substances. II. Hydroxy-derivatives of nitrogenous six-membered ring-compounds. J. Chem. Soc. 1956;1294-1304.
    • (1956) J. Chem. Soc. , pp. 1294-1304
    • Albert, A.1    Phillips, J.N.2
  • 4
    • 0030445764 scopus 로고    scopus 로고
    • Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP
    • Arnez J. G., Steitz T. A. Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP. Biochemistry. 35:1996;14725-14733.
    • (1996) Biochemistry , vol.35 , pp. 14725-14733
    • Arnez, J.G.1    Steitz, T.A.2
  • 5
    • 0029822046 scopus 로고    scopus 로고
    • A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson-Crick base pairing
    • Baeyens K. J., De Bondt H. L., Pardi A., Holbrook S. R. A curved RNA helix incorporating an internal loop with G·A and A·A non-Watson-Crick base pairing. Proc. Natl Acad. Sci. USA. 93:1996;12851-12855.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 12851-12855
    • Baeyens, K.J.1    De Bondt, H.L.2    Pardi, A.3    Holbrook, S.R.4
  • 6
    • 0025815046 scopus 로고
    • The 3 Å crystal structure of yeast initiator tRNA: Functional implications in initiator/elongator discrimination
    • Basavappa R., Sigler P. B. The 3 Å crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination. EMBO J. 10:1991;3105-3111.
    • (1991) EMBO J. , vol.10 , pp. 3105-3111
    • Basavappa, R.1    Sigler, P.B.2
  • 9
    • 0028105601 scopus 로고
    • The 2.9 Å crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser)
    • Biou V., Yaremchuk A., Tukalo M., Cusack S. The 2.9 Å crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science. 263:1994;1404-1410.
    • (1994) Science , vol.263 , pp. 1404-1410
    • Biou, V.1    Yaremchuk, A.2    Tukalo, M.3    Cusack, S.4
  • 10
    • 0031552350 scopus 로고    scopus 로고
    • Solution structure of the HIV-2 TAR-argininamide complex
    • Brodsky A. S., Williamson J. R. Solution structure of the HIV-2 TAR-argininamide complex. J. Mol. Biol. 267:1997;624-639.
    • (1997) J. Mol. Biol. , vol.267 , pp. 624-639
    • Brodsky, A.S.1    Williamson, J.R.2
  • 11
    • 0002084217 scopus 로고    scopus 로고
    • The interactions that shape RNA structure
    • R. F. Gesteland, T. R. Cech, & J. F. Atkins. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
    • Burkard M. E., Turner D. H., Tinoco I. Jr. The interactions that shape RNA structure. Gesteland R. F., Cech T. R., Atkins J. F. The RNA World. 1999a;233-264 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
    • (1999) The RNA World , pp. 233-264
    • Burkard, M.E.1    Turner, D.H.2    Tinoco I., Jr.3
  • 12
    • 0003251937 scopus 로고    scopus 로고
    • Appendix 1: Structures of base pairs involving at least two hydrogen bonds
    • R. F. Gesteland, T. R. Cech, & J. F. Atkins. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
    • Burkard M. E., Turner D. H., Tinoco I. Jr. Appendix 1: Structures of base pairs involving at least two hydrogen bonds. Gesteland R. F., Cech T. R., Atkins J. F. The RNA World. 1999b;675-680 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
    • (1999) The RNA World , pp. 675-680
    • Burkard, M.E.1    Turner, D.H.2    Tinoco I., Jr.3
  • 13
    • 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
  • 15
    • 0027860348 scopus 로고
    • Yeast aspartyl-tRNA synthetase: A structural view of the aminoacylation reaction
    • Cavarelli J., Rees B., Thierry J. C., Moras D. Yeast aspartyl-tRNA synthetase: a structural view of the aminoacylation reaction. Biochimie. 75:1993;1117-1123.
    • (1993) Biochimie , vol.75 , pp. 1117-1123
    • Cavarelli, J.1    Rees, B.2    Thierry, J.C.3    Moras, D.4
  • 16
    • 0027053974 scopus 로고
    • Base-pairing geometry in GA mismatches depends entirely on the neighboring sequence
    • Cheng J.-W., Chou S.-H., Reid B. R. Base-pairing geometry in GA mismatches depends entirely on the neighboring sequence. J. Mol. Biol. 228:1992;1037-1041.
    • (1992) J. Mol. Biol. , vol.228 , pp. 1037-1041
    • Cheng, J.-W.1    Chou, S.-H.2    Reid, B.R.3
  • 17
    • 0030856333 scopus 로고    scopus 로고
    • Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain
    • Correll 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
    • Correll, C.C.1    Freeborn, B.2    Moore, P.B.3    Steitz, T.A.4
  • 18
    • 0031574326 scopus 로고    scopus 로고
    • The loop E-loop D region of Escherichia coli 5S rRNA: The solution structure reveals an unusual loop that may be important for binding ribosomal proteins
    • Dallas A., Moore P. B. The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins. Structure. 5:1997;1639-1653.
    • (1997) Structure , vol.5 , pp. 1639-1653
    • Dallas, A.1    Moore, P.B.2
  • 19
    • 0014243665 scopus 로고
    • Temperature-dependent properties of dinucleoside phosphates
    • Davis R. C., Tinoco I. Jr. Temperature-dependent properties of dinucleoside phosphates. Biopolymers. 6:1968;223-242.
    • (1968) Biopolymers , vol.6 , pp. 223-242
    • Davis, R.C.1    Tinoco I., Jr.2
  • 20
    • 0029864853 scopus 로고    scopus 로고
    • Molecular recognition in the FMN-RNA aptamer complex
    • Fan P., Suri A. K., Fiala R., Live D., Patel D. J. Molecular recognition in the FMN-RNA aptamer complex. J. Mol. Biol. 258:1996;480-500.
    • (1996) J. Mol. Biol. , vol.258 , pp. 480-500
    • Fan, P.1    Suri, A.K.2    Fiala, R.3    Live, D.4    Patel, D.J.5
  • 21
    • 0000339640 scopus 로고
    • The calculation of ab initio molecular geometries: Efficient optimization by natural internal coordinates and empirical correction by offset forces
    • Fogarasi G., Zhou X., Taylor P. W., Pulay P. The calculation of ab initio molecular geometries: efficient optimization by natural internal coordinates and empirical correction by offset forces. J. Am. Chem. Soc. 114:1992;8191-8201.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 8191-8201
    • Fogarasi, G.1    Zhou, X.2    Taylor, P.W.3    Pulay, P.4
  • 22
    • 0029825658 scopus 로고    scopus 로고
    • Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic
    • Fourmy D., Recht M. I., Blanchard S. C., Puglisi J. D. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science. 274:1996;1367-1371.
    • (1996) Science , vol.274 , pp. 1367-1371
    • Fourmy, D.1    Recht, M.I.2    Blanchard, S.C.3    Puglisi, J.D.4
  • 23
    • 0018788364 scopus 로고
    • Thermal perturbation differential spectra of ribonucleic acids. II. Nearest neighbour interactions
    • Frechet D., Ehrlich R., Remy P., Gabarro-Arpa J. Thermal perturbation differential spectra of ribonucleic acids. II. Nearest neighbour interactions. Nucl. Acids Res. 7:1979;1981-2001.
    • (1979) Nucl. Acids Res. , vol.7 , pp. 1981-2001
    • Frechet, D.1    Ehrlich, R.2    Remy, P.3    Gabarro-Arpa, J.4
  • 24
    • 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
  • 25
    • 0022424620 scopus 로고
    • Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes
    • Freier S. M., Alkema D., Sinclair A., Neilson T., Turner D. H. Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry. 24:1985;4533-4539.
    • (1985) Biochemistry , vol.24 , pp. 4533-4539
    • Freier, S.M.1    Alkema, D.2    Sinclair, A.3    Neilson, T.4    Turner, D.H.5
  • 26
    • 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
  • 27
    • 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. 25:1986b;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
  • 29
    • 0027956537 scopus 로고
    • A major family of motifs involving G·A mismatches in ribosomal RNA
    • Gautheret D., Konings D., Gutell R. R. A major family of motifs involving G·A mismatches in ribosomal RNA. J. Mol. Biol. 242:1994;1-8.
    • (1994) J. Mol. Biol. , vol.242 , pp. 1-8
    • Gautheret, D.1    Konings, D.2    Gutell, R.R.3
  • 30
    • 0024602182 scopus 로고
    • The synthesis of 2-pyrimidinone nucleosides and their incorporation into oligodeoxynucleotides
    • Gildea B., McLaughlin L. W. The synthesis of 2-pyrimidinone nucleosides and their incorporation into oligodeoxynucleotides. Nucl. Acids Res. 17:1989;2261-2281.
    • (1989) Nucl. Acids Res. , vol.17 , pp. 2261-2281
    • Gildea, B.1    McLaughlin, L.W.2
  • 31
    • 0030585428 scopus 로고    scopus 로고
    • Solution structure of the donor site of a trans-splicing RNA
    • Greenbaum N. L., Radhakrishnan I., Patel D. J., Hirsh D. Solution structure of the donor site of a trans-splicing RNA. Structure. 4:1996;725-733.
    • (1996) Structure , vol.4 , pp. 725-733
    • Greenbaum, N.L.1    Radhakrishnan, I.2    Patel, D.J.3    Hirsh, D.4
  • 32
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base-pair morphology
    • Gorin A. A., Zhurkin V. B., Olson W. K. B-DNA twisting correlates with base-pair morphology. J. Mol. Biol. 247:1995;34-48.
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 33
    • 0028071557 scopus 로고
    • Collection of small subunit (16S- And 16S-like) ribosomal RNA structures: 1994
    • Gutell R. R. Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. Nucl. Acids Res. 22:1994;3502-3507.
    • (1994) Nucl. Acids Res. , vol.22 , pp. 3502-3507
    • Gutell, R.R.1
  • 34
    • 0027225783 scopus 로고
    • A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993
    • Gutell R. R., Gray M. W., Schnare M. N. A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993. 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
  • 35
    • 0026335264 scopus 로고
    • Nearest-neighbor parameters for G·U mismatches: {{\rm 5^\prime GU3^\prime}\atop {\rm 3^\prime UG5^\prime}} is destabilizing in the contexts {{\rm CGUG}\atop \dot {\rm G}{\rm UG}\dot {\rm C}} , {{\rm UGUA}\atop \dot {\rm A}{\rm UG}\dot {\rm U}} , and {{\rm AGUU}\atop \dot {\rm U}{\rm UG}\dot {\rm A}} , but stabilizing in {{\rm GGUC}\atop \dot {\rm C}{\rm UG}\dot {\rm G}}
    • He L., Kierzek R., SantaLucia J. Jr, Walter A. E., Turner D. H. Nearest-neighbor parameters for G·U mismatches: {{\rm 5^\prime GU3^\prime}\atop {\rm 3^\prime UG5^\prime}} is destabilizing in the contexts {{\rm CGUG}\atop \dot {\rm G}{\rm UG}\dot {\rm C}} , {{\rm UGUA}\atop \dot {\rm A}{\rm UG}\dot {\rm U}} , and {{\rm AGUU}\atop \dot {\rm U}{\rm UG}\dot {\rm A}} , but stabilizing in {{\rm GGUC}\atop \dot {\rm C}{\rm UG}\dot {\rm G}} . Biochemistry. 30:1991;11124-11132.
    • (1991) Biochemistry , vol.30 , pp. 11124-11132
    • He, L.1    Kierzek, R.2    Santalucia J., Jr.3    Walter, A.E.4    Turner, D.H.5
  • 36
    • 0025850802 scopus 로고
    • Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: More isn't always better
    • Herschlag D. Implications of ribozyme kinetics for targeting the cleavage of specific RNA molecules in vivo: more isn't always better. Proc. Natl Acad. Sci. USA. 88:1991;6921-6925.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 6921-6925
    • Herschlag, D.1
  • 37
    • 0026423027 scopus 로고
    • Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops
    • Heus H. A., Pardi A. Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science. 253:1991;191-194.
    • (1991) Science , vol.253 , pp. 191-194
    • Heus, H.A.1    Pardi, A.2
  • 38
    • 0343150712 scopus 로고
    • Preparation of acyl derivatives of pyrimidin-2-one nucleosides by the silyl variant of the Hilbert-Johnson reaction
    • Holý A. Preparation of acyl derivatives of pyrimidin-2-one nucleosides by the silyl variant of the Hilbert-Johnson reaction. Coll. Czech. Chem. Commun. 42:1977;902-908.
    • (1977) Coll. Czech. Chem. Commun. , vol.42 , pp. 902-908
    • Holý, A.1
  • 39
    • 0025062410 scopus 로고
    • Mild acid hydrolysis of 2-pyrimidinone-containing DNA fragments generates apurinic/apyrimidinic sites
    • Iocono J. A., Gildea B., McLaughlin L. W. Mild acid hydrolysis of 2-pyrimidinone-containing DNA fragments generates apurinic/apyrimidinic sites. Tetrahedron Letters. 31:1990;175-178.
    • (1990) Tetrahedron Letters , vol.31 , pp. 175-178
    • Iocono, J.A.1    Gildea, B.2    McLaughlin, L.W.3
  • 40
    • 0023040505 scopus 로고
    • Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability
    • Kierzek R., Caruthers M. H., Longfellow C. E., Swinton D., Turner D. H., Freier S. M. Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability. Biochemistry. 25:1986;7840-7846.
    • (1986) Biochemistry , vol.25 , pp. 7840-7846
    • Kierzek, R.1    Caruthers, M.H.2    Longfellow, C.E.3    Swinton, D.4    Turner, D.H.5    Freier, S.M.6
  • 41
    • 0030996773 scopus 로고    scopus 로고
    • The structure of the isolated, central hairpin of the HDV antigenomic ribozyme: Novel structural features and similarity of the loop in the ribozyme and free in solution
    • Kolk M. H., Heus H. A., Hilbers C. W. The structure of the isolated, central hairpin of the HDV antigenomic ribozyme: novel structural features and similarity of the loop in the ribozyme and free in solution. EMBO J. 16:1997;3685-3692.
    • (1997) EMBO J. , vol.16 , pp. 3685-3692
    • Kolk, M.H.1    Heus, H.A.2    Hilbers, C.W.3
  • 42
    • 0026053768 scopus 로고
    • NMR and molecular modeling evidence for a GA mismatch base pair in a purine-rich DNA duplex
    • Li Y., Zon G., Wilson W. D. NMR and molecular modeling evidence for a GA mismatch base pair in a purine-rich DNA duplex. Proc. Natl Acad. Sci. USA. 88:1991;26-30.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 26-30
    • Li, Y.1    Zon, G.2    Wilson, W.D.3
  • 43
    • 0030586821 scopus 로고    scopus 로고
    • The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites
    • Lietzke S. E., Barnes C. L., Berglund J. A., Kundrot C. E. The structure of an RNA dodecamer shows how tandem U-U base pairs increase the range of stable RNA structures and the diversity of recognition sites. Structure. 4:1996;917-930.
    • (1996) Structure , vol.4 , pp. 917-930
    • Lietzke, S.E.1    Barnes, C.L.2    Berglund, J.A.3    Kundrot, C.E.4
  • 44
    • 0000262963 scopus 로고
    • Application of the tetraisopropyldisiloxane-1,3-diyl group in the chemical synthesis of oligoribonucleotides
    • Markiewicz W. T., Biala E., Kierzek R. Application of the tetraisopropyldisiloxane-1,3-diyl group in the chemical synthesis of oligoribonucleotides. Bull. Acad. Polon. Sci. Chem. 32:1984;433-451.
    • (1984) Bull. Acad. Polon. Sci. Chem. , vol.32 , pp. 433-451
    • Markiewicz, W.T.1    Biala, E.2    Kierzek, R.3
  • 45
    • 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
  • 46
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews D. H., Sabina J., Zuker M., Turner D. H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:1999;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
  • 47
    • 0026077710 scopus 로고
    • The combination of symbolic and numerical computation for three-dimensional modeling of RNA
    • Major F., Turcotte M., Gautheret D., Lapalme G., Fillion E., Cedergren R. The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science. 253:1991;1255-1260.
    • (1991) Science , vol.253 , pp. 1255-1260
    • Major, F.1    Turcotte, M.2    Gautheret, D.3    Lapalme, G.4    Fillion, E.5    Cedergren, R.6
  • 48
    • 0029805937 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and simulated annealing
    • 2 by 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
  • 51
    • 0031967099 scopus 로고    scopus 로고
    • The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme
    • Ortoleva-Donnelly L., Szewczak A. A., Gutell R. R., Strobel S. A. The chemical basis of adenosine conservation throughout the Tetrahymena ribozyme. RNA. 4:1998;498-519.
    • (1998) RNA , vol.4 , pp. 498-519
    • Ortoleva-Donnelly, L.1    Szewczak, A.A.2    Gutell, R.R.3    Strobel, S.A.4
  • 52
    • 0028004607 scopus 로고
    • Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin
    • Oubridge C., Ito N., Evans P. R., Teo C. H., Nagai K. Crystal structure at 1.92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature. 372:1994;432-438.
    • (1994) Nature , vol.372 , pp. 432-438
    • Oubridge, C.1    Ito, N.2    Evans, P.R.3    Teo, C.H.4    Nagai, K.5
  • 54
    • 0027165755 scopus 로고
    • Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase
    • Perona J. J., Rould M. A., Steitz T. A. Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. Biochemistry. 32:1993;8758-8771.
    • (1993) Biochemistry , vol.32 , pp. 8758-8771
    • Perona, J.J.1    Rould, M.A.2    Steitz, T.A.3
  • 55
    • 0020674698 scopus 로고
    • Base-stacking and base-pairing contributions to helix stability: Thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp
    • Petersheim M., Turner D. H. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 18:1983;256-263.
    • (1983) Biochemistry , vol.18 , pp. 256-263
    • Petersheim, M.1    Turner, D.H.2
  • 56
    • 0030596005 scopus 로고    scopus 로고
    • Structural change in Rev responsive element RNA of HIV-1 on binding Rev peptide
    • Peterson R. D., Feigon J. Structural change in Rev responsive element RNA of HIV-1 on binding Rev peptide. J. Mol. Biol. 264:1996;863-877.
    • (1996) J. Mol. Biol. , vol.264 , pp. 863-877
    • Peterson, R.D.1    Feigon, J.2
  • 57
    • 0025744320 scopus 로고
    • Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase
    • Rould M. A., Perona J. J., Steitz T. A. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature. 352:1991;213-218.
    • (1991) Nature , vol.352 , pp. 213-218
    • Rould, M.A.1    Perona, J.J.2    Steitz, T.A.3
  • 58
  • 60
    • 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. 113:1991;4313-4322.
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 4313-4322
    • Santalucia J., Jr.1    Kierzek, R.2    Turner, D.H.3
  • 61
    • 0026562625 scopus 로고
    • Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin
    • SantaLucia J. Jr, Kierzek R., Turner D. H. Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science. 256:1992;217-219.
    • (1992) Science , vol.256 , pp. 217-219
    • Santalucia J., Jr.1    Kierzek, R.2    Turner, D.H.3
  • 63
    • 0029073091 scopus 로고
    • The crystal structure of an all-RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage
    • Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 81:1995;991-1002.
    • (1995) Cell , vol.81 , pp. 991-1002
    • Scott, W.G.1    Finch, J.T.2    Klug, A.3
  • 64
    • 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. P., Stoddard B. L., Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science. 274:1996;2065-2069.
    • (1996) Science , vol.274 , pp. 2065-2069
    • Scott, W.G.1    Murray, J.B.2    Arnold, J.R.P.3    Stoddard, B.L.4    Klug, A.5
  • 66
    • 0030965811 scopus 로고    scopus 로고
    • Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping
    • Strobel S. A., Shetty K. Defining the chemical groups essential for Tetrahymena group I intron function by nucleotide analog interference mapping. Proc. Natl Acad. Sci. USA. 94:1997;2903-2908.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 2903-2908
    • Strobel, S.A.1    Shetty, K.2
  • 67
    • 0023653195 scopus 로고
    • Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid
    • Sugimoto N., Kierzek R., Turner D. H. Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry. 26:1987;4554-4558.
    • (1987) Biochemistry , vol.26 , pp. 4554-4558
    • Sugimoto, N.1    Kierzek, R.2    Turner, D.H.3
  • 68
    • 0029907866 scopus 로고    scopus 로고
    • Image library of biological macromolecules
    • Sühnel J. Image library of biological macromolecules. Comput. Appl. Biosci. 12:1996;227-229.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 227-229
    • Sühnel, J.1
  • 69
    • 0018077590 scopus 로고
    • Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement
    • Sussman J. L., Holbrook S. R., Warrant R. W., Church G. M., Kim S. H. Crystal structure of yeast phenylalanine transfer RNA. I. Crystallographic refinement. J. Mol. Biol. 123:1978;607-630.
    • (1978) J. Mol. Biol. , vol.123 , pp. 607-630
    • Sussman, J.L.1    Holbrook, S.R.2    Warrant, R.W.3    Church, G.M.4    Kim, S.H.5
  • 70
    • 0028953727 scopus 로고
    • The sarcin/ricin loop, a modular RNA
    • Szewczak A. A., Moore P. B. The sarcin/ricin loop, a modular RNA. J. Mol. Biol. 247:1995;81-98.
    • (1995) J. Mol. Biol. , vol.247 , pp. 81-98
    • Szewczak, A.A.1    Moore, P.B.2
  • 71
    • 0001409790 scopus 로고
    • Thermodynamic considerations for evolution by RNA
    • R. F. Gesteland, & J. F. Atkins. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
    • Turner D. H., Bevilacqua. Thermodynamic considerations for evolution by RNA. Gesteland R. F., Atkins J. F. The RNA World. 1993;447-464 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
    • (1993) The RNA World , pp. 447-464
    • Turner, D.H.1    Bevilacqua2
  • 72
    • 0000789168 scopus 로고
    • Free energy increments for hydrogen bonds in nucleic acid base pairs
    • Turner D. H., Sugimoto N., Kierzek R., Dreiker S. D. Free energy increments for hydrogen bonds in nucleic acid base pairs. J. Am. Chem. Soc. 109:1987a;3783-3785.
    • (1987) J. Am. Chem. Soc. , vol.109 , pp. 3783-3785
    • Turner, D.H.1    Sugimoto, N.2    Kierzek, R.3    Dreiker, S.D.4
  • 75
    • 0001179951 scopus 로고
    • Hydrogen-bond geometry around sugar molecules: Comparison of crystal statistics with simulated aqueous solutions
    • Van Eijck B. P., Kroon-Batenburg L. M. J., Kroon J. Hydrogen-bond geometry around sugar molecules: comparison of crystal statistics with simulated aqueous solutions. J. Mol. Struct. 237:1990;315-325.
    • (1990) J. Mol. Struct. , vol.237 , pp. 315-325
    • Van Eijck, B.P.1    Kroon-Batenburg, L.M.J.2    Kroon, J.3
  • 76
    • 0022551018 scopus 로고
    • Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles
    • Westhof E., Sundaralingam M. Restrained refinement of the monoclinic form of yeast phenylalanine transfer RNA. Temperature factors and dynamics, coordinated waters, and base-pair propeller twist angles. Biochemistry. 25:1986;4868-4878.
    • (1986) Biochemistry , vol.25 , pp. 4868-4878
    • Westhof, E.1    Sundaralingam, M.2
  • 77
    • 0000521158 scopus 로고
    • Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals
    • Westhof E., Dumas P., Moras D. Restrained refinement of two crystalline forms of yeast aspartic acid and phenylalanine transfer RNA crystals. Acta Crystallog. sect. A. 44:1988;112-123.
    • (1988) Acta Crystallog. Sect. a , vol.44 , pp. 112-123
    • Westhof, E.1    Dumas, P.2    Moras, D.3
  • 78
    • 0030929777 scopus 로고    scopus 로고
    • 2 by two-dimensional NMR and the iterative relaxation matrix approach
    • 2 by two-dimensional NMR and the iterative relaxation matrix approach. Biochemistry. 36:1997;4449-4460.
    • (1997) Biochemistry , vol.36 , pp. 4449-4460
    • Wu, M.1    Santalucia J., Jr.2    Turner, D.H.3
  • 79
    • 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;12486-12497.
    • (1997) Biochemistry , vol.36 , pp. 12486-12497
    • Xia, T.1    McDowell, J.A.2    Turner, D.H.3
  • 80
    • 0029972909 scopus 로고    scopus 로고
    • Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy
    • Yang Y., Kochoyan M., Burgstaller P., Westhof E., Famulok M. Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science. 272:1996;1343-1347.
    • (1996) Science , vol.272 , pp. 1343-1347
    • Yang, Y.1    Kochoyan, M.2    Burgstaller, P.3    Westhof, E.4    Famulok, M.5
  • 81
    • 0029613238 scopus 로고
    • Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex
    • Ye X. M., Kumar R. A., Patel D. J. Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex. Chem. Biol. 2:1995;827-840.
    • (1995) Chem. Biol. , vol.2 , pp. 827-840
    • Ye, X.M.1    Kumar, R.A.2    Patel, D.J.3
  • 82
    • 0030475417 scopus 로고    scopus 로고
    • Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex
    • Ye X. M., Gorin A., Ellington A. D., Patel D. J. Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex. Nature Struct. Biol. 3:1996;1026-1033.
    • (1996) Nature Struct. Biol. , vol.3 , pp. 1026-1033
    • Ye, X.M.1    Gorin, A.2    Ellington, A.D.3    Patel, D.J.4
  • 83
    • 0029006896 scopus 로고
    • Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes
    • Young M. A., Ravishanker G., Beveridge D. L., Berman H. M. Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. Biophys. J. 68:1995;2454-2468.
    • (1995) Biophys. J. , vol.68 , pp. 2454-2468
    • Young, M.A.1    Ravishanker, G.2    Beveridge, D.L.3    Berman, H.M.4
  • 84
    • 0030752211 scopus 로고    scopus 로고
    • Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA
    • Zimmermann G. R., Jenison R. D., Wick C. L., Simorre J. P., Pardi A. Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA. Nature Struct. Biol. 4:1997;644-649.
    • (1997) Nature Struct. Biol. , vol.4 , pp. 644-649
    • Zimmermann, G.R.1    Jenison, R.D.2    Wick, C.L.3    Simorre, J.P.4    Pardi, A.5


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