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RNA structure and NMR spectroscopy

Published online by Cambridge University Press:  17 March 2009

Gabriele Varani  and
Ignacio Tinoco Jr.
Gabriele Varani
Affiliation:
Department of Chemistry and Laboratory of Chemical Biodynamics, University of California, Berkeley, CA 94720USA
Ignacio Tinoco Jr.
Affiliation:
Department of Chemistry and Laboratory of Chemical Biodynamics, University of California, Berkeley, CA 94720USA
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Extract

RNA molecules perform a wide variety of biological functions, from enzymic activity to storage and propagation of genetic information.

Type
Research Article
Information
Quarterly Reviews of Biophysics , Volume 24 , Issue 4 , November 1991 , pp. 479 - 532
Copyright
Copyright © Cambridge University Press 1991

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References

Altona, C. (1982). Conformational analysis of nucleic acids. Determination of backbone geometry of single-helical RNA and DNA in aqueous solution. Recl. Trav. Chim. Pays-Bas, 101, 413–433.CrossRefGoogle Scholar
Andersen, J., Delihas, N., Hanas, J. S. & Wu, C.-W. (1984). 5s RNA structure and interaction with transcription factor A. 1. Ribonuclease probe of the structure of 5S RNA from Xenopus laevis oocytes. Biochemistry 23, 5752–5759.CrossRefGoogle ScholarPubMed
Antao, V. P., Lee, S. Y. & Tinoco, I. Jr. (1991). Nucl. Acids Res., submitted.Google Scholar
Ashcroft, J., Live, D. H., Patel, D. J. & Cowburn, D. (1991). Heteronuclear 2D 15N and 13C NMR studies of DNA oligomers and their netrospin complexes using indirect proton detection. Biopolymers 31, 45–55.CrossRefGoogle Scholar
Banks, K. M., Hare, D. R. & Reid, B. R. (1989). Three-dimensional solution structure of a DNA duplex containing the Bell restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum. Biochemistry 28, 6996–7010.CrossRefGoogle Scholar
Bax, A. & Davis, D. G. (1985). MLEV-17 based two-dimensional homonuclear magnetization transfer spectroscopy. J. magn. Reson. 65, 355–360.Google Scholar
Bax, A., Griffey, R. H. & Hawkins, B. L. (1983). Correlation of proton and nitrogen-15 chemical shifts by multiple quantum NMR. J. magn. Reson. 55, 301–315.Google Scholar
Blommers, M. J. J. (1990). Aspects of loop folding in DNA hairpins. Thesis, University of Nijmegen.Google Scholar
Blommers, M. J. J., Walters, J. A. L. I., Haasnoot, C. A. G., Aelen, J. M. A., van Der Marel, G. A., van Boom, J. H. & Hilbers, C. W. (1989). Effects of base sequence on the loop folding in DNA hairpins. Biochemistry 28, 7491–7498.CrossRefGoogle ScholarPubMed
Boelens, R., Koning, T. M. G., van Der Marel, G. A., van Boom, J. H. & Kaptein, R. (1989). Iterative procedure for a structure determination from proton–proton NOE's using a full relaxation matrix approach. Application to a DNA octamer. J. magn. Reson. 82, 290–308.Google Scholar
Borgias, B. A. & James, T. L. (1989). Two-dimensional nuclear Overhauser effect: complete relaxation matrix analysis. Meth. Enzym. 176, 169–183.CrossRefGoogle ScholarPubMed
Braun, W. & Go, N. (1985). Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J. molec. Biol. 186, 611–626.CrossRefGoogle ScholarPubMed
Braunschwiler, L., Bodenhausen, G. & Ernst, R. R. (1983). Analysis of networks of coupled spins by multiple quantum NMR. Molec. Phys. 48, 535–560.CrossRefGoogle Scholar
Brush, C. K., Stone, M. P. & Harris, T. M. (1988). Selective deuteration of oligonucleotides: simplification of two-dimensional nuclear Overhauser effect NMR spectral assignments of non-self complementary dodecamer duplex. Biochemistry 27, 115–122.CrossRefGoogle ScholarPubMed
Buzayan, J. M., van Tol, H., Feldstein, P. A. & Bruening, G. (1990). Identification of a non-junction phosphodiester that influences an autolytic processing reaction of RNA. Nucl. Acids Res. 18, 4447–4451.CrossRefGoogle ScholarPubMed
Celander, D. W. & Cech, T. R. (1991). Visualizing the higher order folding of a catalytic RNA molecule. Science, Wash. 251, 401–407.CrossRefGoogle ScholarPubMed
Celda, B., Widmer, H., Leupin, W., Chazin, W. J., Denny, W. A. & Wüthrich, K. (1989). Conformational studies of d(AAAAATTTTT)2 using constraints from nuclear Overhauser effects and from quantitative analysis of the cross-peak fine structures in two-dimensional nuclear magnetic resonance spectra. Biochemistry 28, 1462–1471.CrossRefGoogle Scholar
Chastain, M. A. & Tinoco, I. Jr., (1991). Structural elements of RNA. Prog. nucl. Acids Res. molec. Biol. 40, 131–177.CrossRefGoogle Scholar
Chazin, W. J., Wüthrich, K., Hyberts, S., Rance, M., Denny, W. A. & Leupin, W. (1986). 1H nuclear magnetic resonance assignments for d(GCATTAATGC)2 using experimental refinements of established procedures. J. molec. Biol. 190, 439–453.CrossRefGoogle ScholarPubMed
Cheong, C, Varani, G. & Tinoco, I. Jr. (1990). Solution structure of an unusually stable RNA hairpin, 5′GGAC(UUCG)GUCC. Nature, Lond. 346, 680–682.CrossRefGoogle ScholarPubMed
Chou, S.-H., Flynn, P. & Reid, B. (1989). Solid-phase synthesis and high-resolution NMR studies of two synthetic double-helical RNA dodecamers: r(CGCGAAUUCGCG) and r(CGCGUAUACGCG). Biochemistry 28, 2422–2435.CrossRefGoogle Scholar
Christiansen, J., Brown, R. S., Sproat, B. S. & Garrett, R. A. (1987). Xenopus transcription factor III A binds primarily at junctions between double helical stems and internal loops in oocyte 5S RNA. EMBO J. 6, 453–460.CrossRefGoogle Scholar
Clore, G. M., Gronenborn, A. M., Piper, E. A., McLaughlin, L. W., Graeser, E. & van Boom, J. H. (1984). The solution structure of a RNA pentadecamer comprising the anticodon loop and stem of yeast tRNAphe. Biochem J. 221, 737–751.CrossRefGoogle ScholarPubMed
D'Aubenton Carafa, Y., Brody, E. & Thermes, C. (1990). Prediction of Rhoindependent Escherichia coli transcription terminators. A statistical analysis of their stem-loop structures. J. molec. Biol. 216, 835–858.CrossRefGoogle Scholar
Davis, P. W. (1989). Solution structure and dynamics of Z-RNA: an NMR study of the ribooligonucleotide rCGCGCG. Thesis, University of California, Berkeley.Google Scholar
Davis, D. R., Yamaizumi, Z., Nishimura, S. & Poulter, C. D. (1989). 13N-labeled 5S RNA. Identification of uridine base pairs in Escherichia coli 5S RNA by 1H–15N multiple quantum NMR. Biochemistry 28, 4105–4108.CrossRefGoogle Scholar
de Leeuw, F. A. A. M. & Altona, C. (1982). Conformational analysis of β-D-ribo-,β-D-arabino-, β-D-xylo-, and β-D-lyxo-nucleosides from proton–proton coupling constants. J. chem. Soc. Perkin Trans. II 2, 375–384.CrossRefGoogle Scholar
de Leeuw, F. A. A. M., van Kampeqswn, P. N., Altona, C, Diez, E. & Esteban, A. L. (1984). Relationship between torsion angles and ring-puckering coordinates. III. Application to heterocyclic puckered five-membered rings. J. molec. Struct. 125, 67–88.CrossRefGoogle Scholar
de Los Santos, C, Rosen, M. & Patel, D. (1989). NMR studies of DNA (R+)n (Y-)n (Y+)n triple helices in solution: imino and amino proton markers of T. A. T and C. G. C+ base-triple formation. Biochemistry 28, 7282–7289.CrossRefGoogle Scholar
Derome, A. E. & Williamson, M. P. (1990). Rapid-pulsing artifacts in doublequantum-filtered COSY. J. magn. Reson. 88, 177–185.Google Scholar
Dock-Bregeon, A. C., Chevrier, B., Podjarny, A., Moras, D., DeBear, J. S., Gough, G. R., Gilham, P. T. & Johnson, J. E. (1988). High resolution structure of the RNA duplex [U(U-A)6]2. Nature, Lond. 335, 375–378.CrossRefGoogle Scholar
Ehresmann, C, Baudin, F., Mongel, M., Romby, P., Ebel, J.-P. & Ehresmann, B. (1987). Probing the structure of RNA's in solution. Nucl. Acids Res. 15, 9109–9128.CrossRefGoogle Scholar
Feigon, J., Leupin, W., Denny, W. A. & Kearns, D. R. (1983). Two-dimensional proton nuclear magnetic resonance investigation of the synthetic deoxyribonucleic acid decamer d(ATATCGATAT)2. Biochemistry 22, 5943–5951.CrossRefGoogle ScholarPubMed
Fesik, S. W. & Zuiderweg, E. R. P. (1990). Heteronuclear three-dimensional NMR spectroscopy of isotopically labeled biological macromolecules. Q. Rev. Biophys. 23, 97–131.CrossRefGoogle ScholarPubMed
Flynn, P. F., Kintanar, A., Reid, B. R. & Drobny, G. (1988). Coherence transfer in deoxyribose sugars produced by isotropic mixing: an improved intraresidue assignment strategy for the two-dimensional NMR spectra of DNA. Biochemistry 27, 1191–1197.CrossRefGoogle ScholarPubMed
Forster, A. C. & Simons, R. H. (1987). Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active site. Cell 49, 211–220.CrossRefGoogle Scholar
Freier, S. M., Kierzek, R., Jaeger, J. A., Sugimoto, N., Caruthers, M. H., Neilson, T. & Turner, D. H. (1986). Improved free energy parameters for predictions of RNA duplex stability. Proc. natn. Acad. Sci. U.S.A. 83, 9373–9377.CrossRefGoogle ScholarPubMed
Frey, M. H., Leupin, W., Sorensen, O. W., Denny, W. A., Ernst, R. R. & Wüthrich, K. (1985). Sequence-specific assignments of the backbone 1H and 31P-NMR lines in a short DNA duplex with homo- and heteronuclear correlated spectroscopy. Biopolymers 24, 2371–2380.CrossRefGoogle Scholar
Fu, J. M., Schroeder, S. A., Jones, C. R., Santini, R. & Gorenstein, D. G. (1988). Use of pure-absorption-phase 31P–1H 2D COLOC NMR spectra for assignment of 31P signals of oligonucleotides. J. magn. Reson. 77, 577–582.Google Scholar
Gewirth, D. T., Abo, S. R., Leontis, N. B. & Moore, P. B. (1987). Secondary structure of 5S RNA: NMR experiments on RNA molecules partially labeled with nitrogen-15. Biochemistry 26, 5213–5220.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C, Pullman, B., Ribas Prado, F., Cheng, D. M., Iuorno, V. & Tso, P. O. P. (1984). Contributions of the PO ester and CO torsion angles of the phosphate group to 31P-nuclear magnetic shielding constant in nucleic acids: theoretical and experimental study of model compounds. Biopolymers 23, 377–388.CrossRefGoogle ScholarPubMed
Glaser, S. J., Remerowski, M. L. & Drobny, G. P. (1989). Complete assignment of the deoxyribose 5′/5′ proton resonances of the EcoRl DNA sequence with isotropic mixing. Biochemistry 28, 1483–1487.CrossRefGoogle Scholar
Gochin, M. & James, T. L. (1990). Solution structure studies of d(AC)4d(GT)4 via restrained molecular dynamics simulations with NMR constraints derived from twodimensional NOE and double-quantum filtered COSY experiments. Biochemistry 29, 11172–11180.CrossRefGoogle ScholarPubMed
Gochin, M., Zon, G. & James, T. L. (1990). Two-dimensional COSY and twodimensional NOE spectroscopy of d(AC)4 d(GT)4: extraction of structural constraints. Biochemistry 29, 11161–11171.CrossRefGoogle ScholarPubMed
Gorenstein, D. (1984). 31P NMR, Principles and Applications. New York: Academic Press.Google Scholar
Griesinger, C., Sørensen, O. W. & Ernst, R. R. (1987). Practical aspects of the E.COSY technique. Measurement of scalar spin–spin coupling constants in peptides. J. magn. Reson. 75, 474–492.Google Scholar
Gutell, R. R., Weiser, B., Woese, C. R. & Nolleer, H. F. (1985). Comparative anatomy of 16S-like ribosomal RNA. Prog. nucl. Acids Res. molec. Biol. 32, 155–216.CrossRefGoogle Scholar
Haasnoot, C. A. G., de Leeuw, F. A. A. M. & Altona, C. (1980). The relationship between proton–proton NMR coupling constants and substituent electronegatives. I, An empirical generalization of the Karplus equation. Tetrahedron 36, 2783–2792.CrossRefGoogle Scholar
Haasnoot, C. A. G., de Leeuw, F. A. A. M., de Leeuw, H. P. M. & Altona, C. (1981). The relationship between proton–proton NMR coupling constants and substituent electronegatives. II, Conformational analysis of the sugar ring in nucleosides and nucleotides in solution using a generalized Karplus equation. Org. magn. Reson. 15, 43–52.CrossRefGoogle Scholar
Haasnoot, C. A. G., Hilbers, C. W., van der Marel, G. A., van Boom, J. H., Singh, U. C., Pattabiraman, N. & Kollman, P. A. (1986). On loopfolding in nucleic acids hairpin-type structures. J. biomol. Struct. Dyn. 3, 843–857.CrossRefGoogle Scholar
Hare, D. R., Wemmer, D. E., Chou, S.-H., Drobny, G. & Reid, B. R. (1983). Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-CG-C-G) using two-dimensional nuclear magnetic resonance methods. J. molec. Biol. 171, 319–336.CrossRefGoogle ScholarPubMed
Havel, T. F. & Wüthrich, K. (1984). An evaluation of the combined use of nuclear magnetic resonance and distance geometry for the determination of protein conformations in solution. J. molec. Biol. 182, 281–294.CrossRefGoogle Scholar
Heus, H. A. & Pardi, A. (1991a). Nuclear magnetic resonance studies of the hammerhead ribozyme domain. Secondary structure formation and magnesium ion dependence, J. molec. Biol. 217, 113–124.CrossRefGoogle ScholarPubMed
Heus, H. A. & Pardi, A. (1991b). Novel 1H nuclear magnetic resonance assignment procedure for RNA duplexes. J. Am. Chem. Soc. 113, 4360–4361.CrossRefGoogle Scholar
Heus, H. A. & Pardi, A. (1991c). Structural features that give rise to the unusual stability for RNA hairpins containing GNRA loops. Science, Wash. 253, 191–194.CrossRefGoogle Scholar
Heus, H. A., Uhlenbeck, O. C. & Pardi, A. (1990). Sequence-dependent structural variations of hammerhead RNA enzymes. Nucl. Acids Res. 18, 1103–1108.CrossRefGoogle ScholarPubMed
Hilbers, C. W., Heerschap, A., Haasnoot, C. A. G. & Walters, J. A. L. I. (1983). The solution structure of Yeast tRNAphe as studied by nuclear Overhauser effects in NMR. J. biomol. Struct. Dyn. 1, 183–207.CrossRefGoogle ScholarPubMed
Hirao, I., Nishimura, Y., Naraoka, T., Watanabe, K., Arata, Y. & Miura, K. (1989). Extraordinary stable structure of short single-stranded DNA fragments containing a specific base-sequence: d(GCGAAAGC). Nucl. Acids Res. 17, 2223–2231.CrossRefGoogle ScholarPubMed
Hosur, R. V., Chary, K. V. R., Saran, A., Govil, G. & Miles, H. T. (1990). Determination of solution conformation of DNA backbone: application of homonuclear (J, δ) spectroscopy. Biopolymers 29, 953–959.CrossRefGoogle ScholarPubMed
Huber, P. W. & Wool, I. G. (1986). Use of the cytotoxic nuclease a-sarcin to identify the binding site on eukaryotic 5S ribosomal ribonucleic acid for the ribosomal protein L5. J. biol. Chem. 7, 3002–3005.CrossRefGoogle Scholar
Jaeger, J. A., Turner, D. H. & Zuker, M. (1989). Improved predictions of secondary structures for RNA. Proc. natn. Acad. Sci. U.S.A. 86, 7706–7710.CrossRefGoogle ScholarPubMed
Jaeger, J. A., Zuker, M. & Turner, D. H. (1990). Melting and chemical modification of a cyclized self-splicing group I intron. Similarity of structures in 1 M Na+, in 10 raM Mg2+, and in the presence of substrate. Biochemistry 29, 10147–10158.CrossRefGoogle Scholar
Kessler, H., Muller, A. & Oschinat, H. (1985). Differences and sums of traces within COSY spectra (DISCO) for the extraction of coupling constants: ‘decoupling’ after the measurement. Magn. Res. Chem. 23, 844–852.CrossRefGoogle Scholar
Kim, Y. & Prestegard, J. H. (1989). Measurement of vicinal couplings from cross peaks in COSY spectra. J. magn. Res. 84, 9–13.Google Scholar
Kline, P. C. & Serianni, A. S. (1990). 13C-enriched ribonucleosides: synthesis and application of 1H–13C and 13C–13C spin–spin coupling constants to assess furanose and N-glycoside bond conformation. J. Am. Chem. Soc. 112, 7373–7381.CrossRefGoogle Scholar
Koning, T. M. G., Boelens, R. & Kaptein, R. (1990). Calculation of the Nuclear Overhauser Effect and the determination of proton–proton distances in the presence of internal motion. J. magn. Res. 90, 111–123.Google Scholar
Kupferschmidt, G., Schmidt, J., Schmidt, Th., Fera, B., Buck, F. & Ruterjans, H. (1987). 15N labeling of oligodeoxynucleotides for NMR studies of DNA-ligand interactions. Nucl. Acids Res. 15, 6225–6241.CrossRefGoogle Scholar
Lane, A. N., Jenkins, T. C., Brown, T. & Neidle, S. (1991). Interaction of berenil with the EcoRl dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR. Biochemistry 30, 1372–1385.CrossRefGoogle Scholar
Lankhorst, P. P., Haasnoot, C. A. G., Erkelens, C. & Altona, C. (1984). Carbon-13 NMR in conformational analysis of nucleic acid fragments. 2. A reparametrization of the Karplus equation for vicinal NMR coupling constants in CCOP and HCOP fragments. J. biomol. Struct. Dyn. 1, 1387–1405.CrossRefGoogle ScholarPubMed
LaPlante, S. R., Ashcroft, J., Cowburn, D., Levy, G. C. & Borer, P. N. (1988). 13C NMR assignments of the protonated carnons of [d(TAGCGCTA)]2 by twodimensional proton-detected heteronuclear correlation. J. Biomol. Struct. Dyn. 5, 1089–1099.CrossRefGoogle ScholarPubMed
LeMaster, D. M. (1990). Deuterium labeling in NMR structural analysis of larger proteins. Q. Rev. Biophys. 23, 133–174.CrossRefGoogle ScholarPubMed
Leroy, J.-L., Broseta, D. & Gueron, M. (1985). Proton exchange and base-pair kinetics of poly(rA) poly(rU) and poly(rI) poly(rC). J. molec. Biol. 184, 165–178.CrossRefGoogle ScholarPubMed
Leupin, W., Wagner, G., Denny, W. A. & Wüthrich, K. (1987). Assignment of the 13C nuclear magnetic resonance spectrum of a short DNA-duplex with 1H-detected two-dimensional heteronuclear correlation spectroscopy. Nucl. Acids Res. 15, 267–275.CrossRefGoogle Scholar
Levitt, M. & Warshell, A. (1978). Extreme conformational flexibility of the furanose ring in DNA and RNA. J. Am. Chem. Soc. 100, 2607–2613.CrossRefGoogle Scholar
Li, S.-J., Wu, J. & Marshall, A. G. (1987). 500-MHz proton homonuclear overhauser evidence for additional base pairs in the common arm of eukaryotic ribosomal 5s RNA: wheat germ. Biochemistry 26, 1578–1585.CrossRefGoogle ScholarPubMed
Li, Y., Wilson, W. D. & Zon, G. (1991). NMR and molecular modeling evidence for a G. A mismatch base pair in a purine-rich DNA duplex. Proc. natn. Acad. Sci. U.S.A. 88, 28–30.CrossRefGoogle Scholar
Manoharan, M., Gertl, J. A., Wilde, J. A., Withka, J. M. & Bolton, P. H. (1987). Coexistence of conformations in a DNA heteroduplex revealed by site specific labeling with 13C-labeled nucleotides. J. Am. Chem. Soc. 109, 7217–7219.CrossRefGoogle Scholar
Metzler, W. J., Wang, C, Kitchen, D. B., Levy, R. M. & Pardi, A. (1990). Determining local conformational variations in DNA. Nuclear magnetic resonance structures of the DNA duplexes d(CGCCTAATCG) and d(CGTCACGCGC) generated using back-calculation of the nuclear Overhauser effect spectra, a distance geometry algorithm and constrained molecular dynamics. J. molec. Biol. 214, 711–736.CrossRefGoogle Scholar
Michel, F., Ellington, A. D., Couture, S. & Szostak, J. W. (1990). Phylogenetic and genetic evidence for base-triples in the catalytic domain of group I introns. Nature, Lond. 347, 578–580.CrossRefGoogle ScholarPubMed
Milligan, J. F., Groebe, D. R., Witherell, G. W. & Uhlenbeck, O. C. (1987). Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 15, 8783–8798.CrossRefGoogle ScholarPubMed
Moazed, D., Stern, S. & Noller, H. F. (1986). Rapid chemical probing of conformation in 16S ribosomal RNA and 30S ribosomal subunits using primer extension, J. molec. Biol. 187, 399–416.CrossRefGoogle Scholar
Molinaro, M. & Tinoco, I. Jr (1991). Effect of stem and loop sequence on thermodynamics and structure of an RNA tetraloop hairpin.Biophysical Society, 35th Annual Meeting,San Francisco, CA.Google Scholar
Montelione, G. T., Winkler, M. E., Ranenbuehler, P. & Wagner, C. (1989). Accurate measurements of long-range heteronuclear coupling constants from. homonuclear 2D NMR spectra of isotope-enriched proteins. J. magn. Reson. 82, 198–204.Google Scholar
Müller, N., Ernst, R. R. & Wüthrich, K. (1986). Multiple-quantum-filtered two dimensional correlated spectroscopy of proteins, J. Am. Chem. Soc. 108, 6482–6492.CrossRefGoogle Scholar
Odai, O., Kodama, H., Hiroaki, H., Sakata, T., Tanaka, T. & Uesugi, S. (1990). Synthesis and NMR studies of ribooligonculeotides forming a hammerhead-type ribozyme system. Nucl. Acids Res. 18, 5955–5960.CrossRefGoogle Scholar
Orban, J. & Bell, R. A. (1990). 1H NMR assignments and conformational analysis of the oligoribonucleotides CA, CAU, CAUG, ACAUG and UCAUG: observation of pyrimidine H5–H1′ long-range scalar couplings, J. Biomol. Struct. Dyn. 7, 837–848.CrossRefGoogle ScholarPubMed
Otting, G. & Wüthrich, K. (1990). Heteronuclear filters in two-dimensional [1H-1H] NMR spectroscopy: combined use with isotope labelling for studies of macromolecular conformation and intermolecular interactions. Q. Rev. Biophys. 23, 39–96.CrossRefGoogle ScholarPubMed
Pardi, A., Hare, D. R. & Wang, C. (1988). Determination of DNA structures by NMR and distance geometry techniques: a computer simulation. Proc. natn. Acad. Sci. U.S.A. 85, 8785–8789.CrossRefGoogle ScholarPubMed
Pardi, A., Walker, R., Rapoport, H., Wider, G. & Wüthrich, K. (1983). Sequential assignments for the 1H and 31P atoms in the backbone of oligonucleotides by two dimensional nuclear magnetic resonance, J. Am. Chem. Soc. 105, 1652–1653.CrossRefGoogle Scholar
Patel, D. J., Shapiro, L. & Hare, D. (1987). Nuclear magnetic resonance and distance geometry studies of DNA structures in solution. A. Rev. Biophys. biophys. Chem. 16, 423–453.CrossRefGoogle ScholarPubMed
Pease Caviani, A. & Wemmer, D. E. (1990). Characterization of the secondary structure and melting of a self-cleaved RNA hammerhead domain by H NMR spectroscopy. Biochemistry 29, 9039–9046.CrossRefGoogle Scholar
Perrault, J.-P., Wu, T., Cousineau, B., Olgivie, K. K. & Cedergren, R. (1990). Mixed deoxyribo- and ribooligonucleotides with catalytic activity. Nature, Lond. 344, 565–567.CrossRefGoogle Scholar
Post, C. B., Meadows, R. & Gorenstein, D. G. (1990). On the evaluation of interproton distances for three-dimensional structural analysis by NMR using a relaxation rate matrix analysis, J. Am. Chem. Soc. 112, 6796–6803.CrossRefGoogle Scholar
Puglisi, J. D., Wyatt, J. R. & Tinoco, I. Jr. (1990a). Solution conformation of an RNA hairpin loop. Biochemistry 29, 4215–4226.CrossRefGoogle ScholarPubMed
Puglisi, J. D., Wyatt, J. R. & Tinoco, I. Jr. (1990b). Conformation of an RNA pseudoknot. J. molec. Biol. 214, 437–453.CrossRefGoogle ScholarPubMed
Pyle, A. M., McSwiggen, J. & Cech, T. R. (1990). Direct measurement of RNA structure and NMR spectroscopy 531 oligonucleotide substrate binding to wild-type and mutant ribozymes from Tetrahymena. Proc. natn. Acad. Sci. U.S.A. 87, 8187–8191.CrossRefGoogle Scholar
Rhemin, M. & Shugar, D. (1972). Conformation of the exocyclic 5′-CH2OH in nucleosides and nucleotides in acqueous solutions from specific assignments of the H5′ and H5″ signals in the NMR spectra. Biochem. biophys. Res. Commun. 48, 636–642.CrossRefGoogle Scholar
Rinkel, L. J. & Altona, C. (1987). Conformational analysis of the deoxyribofuranose ring in DNA by means of sums of proton-proton coupling constants: a graphical method, J. Biomol. Struct. Dyn. 4, 621–649.CrossRefGoogle ScholarPubMed
Romaniuk, P. J., de Stevenson, I. L., Ehresmann, C, Romby, P. & Ehresmann, B. (1988). A comparison of the solution structures and conformational properties of the somatic and oocyte 5S rRNA's of Xenopus Laevis. Nucl. Acids Res. 16, 2295–2312.CrossRefGoogle ScholarPubMed
Roy, S. & Redfield, A. G. (1983). Assignment of the imino proton spectra of yeast phenilalanine transfer ribonucleic acid. Biochemistry 22, 1386–1390.CrossRefGoogle Scholar
Ruffner, D. E. & Uhlenbeck, O. C. (1990). Thiophosphate interference experiments locate phosphates important for the hammerhead RNA self-cleavage reaction. Nucl. Acids Res. 18, 6025–6029.CrossRefGoogle ScholarPubMed
Saenger, W. (1984). Principles of Nucleic Acid Structure. New York: Springer-Verlag.CrossRefGoogle Scholar
Sakata, T., Hiroaki, H., Oda, Y., Tanaka, T., Ikehara, M. & Uesugi, S. (1990). Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides. Nucl. Acids Red. 18, 3831–3839.CrossRefGoogle ScholarPubMed
SantaLucia, J., Kierzek, R. & Turner, D. H. (1990). Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry 29, 8813–8819.CrossRefGoogle ScholarPubMed
Scheek, R. M., Russo, N., Boelens, R., Kaptein, R. & van Boom, I. H. (1983). Sequential resonance assignments in DNA 1H NMR spectra by two-dimensional NOE spectroscopy. J. Am. Chem. Soc. 105, 2914–2916.CrossRefGoogle Scholar
Simon, E. S., Grabowski, S. & Whitesides, G. M. (1990). Convenient synthesis of cytidine 5′-triphosphates, guanosine 5′-triphosphate and uridine 5′-triphosphate and their use in the preparation of UDP-glucose, UDP-glucoronic acid and GDP mannose. J. org. Chem. 55, 1834–1841.CrossRefGoogle Scholar
Sklenar, V. & Bax, A. (1987). Measurement of 1H–31P NMR coupling constants in double stranded DNA fragments. J. Am. Chem. Soc. 109, 7525–7526.CrossRefGoogle Scholar
Sklenar, V. & Feigon, J. (1990). Formation of a stable triplex from a single DNA strand. Nature, Lond. 345, 836–838.CrossRefGoogle ScholarPubMed
Sklenar, V., Miyashiro, H., Zon, G., Miles, H. T. & Bax, A. (1986). Assignment of the 31P and 1H resonances in oligonucleotides by two-dimensional NMR spectroscopy. FEBS Lett. 208, 94–99.CrossRefGoogle ScholarPubMed
Stone, M. P., Winkle, S. A. & Borer, P. N. (1986). 13C-NMR of ribosyl ApApA, ApApG and ApUpG. J. Biomol. Struct. Dyn. 3, 767–781.CrossRefGoogle ScholarPubMed
Tinoco, I. Jr., Puglisi, J. D. & Wyatt, J. R. (1990). RNA folding, In Nucleic Acid and Molecular Biology, vol. 4 (ed. Eckstein, F. and Lilley, D. M. J.), Berlin: Springer.Google Scholar
Titman, J. J. & Keeler, J. (1990). Measurement of homonuclear coupling constants from NMR correlation spectra. J. magn. Reson. 89, 640–646.Google Scholar
Tuerk, C, Gauss, P., Thermes, C, Groebe, D., Guild, N., Stormo, G., Gayle, M., D'Aubenton-Carafa, Y., Uhlenbeck, O., Tinoco, I. Jr., Brody, E. N. & Gold, L. (1988). Extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc. natn. Acad. Sci. U.S.A. 85, 1364–1368.CrossRefGoogle ScholarPubMed
Turner, D. H., Sugimoto, N. & Freier, S. M. (1988). RNA structure prediction. A. Rev. Biophys. Biophys. Chem. 17, 167–192.CrossRefGoogle Scholar
Uhlenbeck, O. C. (1990). Tetraloops and RNA folding. Nature, Lond. 346, 613–614.CrossRefGoogle ScholarPubMed
van de Ven, F. J. N. & Hilbers, C. W. (1988). Nucleic acid and magnetic resonance. Eur. J. Biochem. 178, 1–38.CrossRefGoogle Scholar
Varani, G., Cheong, C. & Tinoco, I. Jr. (1991). Structure of an unusually stable RNA hairpin. Biochemistry 30, 3280–3289.CrossRefGoogle ScholarPubMed
Varani, G. & Tinoco, I. Jr. (1991). Carbon assignments and heteronuclear coupling constants for an RNA oligonucleotide from natural abundance 13C-1H correlated experiments. J. Am. Chem. Soc. (in the press).Google Scholar
Varani, G., Wimberly, B. & Tinoco, I. Jr. (1989). Conformation and dynamics of an RNA internal loop. Biochemistry 28, 7760–7772.CrossRefGoogle ScholarPubMed
Waring, R. B. (1989). Identification of phosphate groups important to self-splicing of the Tetrahymena rRNA intron as determined by phosphorothioate substitution. Nucl. Acids Res. 17, 10281–10293.CrossRefGoogle ScholarPubMed
Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Alagona, G., Profeta, S. Jr, & Weiner, P. (1984). A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765–784.CrossRefGoogle Scholar
Widmer, H. & Wüthrich, K. (1987). Simulated two-dimensional NMR cross-peak fine structures for 1H spin systems in polypeptides and polydeoxynucleotides. J. magn. Res. 74, 316–336.Google Scholar
Widmer, G., Neri, D., Otting, G. & Wüthrich, K. (1989). A heteronuclear threedimensional NMR experiment for measurement of small heteronuclear coupling constants in biological macromolecules. J. magn. Res. 85, 426–431.Google Scholar
Williamson, J. R. & Boxer, S. G. (1989a). Multinuclear NMR studies of DNA hairpins. 1. Structure and dynamics of d(CGCGTTGTTCGCG). Biochemistry 28, 2819–2831.CrossRefGoogle ScholarPubMed
Williamson, J. R. & Boxer, S. G. (1989b). Multinuclear NMR studies of DNA hairpins. 2. Sequence dependent structural variations. Biochemistry 28, 2831–2836.CrossRefGoogle ScholarPubMed
Woese, C. R., Winker, S. & Guttel, R. R. (1990). Architecture of ribosomal RNA: constraints on the sequences of ‘tetraloops’. Proc. natn. Acad. Sci. U.S.A. 87, 8467–8471.CrossRefGoogle ScholarPubMed
Wu, J. & Marshall, A. G. (1990a). 500-MHz proton NMR evidence for two solution structures of the common arm base-paired segment of wheat germ 5S ribosomal RNA. Biochemistry 29, 1722–1730.CrossRefGoogle ScholarPubMed
Wu, J. & Marshall, A. G. (1990b). Wheat germ 5S ribosomal RNA common arm fragment conformations observed by 1H and 31P nuclear magnetic resonance spectroscopy. Biochemistry 29, 1730–1736.CrossRefGoogle ScholarPubMed
Wüthrich, K. (1986). NMR of Proteins and Nucleic Acids. New York: Wiley.CrossRefGoogle Scholar
Wüthrich, K. (1989). Protein structure determination in solution by nuclear magnetic resonance spectroscopy. Science, Wash. 243, 45–50.CrossRefGoogle ScholarPubMed
Wyatt, J. R., Puglisi, J. D. & Tinoco, I. Jr. (1990). RNA pseudoknots. Stability and loop size requirements. J. molec. Biol. 214, 455–470.CrossRefGoogle ScholarPubMed