Recent Advances in RNA Structure Determination by NMR

M. Hennig1, J.R. Williamson1, A.S. Brodsky2, J.L. Battiste3

1 The Scripps Research Institute, La Jolla, California, 2 Dana‐Farber Cancer Institute, Boston, Massachusetts, 3 Harvard Medical School, Boston, Massachusetts
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 7.7
DOI:  10.1002/0471142700.nc0707s02
Online Posting Date:  May, 2001
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Despite recent advances in the solution of NMR structures of RNA and RNA‐ligand complexes, the rate limiting step remains the gathering of a large number of NOE and torsion restraints. Additional sources of information for structure determination of larger RNA molecules have recently become available, and it is possible to supplement NOE and J‐coupling data with the measurement of dipolar couplings and cross‐correlated relaxation rates in high‐resolution NMR spectroscopy.

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Table of Contents

  • Isotopic Labeling of RNA
  • Assignment of RNA NMR Resonances
  • NOE Measurement
  • Hydrogen Bonds in RNA NMR Structures
  • Measurement of Backbone Torsions
  • Novel Parameters for Liquid‐State NMR Structure Determination
  • RNA Structures
  • Prospects for Large RNA Molecules
  • Figures
  • Tables
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Literature Cited

Literature Cited
   Aboul‐ela, F., Karn, J., and Varani, G. 1995. The structure of the human immunodeficiency virus Type‐1 TAR RNA reveals principles of RNA recognition by Tat protein. J. Mol. Biol. 253:313‐332.
   Allain, F.H.‐T. and Varani, G. 1995. Structure of the P1 helix from group I self‐splicing introns. J. Mol. Biol. 250:333‐353.
   Allain, F.H.‐T. and Varani, G. 1997. How accurately and precisely can RNA structure be determined by NMR. J. Mol. Biol. 267:338‐351.
   Allain, F.H.‐T., Gubser, C.C., Howe, P.W.A., Nagai, K., Neuhaus, D., and Varani, G. 1996. Specificity of ribonucleoprotein interaction determined by RNA folding during complex formation. Nature 380:646‐650.
   Batey, R.T., Inada, M., Kujawinski, E., Puglisi, J.D., and Williamson, J.R. 1992. Preparation of isotopically labeled ribonucleotides for multidimensional NMR spectroscopy of RNA. Nucl. Acids Res. 20:4515‐4523.
   Batey, R.T., Battiste, J.L., and Williamson, J.R. 1995. Preparation of isotopically enriched RNAs for heteronuclear NMR. Methods Enzymol. 261:300‐322.
   Battiste, J.L., Tan, R., Frankel, A.D., and Williamson, J.R. 1995. Assignment and modeling of the Rev Response Element RNA bound to a Rev peptide using 13C‐heteronuclear NMR. J. Biomol. NMR 6:375‐389.
   Battiste, J.L., Mao, H., Rao, N.S., Tan, R., Muhandiram, D.R., Kay, L.E., Frankel, A.D., and Williamson, J.R. 1996. α‐helix‐RNA major groove recognition in an HIV‐1 Rev peptide‐RRE RNA complex. Science 273:1547‐1551.
   Brodsky, A.S. and Williamson, J.R. 1997. Solution structure of the HIV‐2 TAR‐argininamide complex. J. Mol. Biol. 267:624‐39.
   Brünger, A.T. and Karplus, M. 1991. Molecular dynamics simulations with experimental restraints. Acc. Chem. Res. 24:54‐61.
   Brutscher, B., Boisbouvier, J., Pardi, A., Marion, D., and Simorre, J.‐P. 1998. Improved sensitivity and resolution in 1H‐13C NMR experiments of RNA. J. Am. Chem. Soc. 120:11845‐11851.
   Cai, Z. and Tinoco, I. 1996. Solution structure of loop A from the hairpin ribozyme from tobacco ringspot virus satellite. Biochemistry 35:6026‐6036.
   Cate, J.H., Gooding, A.R., Podell, E., Zhou, K., Golden, B.L., Kondrot, C.E., Cech, T.R., and Doudna, J.A. 1996. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273:1678‐1685.
   Cilley, C.D. and Williamson, J.R. 1997. Analysis of bacteriophage N protein and peptide binding to boxB RNA using polyacrylamide gel coelectrophoresis (PACE). RNA 3:57‐67.
   Clore, G.M., Murphy, E.C., Gronenborn, A.M., and Bax, A. 1998. Determination of three‐bond 1H3′‐31P couplings in nucleic acids and protein‐nucleic acid complexes by quantitative J correlation spectroscopy. J. Magn. Reson. 134:164‐7.
   Dayie, K.T., Tolbert, T.J., and Williamson, J.R. 1998. 3D C(CC)H TOCSY experiment for assigning protons and carbons in uniformly 13C‐ and selectively 2H‐labeled RNA. J. Magn. Reson. 130:97‐101.
   de Vlieg, J. and van Gunsteren, W.F. 1991. Combined procedures of distance geometry and molecular dynamics for determining protein structure from nuclear magnetic resonance data. Methods Enzymol. 202:268‐300.
   Dieckmann, T. and Feigon, J. 1994. Heteronuclear techniques in NMR studies of RNA and DNA. Curr. Opin. Struct. Biol. 4:745‐749.
   Dieckmann, T., Suzuki, E., Nakamura, G.D., and Feigon, J. 1996. Solution structure of an ATP‐binding RNA aptamer reveals a novel fold. RNA 2:628‐640.
   Dingley, A.J. and Grzesiek, S. 1998. Direct observation of hydrogen bonds in nucleic acid base pairs by internucleotide 2JNN couplings. J. Am. Chem. Soc. 120:8293‐8297.
   Fan, P., Suri, A.K., Fiala, R., Live, D., and Patel, D.J. 1996. Molecular recognition in the FMN‐RNA aptamer complex. J. Mol. Biol. 258:480‐500.
   Farmer, B.T., Muller, L., Nikonowicz, E.P., and Pardi, A. 1993. Unambiguous resonance assignments in 13C,15N‐labeled nucleic acids by 3D triple‐resonance NMR. J. Am. Chem. Soc. 115:11040‐11041.
   Farmer, B.T., Mueller, L., Nikonowicz, E.P., and Pardi, A. 1994. Unambiguous through‐bond sugar‐to‐base correlations for purines in 13C,15N‐labeled nucleic acids: The HsCsNb, HsCs(N)bCb, and HbNbCb experiments. J. Biomol. NMR 4:129‐133.
   Felli, I.C., Richter, C., Griesinger, C., and Schwalbe, H. 1999. Determination of RNA sugar pucker mode from cross‐correlated relaxation in solution NMR. J. Am. Chem. Soc. 121:1956‐1957.
   Fesik, S., Eaton, H., Olejniczak, E., and Zuiderweg, E. 1990. 2D and 3D NMR spectroscopy employing 13C‐13C magnetization transfer by isotropic mixing. Spin identification in large proteins. J. Am. Chem. Soc. 112:886‐888.
   Fiala, R., Jiang, F., and Patel, D.J. 1996. Direct correlation of exchangeable and nonexchageable protons on purine bases in 13C,15N‐labeled RNA using a HCCNH‐TOCSY experiment. J. Am. Chem. Soc. 118:689‐690.
   Fiala, R., Jiang, F., and Sklenar, V. 1998. Sensitivity optimized HCN and HCNCH experiments for 13C/15N‐labeled oligonucleotides. J. Biomol. NMR 12:373‐383.
   Foldesi, A., Nilsson, F.P.R., Glemarec, C., Gioeli, C., and Chattopadhyaya, J. 1992. Synthesis of 1′#, 2′, 3′, 4′#, 5′, 5′′‐2H6‐beta‐D‐ribonucleosides and 1′#, 2′, 3′, 4′#, 5′, 5′′‐2H7‐beta‐D‐2′‐deoxyribonucleosides for selective suppression of proton resonances in partially deuterated oligo‐DNA, oligo‐RNA and in 2,4A core (1H‐NMR window). Tetrahedron 48:9033‐9072.
   Foldesi, A., Yamakage, S.‐I., Nilsson, F.P.R., Maltseva, T.V., and Chattopadhyaya, J. 1996. The use of non‐uniform deuterium labelling [“NMR‐window”] to study the NMR structure of a 21mer RNA hairpin. Nucl. Acids Res. 24:1187‐1194.
   Fourmy, D., Recht, M.I., Blanchard, S.C., and Puglisi, J.D. 1996. Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an aminoglycoside antibiotic. Science 274:1367‐1371.
   Giessner‐Prettre, C. and Pullman, B. 1987. Quantum mechanical calculations of NMR chemical shifts in nucleic acids. Q. Rev. Biophys. 20:113‐172.
   Glaser, S.J., Schwalbe, H., Marino, J.P., and Griesinger, C. 1996. Directed TOCSY, a method for selection of directed correlations by optimal combinations of isotropic and longitudinal mixing. J. Magn. Reson. B112:160‐180.
   Glemarec, C., Kukel, J., Foldesi, A., Maltseva, T., Sandstrom, A., Kirsebom, L.A., and Chattopadhyaya, J. 1996. The NMR structure of 31mer RNA domain of Escherichia coli RNase P RNA using its non‐uniformly deuterium labelled counterpart [the “NMR‐window” concept]. Nucl. Acids Res. 24:2022‐2035.
   Gorenstein, D.G. and Luxon, B.A. 1979. High‐resolution phosphorus nuclear magnetic resonance spectra of yeast phenylalanine transfer ribonucleic acid. melting curves and relaxation effects. Biochemistry 18:3796‐3804.
   Gueron, M. and Leroy, J.L. 1995. Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol. 261:383‐413.
   Gueron, M. and Shulman, R.G. 1975. 31P magnetic resonance of tRNA. Proc. Natl. Acad. Sci. U.S.A. 72:3482‐3485.
   Hansen, M.R., Mueller, L., and Pardi, A. 1998a. Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nature Struct. Biol. 5:1065‐1074.
   Hansen, M.R., Rance, M., and Pardi, A. 1998b. Observation of long‐range 1H‐1H distances in solution by dipolar coupling interactions. J. Am. Chem. Soc. 120:11210‐11211.
   Hennig, M. and Williamson, J.R. 2000. Detection of N‐H...N hydrogen bonding in RNA via scalar coupling in the absence of observable imino proton resonances. Nucl. Acids Res. 28:1585‐1593.
   Heus, H. and Pardi, A. 1991. Structural features that give rise to unusual stability of RNA hairpins containing GNRA loops. Science 253:191‐194.
   Heus, H.A., Wijmenga, S.S., van de Ven, F.J.M., and Hilbers, C.W. 1994. Sequential backbone assignment in 13C‐labeled RNA via through‐bond coherence transfer using three‐dimensional triple resonance spectroscopy(1H,13C, 31P) and two‐dimensional hetero TOCSY. J. Am. Chem. Soc. 116:4983‐4984.
   Hines, J.V., Varani, G., Landry, S.M., and Tinoco, J.I. 1993. The stereospecific assignment of H5′ and H5′′ in RNA using the sign of two‐bond carbon‐proton scalar coupling. J. Am. Chem. Soc. 115:11002‐11003.
   Hines, J.V., Landry, S.M., Varani, G., and Tinoco, J.I. 1994. Carbon‐proton scalar couplings in RNA: 3D heteronuclear and 2D isotope‐edited NMR of a 13C‐labeled extra‐stable hairpin. J. Am. Chem. Soc. 116:5823‐5831.
   Hoogstraten, C.G. and Pardi, A. 1998a. Improved distance analysis in RNA using network‐editing techniques for overcoming errors due to spin diffusion. J. Biomol. NMR 11:85‐95.
   Hoogstraten, C.G. and Pardi, A. 1998b. Measurement of carbon‐phosphorus J coupling constants in RNA using spin‐echo difference constant‐time HCCH‐COSY. J. Magn. Reson. 133:236‐240.
   Hu, W., Kakalis, L.T., Jiang, L., Jiang, F., Ye, X., and Majumdar, A. 1998. 3D HCCH‐COSY‐TOCSY experiment for the assignment of ribose and amino acid side chains in 13C labeled RNA and protein. J. Biomol. NMR 12:559‐564.
   Jiang, F., Kumar, R.A., Jones, R.A., and Patel, D.J. 1996. Structural basis of RNA folding and recognition in an AMP‐RNA aptamer complex. Nature 382:183‐186.
   Jucker, F.M. and Pardi, A. 1995. Solution structure of the CUUG hairpin loop: A novel RNA tetraloop motif. Biochemistry 34:14416‐27.
   Jucker, F.M., Heus, H.A., Yip, P.F., Moors, E.H.M., and Pardi, A. 1996. A network of heterogeneous hydrogen bonds in GNRA tetraloops. J. Mol. Biol. 264:968‐980.
   Karplus, M. 1959. Contact electron‐spin coupling of nuclear magnetic moments. J. Chem. Phys. 30:11‐15.
   Kay, L.E., Ikura, M., and Bax, A. 1990. Proton‐proton correlation via carbon‐carbon couplings: A three‐dimensional NMR approach for the assignment of aliphatic resonances in proteins labeled with carbon‐13. J. Am. Chem. Soc. 112:888‐889.
   Kellogg, G.W. 1992. Proton‐detected hetero‐TOCSY experiments with application to nucleic acids. J. Magn. Reson. 98:176‐182.
   Kellogg, G.W. and Schweitzer, B.I. 1993. Two‐ and three‐dimensional 31P‐driven NMR procedures for complete assignment of backbone resonances in oligodeoxyribonucleotides. J. Biomol. NMR 3:577‐95.
   Krishnan, V.V. and Rance, M. 1995. Influence of chemical exchange among homonuclear spins in heteronuclear coherence‐transfer experiments in liquids. J. Magn. Reson. A A116:97‐106.
   Kundrot, C. 1996. Rapid identification of ordered and disordered domains in NMR structures. J. Am. Chem. Soc. 118:8725‐8726.
   Legault, P., Farmer, B.T., II, Mueller, L., and Pardi, A. 1994. Through‐bond correlation of adenine protons in a 13C‐labeled ribozyme. J. Am. Chem. Soc. 116:2203‐2204.
   Legault, P., Jucker, F.M., and Pardi, A. 1995. Improved measurement of 13C, 31P J coupling constants in isotopically labeled RNA. FEBS Lett. 362:156‐160.
   Liu, Y., Zhao, D., Altman, R., and Jardetzky, O. 1992. A systematic comparison of three structure determination methods from NMR data: Dependence upon quality and quantity of data. J. Biomol. NMR 2:373‐388.
   Mao, H. and Williamson, J.R. 1999. Assignment of the L30‐mRNA complex using selective isotopic labeling and RNA mutants. Nucl. Acids Res. 27:4059‐4070.
   Mao, H., White, S.A., and Williamson, J.R. 1999. A novel loop‐loop recognition motif in the yeast ribosomal protein L30 autoregulatory RNA complex [see comments]. Nature Struct. Biol. 6:1139‐1147.
   Marino, J.P., Prestegard, J.H., and Crothers, D.M. 1994a. Correlation of adenine H2/H8 resonances in uniformly 13C labeled RNAs by 2D HCCH‐TOCSY: A new tool for 1H assignment. J. Am. Chem. Soc. 116:2205‐2206.
   Marino, J.P., Schwalbe, H., Anklin, C., Bermel, W., Crothers, D.M., and Griesinger, C. 1994b. A three‐dimensional triple‐resonance 1H, 13C, 31P experiment: Sequential through‐bond correlation of ribose protons and intervening phosphorous along the RNA oligonucleotide backbone. J. Am. Chem. Soc. 116:6472‐6473.
   Marino, J.P., Schwalbe, H., Anklin, C., Bermel, W., Crothers, D.M., and Griesinger, C. 1995. Sequential correlation of anomeric ribose protons and intervening phosphorus in RNA oligonucleotides by a 1H,13C,31P triple resonance experiment: HCP‐CCH‐TOCSY. J. Biomol. NMR 5:87‐92.
   Marino, J.P., Diener, J.L., Moore, P.B., and Griesinger, C. 1997. Multiple‐quantum coherence dramatically enhance the sensitivity of CH and CH2 correlations in uniformly 13C‐labeled RNA. J. Am. Chem. Soc. 119:7361‐7366.
   Marino, J.P., Schwalbe, H., and Griesinger, C. 1999. J‐coupling restraints in RNA structure determination. Acc. Chem. Res 32:614‐623.
   Meissner, A. and Sorensen, O.W. 1999a. Optimization of three‐dimensional TROSY‐type HCCH NMR correlation of aromatic 1H‐13C groups in proteins. J. Magn. Reson. 139:447‐450.
   Meissner, A. and Sorensen, O.W. 1999b. Suppression of diagonal peaks in TROSY‐type 1H NMR NOESY spectra of 15N‐labeled proteins. J. Magn. Reson. 140:499‐503.
   Meissner, A. and Sorensen, O.W. 2000. Three‐dimensional protein NMR TROSY‐type (15)N‐resolved (1)H(N)‐(1)H(N) NOESY spectra with diagonal peak suppression. J. Magn. Reson. 142:195‐198.
   Mohebbi, A. and Shaka, A.J. 1991. Improvements in carbon‐13 broadband homonuclear cross‐polarization for 2D and 3D NMR. Chem. Phys. Lett. 178:374‐378.
   Mueller, L., Legault, P., and Pardi, A. 1995. Improved RNA structure determination by detection of NOE contacts to exchange‐broadened amino protons. J. Am. Chem. Soc. 117:11043‐11048.
   Nikonowicz, E.P. and Pardi, A. 1992. Three‐dimensional heteronuclear NMR studies of RNA. Nature 355:184‐186.
   Nikonowicz, E.P. and Pardi, A. 1993. An efficient procedure for assignment of the proton, carbon and nitrogen resonances in 13C/15N labeled nucleic acids. J. Mol. Biol. 232:1141‐1156.
   Nikonowicz, E.P., Sirr, A., Legault, P., Jucker, F.M., Baer, L.M., and Pardi, A. 1992. Preparation of 13C and 15N labelled RNAs for heteronuclear multi‐dimensional NMR studies. Nucl. Acids Res. 20:4507‐4513.
   Nilges, M. 1996. Structure calculation from NMR data. Curr. Opin. Struct. Biol. 6:617‐623.
   Otting, G. and W¨thrich, K. 1989a. Extended heteronuclear editing of 2D 1H NMR spectra of isotope‐labeled proteins, using the X(ω1, ω2) double half filter. J. Magn. Reson. 85:586‐594.
   Otting, G. and Wüthrich, K. 1989b. Studies of protein hydration in aqueous solution by direct NMR observation of individual protein‐bound water molecules. J. Am. Chem. Soc. 111:1871‐1875.
   Otting, G. and 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.
   Otting, G., Liepinsh, E., and Wüthrich, K. 1991. Protein hydration in aqueous solution. Science 254:974‐980.
   Pardi, A. 1995. Multidimensional heteronuclear NMR experiments for structure determination of isotopically labeled RNA. Methods Enzymol. 261:350‐380.
   Pardi, A. and Nikonowicz, E.P. 1992. Simple procedure for resonance assignment of the sugar protons in 13C‐labeled RNAs. J. Am. Chem. Soc. 114:9202‐9203.
   Pervushin, K., Riek, R., Wider, G., and Wüthrich, K. 1997. Attenuated T2 relaxation by mutual cancellation of dipole‐dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc. Natl. Acad. Sci. U.S.A. 94:12366‐71.
   Pervushin, K., Ono, A., Fernandez, C., Szyperski, T., Kainosho, M., and Wüthrich, K. 1998a. NMR scalar couplings across Watson‐Crick base pair hydrogen bonds in DNA observed by transverse relaxation‐optimized spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 95:14147‐14151.
   Pervushin, K., Riek, R., Wider, G., and Wüthrich, K. 1998b. Transverse relaxation‐optimized spectroscopy (TROSY) for NMR studies of aromatic spin systems in 13C‐labeled proteins. J. Am. Chem. Soc. 120:6394‐6400.
   Pervushin, K., Wider, G., Riek, R., and Wüthrich, K. 1999. The 3D NOESY‐[1H,15N,1H]‐ZQ‐TROSY NMR experiment with diagonal peak suppression. Proc. Natl. Acad. Sci. U.S.A. 96:9607‐9612.
   Pley, H., Flaherty, K.M., and McKay, D.B. 1994a. Three‐dimensional structure of a hammerhead ribozyme. Nature 372:68‐74.
   Pley, H.W., Flaherty, K.M., and McKay, D.B. 1994b. Model of an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. Nature 372:111‐113.
   Prestegard, J.H. 1998. New techniques in structural NMR—Anisotropic interactions. Nature Struct. Biol. 5:517‐522.
   Puglisi, J.D., Chen, L., Blanchard, S., and Frankel, A.D. 1995. Solution structure of a bovine immunodeficiency virus tat TAR RNA‐peptide complex. Science 270:1200‐1203.
   Quant, S., Wechselberger, R.W., Wolter, M.A., Wörner, K.‐H., Schell, P., Engels, J.W., Griesinger, C., and Schwalbe, H. 1994. Chemical synthesis of 13C‐labelled monomers for the solid‐phase and template controlled enzymatic synthesis of DNA and RNA oligomers. Tetrahedron Lett. 35:6649‐6652.
   Reif, B., Hennig, M., and Griesinger, C. 1997. Direct measurement of angles between bond vectors in high‐resolution NMR. Science 276:1230‐1233.
   Richter, C., Reif, B., Wörner, K.‐H., Quant, S., Marino, J.P., Engels, J.W., Griesinger, C., and Schwalbe, H. 1998. A new experiment for the measurement of nJ(C,P) coupling constants including 3J(C4′i,Pi) and 3J(C4′i,Pi+1) in oligonucleotides. J. Biomol. NMR 12:223‐230.
   Richter, C., Griesinger, C., Felli, I.C., Cole, P.T., Varani, G., and Schwalbe, H. 1999. Determination of sugar conformation in large RNA oligonucleotides from analysis of dipole‐dipole cross‐correlated relaxation by solution NMR spectroscopy. J. Biomol. NMR 15:241‐250.
   Salemink, P.J.M., Swarthof, T., and Hilbers, C.W. 1979. Studies of yeast phenylalanine‐accepting transfer ribonucleic acid backbone structure in solution by phosphorous‐31 nuclear magnetic resonance spectroscopy. Biochemistry 18:3477‐3485.
   SantaLucia, J., Shen, L.X., Cai, Z., Lewis, H., and Tinoco, I. 1995. Synthesis and NMR of RNA with selective isotopic enrichment in the bases. Nucl. Acids Res 23:4913‐4921.
   Schwalbe, H., Samstag, W., Engels, J.W., Bermel, W., and Griesinger, C. 1993. Determination of 3J(C,P) and 3J(H,P) coupling constants in nucleotide oligomers with FIDS‐HSQC. J. Biomol. NMR 3:479‐486.
   Schwalbe, H., Marino, J.P., King, G.C., Wechselberger, R., Bermel, W., and Griesinger, C. 1994. Determination of a complete set of coupling constants in 13C‐labeled oligonucleotides. J. Biomol. NMR 4:631‐644.
   Schwalbe, H., Marino, J.P., Glaser, S.J., and Griesinger, C. 1995. Measurement of H,H‐coupling constants associated with v1,v2, and v3 in uniformly 13C labeled RNA by HCC‐TOCSY‐CCH‐E. COSY. J. Am. Chem. Soc. 117:7251‐7252.
   Scott, W.G., Finch, J.T., and Klug, A. 1995. The crystal structure of an all‐RNA hammerhead ribozyme: A proposed mechanism for RNA catalytic cleavage. Cell 81:991‐1002.
   Simorre, J.‐P., Zimmermann, G.R., Pardi, A., Farmer, B.T., II, and Mueller, L. 1995. Triple resonance HNCCCH experiments for correlating exchangeable and nonexchangeable cytidine and uridine base protons in RNA. J. Biomol. NMR 6:427‐432.
   Simorre, J.P., Zimmermann, G.R., Mueller, L., and Pardi, A. 1996a. Correlation of the guanosine exchangeable and nonexchangeable base protons in 13C‐/15N‐labeled RNA with an HNC‐TOCSY‐CH experiment. J. Biomol. NMR 7:153‐156.
   Simorre, J.‐P., Zimmermann, G., Mueller, L., and Pardi, A. 1996b. Triple‐resonance experiments for assignment of adenine base resonances in 13C/15N‐labeled RNA. J. Am. Chem. Soc. 118:5316‐5317.
   Sklenar, V. and Bax, A. 1987. Spin echo water suppression for the generation of pure phase two‐dimensional NMR spectra. J. Magn. Reson. 74:469‐479.
   Sklenar, V., Miyashiro, H., Zon, G., Miles, H.T., and Bax, A. 1986. Assignment of the 31P and 1H resonances in oligonucleotides by two‐dimensional NMR spectroscopy. FEBS Lett. 208:94‐98.
   Sklenar, V., Brooks, B.R., Zon, G., and Bax, A. 1987. Absorption mode two‐dimensional NOE spectroscopy of exchangeable protons in oligonucleotides. FEBS Lett. 216:249‐252.
   Sklenar, V., Peterson, R.D., Rejante, M.R., and Feigon, J. 1993a. Two‐ and three‐dimensional HCN experiments for correlating base and sugar resonances in 15N,13C‐labeled RNA oligonucleotides. J. Biomol. NMR 3:721‐7.
   Sklenar, V., Peterson, R.D., Rejante, M.R., Wang, E., and Feigon, J. 1993b. Two‐dimensional triple‐resonance HCNCH experiment for direct correlation of ribose H1′ and base H8, H6 protons in 13C,15N‐labeled RNA oligonucleotides. J. Am. Chem. Soc. 115:12181‐12182.
   Sklenar, V., Peterson, R.D., Rejante, M.R., and Feigon, J. 1994. Correlation of nucleotide base and sugar protons in a 15N‐labeled HIV‐1 RNA oligonucleotide by 1H‐15N HSQC experiments. J. Biomol. NMR 4:117‐22.
   Sklenar, V., Dieckmann, T., Butcher, S.E., and Feigon, J. 1996. Through‐bond correlation of imino and aromatic resonances in 13C, 15N‐labeled RNA via heteronuclear TOCSY. J. Biomol. NMR 7:83‐87.
   Sklenar, V., Dieckmann, T., Butcher, S.E., and Feigon, J. 1998. Optimization of triple‐resonance HCN experiments for application to larger RNA oligonucleotides. J. Magn. Reson. 130:119‐124.
   Szyperski, T., Fernandez, C., Ono, A., Wüthrich, K., and Kainosho, M. 1999. The 2D [31P] spin‐echo‐difference constant‐time [13C, 1H]‐HMQC experiment for simultaneous determination of 3J(H3′P) and 3J(C4′P) in 13C‐labeled nucleic acids and their protein complexes. J. Magn. Reson. 140:491‐494.
   Tjandra, N. and Bax, A. 1997a. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium [see comments]. Science 278(5340):1111‐1114. [published erratum appears in Science 1997, 278(5344):1697]
   Tjandra, N. and Bax, A. 1997b. Measurement of dipolar contributions to 1JCH splittings from magnetic‐field dependence of J modulation in two‐dimensional NMR spectra. J. Magn. Reson. 124:512‐515.
   Tjandra, N., Grzesiek, S., and Bax, A. 1996. Magnetic field dependance of nitrogen‐proton J splittings in 15N‐enriched human ubiquitin resulting from relaxation interference and residual dipolar coupling. J. Am. Chem. Soc. 118:6264‐6272.
   Tjandra, N., Omichinski, J.G., Gronenborn, A.M., Clore, G.M., and Bax, A. 1997. Use of dipolar 1H‐15N and 1H‐13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nature Struct. Biol. 4:732‐738.
   Tolbert, T.J. and Williamson, J.R. 1996. Preparation of specifically deuterated RNA for NMR studies using a combination of chemical and enzymatic synthesis. J. Am. Chem. Soc. 118:7929‐7940.
   Varani, G. and Tinoco, J.I. 1991. RNA structure and NMR spectroscopy. Q. Rev. Biophys. 24:479‐532.
   Varani, G., Aboul‐ela, F., Allain, F., and Gubser, C.C. 1995. Novel three‐dimensional 1H‐13C‐31P triple resonance experiments for sequential backbone correlations in nucleic acids. J. Biomol. NMR 5:315‐320.
   Varani, G., Aboul‐ela, F., and Allain, F. H.‐T. 1996. NMR investigation of RNA structure. Prog. Nucl. Magn. Reson. Spectrosc. 29:51‐127.
   Wijmenga, S.S. and van Buuren, B.N.M. 1998. The use of NMR methods for conformational studies of nucleic acids. Prog. Nucl. Magn. Reson. Spectrosc. 32:287‐387.
   Wijmenga, S.S., Heus, H.A., Leeuw, H.A.E., Hoppe, H., van der Graaf, M., and Hilbers, C.W. 1995. Sequential backbone assignment of uniformly 13C‐labeled RNAs by a two‐dimensional P(CC)H‐TOCSY triple resonance NMR experiment. J. Biomol. NMR 5:82‐86.
   Wöhnert, J., Ramachandran, R., Görlach, M., and Brown, L.R. 1999. Triple‐resonance experiments for correlation of H5 and exchangeable pyrimidine base hydrogens in 13C,15N‐labeled RNA. J. Magn. Reson. 139:430‐433.
   Wüthrich, K. 1986. NMR of Proteins and Nucleic Acids. John Wiley & Sons, New York.
   Wüthrich, K. 1998. The second decade—into the third millenium. Nature Struct. Biol. 5:492‐495.
   Xu, J., Lapham, J., and Crothers, D.M. 1996. Determining RNA solution structure by segmental isotopic labeling and NMR: Application to Caenorhabditis elegans spliced leader RNA 1. Proc. Natl. Acad. Sci. U.S.A. 93:44‐48.
   Xu, X.‐P., Chiu, W.‐L.A.K., and Au‐Yeung, S.C.F. 1998. Chemical shift and structure relationship in nucleic acids: Correlation of backbone torsion angles γ and α with 13C chemical shifts. J. Am. Chem. Soc. 120:4230‐4231.
   Ye, X., Kumar, R.A., and Patel, D.J. 1995. Molecular recognition in the bovine immunodeficiency virus tat peptide TAR RNA complex. Chem. Biol. 2:827‐840.
   Ye, X., Gorin, A., Ellington, A.D., and Patel, D.J. 1996. Deep penetration of an a‐helix into a widened RNA major groove in the HIV‐1 rev peptide‐RNA aptamer complex. Nature Struct. Biol. 3:1026‐1033.
   Zhang, X., Gaffney, B.L., and Jones, R.A. 1998. 15N NMR of RNA fragments containing specifically labeled tandem GA pairs. J. Am. Chem. Soc. 120:6625‐6626.
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