Hostname: page-component-cd9895bd7-p9bg8 Total loading time: 0 Render date: 2024-12-29T11:16:41.550Z Has data issue: false hasContentIssue false

Quantum mechanical calculations of NMR chemical shifts in nucleic acids

Published online by Cambridge University Press:  17 March 2009

C. Giessner-Prettre
Affiliation:
Laboratoire de Biochimie Théorique associé au C.N.R.S., Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
B. Pullman
Affiliation:
Laboratoire de Biochimie Théorique associé au C.N.R.S., Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France

Extract

During the last twenty-five years the development of quantum mechanical calculations and experimental measurements of chemical shifts of the different type of nuclei present in nucleic acids have run parallel in close relation to each other. The first calculations dealt with intramolecular effects on base proton shifts (Veillard, 1962) but the real breakthrough of the theory occurred with the advent of computations of intermolecular shielding due to the ring current effect of the nucleic acid bases (Giessner-Prettre & Pullman, 1970).

Type
Research Article
Copyright
Copyright © Cambridge University Press 1987

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

6. References

Adamiak, R. W., Galat, A. & Skaski, B. (1985). Salt and solvent dependent conformational transitions of ribo-CGCGCG duplex. Biochim. biophys. Acta 825, 345352.CrossRefGoogle Scholar
Alderfer, J. L. & Hazel, G. L. (1981). Nonequivalence of 31P NMR chemical shifts of RNA complexes. J. Am. chem. Soc. 103, 59255926.CrossRefGoogle Scholar
Alderfer, J. L., Lilga, K. T., French, J. B. & Box, H. C. (1984). 13C NMR studies of the effects of the carcinogen acetylaminofluorene on the conformation of dinucleoside monophosphates. Chem. Biol. Interact. 48, 6980.CrossRefGoogle Scholar
Alderfer, J. L. & Ts'o, P. O. P. (1977). Conformation properties of the furanose phosphate backbone in nucleic acids. A carbon-13 nuclear magnetic resonance study. Biochemistry 16, 24102417.CrossRefGoogle ScholarPubMed
Allore, B. D., Queen, A., Blonski, W. J. & Hruska, F. E. (1983). A kinetic and nuclear magnetic resonance study of methylated pyrimidine nucleosides. Can. J. Chem. 61, 23972402.CrossRefGoogle Scholar
Arnott, S., Chandrasekaran, R.Birdsall, D. L., Leslie, A. G. W. & Ratliff, R. L. (1980). Left-handed DNA helices. Nature 283, 743745.CrossRefGoogle ScholarPubMed
Arnott, S., Chandrasekaran, R., Puigjaner, L.C., Walker, J. K., Hall, I. H., Birdsall, D. L. & Ratliff, R. L. (1983). Wrinkled DNA. Nucl. Acids Res. 11, 14571474.CrossRefGoogle ScholarPubMed
Arnott, S. & Hukins, D. W. L. (1972). Optimized parameters for A-DNA and B-DNA. Biochem. biophys. Res. Com. 48, 15041509.CrossRefGoogle Scholar
Arnott, S., Hukins, D. W. L. & Dover, S. D. (1972). Optimized parameters for RNA double-helices. Biochem. biophys. Res. Com. 48, 13921399.CrossRefGoogle Scholar
Arter, D. B. & Schmidt, P. G. (1976). Ring current shielding effects in nucleic acid doubles helices. Nucl. Acids Res. 3, 14371447.CrossRefGoogle ScholarPubMed
Borer, P. N., Kan, L.-S. & Ts'o, P. O. P. (1975). Conformation and interaction in short nucleic acid double stranded helix. I. Proton magnetic resonance studies of the nonexchangeable protons of ribosyl ApApGpCpUpU. Biochemistry 14, 48474863.CrossRefGoogle ScholarPubMed
Borer, P. N., Zanatta, N., Holak, T. A., Levy, G. L.van Boom, J. H. & Wang, A. H. -J. (1984). Conformation and Dynamics of short DNA duplexes: (dC-dG)3 and (dC-dG)4. J. biomol. Struct. Dyn. 1, 13731383.CrossRefGoogle Scholar
Box, H. C., Lilga, K. T., French, J. B. & Alderfer, J. L. (1984). 13C and 31P NMR studies of the conformation of the carcinogen modified nucleic acid dimers. Chem. Biol. Interact. 52, 93102.CrossRefGoogle ScholarPubMed
Brown, T., Kneale, G., Hunter, W. N. & Kennard, O. (1986). Structural characterisation of the bromouracil. guanine base pair mismatch in a Z-DNA fragment. Nucl. Acids Res. 14, 18011809.CrossRefGoogle Scholar
Buchner, P., Maurer, W. & Ruterjans, H. (1978). Nitrogen-15 nuclear magnetic resonance spectroscopy of 15N-labelled nucleotides. J. magn. Reson. 29, 4563.Google Scholar
Buck, F., Hahn, K.-D., Zemann, W., Ruterjans, H., Sadler, J. R., Beyereuter, K., Kapteinc, R., Scheek, R. & Hull, W. E. (1983). NMR study of the interaction between the lac repressor and the lac operator. Eur. J. Biochem. 132, 321327.CrossRefGoogle ScholarPubMed
Buckingham, A. D. (1960). Chemical shift in the nuclear magnetic resonance spectra of molecules containing polar groups. Can. J. Chem. 38, 300307.CrossRefGoogle Scholar
Burgar, M. I., Dhawan, D. & Fiat, D. (1982). 17O and 14N spectroscopy of 17O-labelled nucleic acid bases. Org. magn. Reson. 20, 184190.CrossRefGoogle Scholar
Chen, C.-W. & Cohen, J. S. (1983). Salt- and sequence-dependence of the secondary structure of DNA in solution by 31P-NMR spectroscopy. Biopolymers 22, 879893.CrossRefGoogle Scholar
Cheng, D. M., Kan, L.-S., Frechet, D., Ts'O, P. O. P., Uesugi, S., Shida, T. & Ikehara, M. (1984). 1H and 31p nuclear magnetic resonance studies on the conformation of d(CpGpCpG)2 and d(CpG.pCpGpCpG)2 short helices in B conformation. Biopolymers 23, 775795.CrossRefGoogle Scholar
Cheng, D. M., Kan, L.-S., Ts'o, P. O. P., Giessner-Prettre, C. & Pullman, B. (1980). 1H and 13C nuclear magnetic resonance studies on purine. J. Am. chem. Soc. 102, 525534.CrossRefGoogle Scholar
Chesnut, D. B. & Foley, C. K. (1986). A basis set study of NMR chemical shift in PH3. J. chem. Phys. 85, 28142820.CrossRefGoogle Scholar
Cohen, J. S., Wooten, J. B. & Chatterjee, C. L. (1981). Characterization of alternating deoxyribonucleic acid conformation in solution by phosphorus 31 nuclear magnetic resonance spectroscopy. Biochemistry 20, 30493055.CrossRefGoogle ScholarPubMed
Cozzone, P. J. & Jardetzky, O. (1976). Phosphorus-31 fourier trans-form, nuclear magnetic resonance study of mononucleotides and dinucleotides. 1. Chemical shifts. Biochemistry 15, 48534859.CrossRefGoogle Scholar
Davanloo, P. & Crothers, D. M. (1979). Nuclear magnetic resonance investigation of lysine oligopeptides and a complex with d(pA)3pGpC(pT)3. Biopolymers 18, 22132231.CrossRefGoogle Scholar
Day, B. & Buckingham, A. D. (1976). The ab initio computation of some magnetic properties and their variation with an electric field. The hydrogen fluoride molecule. Molec. Phys. 32, 343351.CrossRefGoogle Scholar
De Leeuw, H. P. M., Haasnoot, C. A. G. & Altona, C. (1980). Empirical correlations between conformational parameters in β-D-furanoside fragments derived from a statistical survey of crystal structures of nucleic acid constituents. Israel J. Chem. 20, 108126.CrossRefGoogle Scholar
Dhingra, M. M., Sarma, R. H., Giessner-Prettre, C. & Pullman, B. (1978). Stereodynamics of dimer segments of RNA in aqueous solution. Biochemistry 17, 58155826.CrossRefGoogle ScholarPubMed
Dickerson, R. E. & Drew, H. R. (1981). Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J. molec. Biol. 149, 761786.CrossRefGoogle ScholarPubMed
Ditchfield, R. (1974). Self consistent field theory of diamagnetism. I. A gauge invariant LCAO method for NMR chemical shifts. Molec. Phys. 27, 789807.CrossRefGoogle Scholar
Dorman, D. E. & Roberts, J. D. (1970). Nuclear magnetic resonance spectroscopy: 13C spectra of some common nucleotides. Proc. natn. Acad. Sci. USA 65, 1926.CrossRefGoogle ScholarPubMed
Dreyfus, M. & Pullman, A. (1970). A non-empirical study of the hydrogen bond between peptide units. Theor. chim. Acta 19, 2037.CrossRefGoogle Scholar
Dugaiszyk, A. (1970). Conformation of pseudouridine and pseudouridine 5'-phosphate. Ultraviolet and nuclear magnetic resonance study. Biochemistry 9, 15571564.CrossRefGoogle Scholar
Dyllick-Brenzinger, C., Sullivan, G. R., Pang, P. P.Roberts, J. D. (1980). Selfassociation and base pairing of guanosine, cytidine, adenosine and uridine in dimethyl sulfoxide solution measured by 15N nuclear magnetic resonance spectroscopy. Proc. natn. Acad. Sci. USA 77, 55805582.CrossRefGoogle ScholarPubMed
Feigon, J., Wang, A. H.-J., van der Marel, G. A., van Boom, J. H. & Rich, A. (1985). Z-DNA forms without an alternating purine-pyrimidine sequence in solution. Science 230, 8284.CrossRefGoogle ScholarPubMed
Ferchiou, S. & Giessner-Prettre, C. (1985). Nonempirical quantum mechanical calculations of contributions of intermolecular interactions to nuclear magnetic shielding constants. II. Applications to conjugated molecules. J. magn. Reson. 61, 262271.Google Scholar
Ferguson, A. F. & Pople, J. A. (1965). Molecular orbital theory of diamagnetism. V. Anisotropies of some aromatic hydrocarbon molecules. J. chem. Phys. 42, 15601563.CrossRefGoogle Scholar
Feuerstein, B. G., Martin, L. J., Keniry, M. A., Wade, D. L. & Shafer, R. H. (1985). Nea DNA polymorphism evidence for a low salt, left handed form of poly(dG-m5dC). Nucl. Acids Res. 13, 41324141.CrossRefGoogle Scholar
Fratini, A. V., Kopka, M. L., Drew, H. R. & Dickerson, R. E. (1982). Reversible bending and helix geometry in a B-DNA dodecamer CGCGAATTBrCGCG. J. biol. Chem. 257, 1468614707.CrossRefGoogle Scholar
Fuji, S., Wang, A. H.-J., van der Marel, G., van Boom, J. & Rich, A. (1982). Molecular structure of (m5dC-dG)3: the role of the methyl group of 5-methyl cytosine in stabilizing Z-DNA. Nucl. Acids Res. 10, 78797890.CrossRefGoogle Scholar
Geerdes, H. A. M. & Hilbers, C. W. (1977). The imino proton NMR spectrum of yeast tRNAphe predicted from crystal coordinates. Nucl. Acids Res. 4, 207221.CrossRefGoogle Scholar
Gerlt, J. A., Demou, P. C. & Mehdi, S. (1982). 17O-NMR spectral properties of simple phosphate esters and adenine nucleotides. J. Am. chem. Soc. 104, 28482856.CrossRefGoogle Scholar
Germann, M. W., Schoenwaelder, K.-H. & van der Sande, J. H. (1985). Right- and left-handed (Z) helical conformations of the hair pin d(C-G)5T4(C-G)5 monomer and dimer. Biochemistry 24, 56985702.CrossRefGoogle Scholar
Gerothanassis, I. P. & Sheppard, N. (1982). Natural abundance 17O-NMR spectra of some inorganic and biologically important phosphates. J. magn. Reson. 46, 423439.Google Scholar
Giessner-Prettre, C. (1984). Ab initio quantum mechanical calculations of NMR chemical shifts in nucleic acid constituents. I. The Watson–Crick base pairs. J. biomol. Struct. Dyn. 2, 233248.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C. (1985). Ab initio quantum mechanical calculations of NMR chemical shifts in nucleic acid constituents. II. Conformational dependence of the 1H and 13C chemical shifts in the ribose. J. biomol. Struct. Dyn. 3, 145160.CrossRefGoogle Scholar
Giessner-Prettre, C. (1986). Ab initio quantum mechanical calculations of NMR chemical shifts in nucleic acid constituents. III. Chemical shift variations due to base stacking. J. biomol. Struct. Dyn. 4, 99110.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C. & Ferchiou, S. (1983). Non-empirical quantum mechanical calculations of three contributions to the variation of nuclear magnetic shielding constants with intermolecular interactions. I. Methods and applications to water and methane. J. magn. Reson. 55, 6477.Google Scholar
Giessner-Prettre, C., Langlet, J.. & Caron, F. (1984a). Theoretical study of GT and GA wobble pairs, in two short duplexes. Proton NMR chemical shifts and interaction energy calculations. J. theoret. Biol. 107, 211228.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C. & Pullman, B. (1965). Sur les courants π dans les bases puriques et pyrimidinques d'intérêjt biochimique. C. R. Acad. Sci. Paris 261, 25212523.Google Scholar
Giessner-Prettre, C. & Pullman, B. (1970). Intermolecular nuclear shielding value of protons of purines and flavines. J. theor. Biol. 27, 8795.CrossRefGoogle Scholar
Giessner-Prettre, C. & Pullman, B. (1976). On the atomic or ‘local’ contributions to proton chemical shifts due to the anisotropy of the diamagnetic susceptibility of the nucleic acid bases. Biochem. biophys. Res. Com. 70, 578581.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C. & Pullman, B. (1977a). On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. I. Proton shifts in the ribose ring of pyrimidine nucleosides as a function of the torsion angle about the glycosyl bond. J. theor. Biol. 65, 171188.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C. & Pullman, B. (1977b). On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. II. Proton shifts in the ribose ring of purine nucleosides as a function of the torsion angle about the glycosyl bond. J. theor. Biol. 65, 189201.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C. & Pullman, B. (1978). On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. IV. Proton chemical shifts in 3′-nucleotides as a function of different conformational parameters. The Jerusalem Symp. Quant. Chem. Biochem. X. Nuclear magnetic resonance spectroscopy in molecular biology (ed. B. Pullman, pp.161181.Dordrecht, Holland: D. Reidel.CrossRefGoogle Scholar
Giessner-Prettre, C. & Pullman, B. (1982a). Ab initio quantum mechanical calculations of the magnetic shielding constants of the different nuclei of cytosine. J. Am. chem. Soc. 104, 7073.CrossRefGoogle Scholar
Giessner-Prettre, C. & Pullman, B. (1982b). Solution conformation of the double helix formed by Dickerson's dodecamer d(CGCGAATTCGCG): a theoretical proton NMR study. Biochem. biophys. Res. Com. 107, 15391544.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C. & Pullman, B. (1983). Theoretical NMR study of the pre-melting transition in the d-(CGCGAATTCGCG) and d-(CGCGTATACGCG) self-complementary duplexes. FEBS Lett. 153, 329331.CrossRefGoogle Scholar
Giessner-Prettre, C., Pullman, B. & Caillet, J. (1977). Theoretical study on the proton chemical shifts of hydrogen bonded nucleic acid bases. Nucl. Acids Res. 4, 99115.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C., Pullman, B., Ribas, Prado F., Cheng, D. M., Iuorno, V. & Ts'o, P. O. P. (1984c). Contribution 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, 377388.CrossRefGoogle ScholarPubMed
Giessner-Prettre, C., Pullman, B., Tran-Dinh, S., Neumann, J.-M., Huynhdinh, T. & Igolen, J. (1984b). Proton NMR study of the B → Z transition of d(CGm5CG)2 and d(CGm5CGCG)2: theory and experiment. Nucl. Acids Res. 12, 32713281.CrossRefGoogle Scholar
Giessner-Prettre, C., Ribas, Prado F., Pullman, B., Kan, L.-S., Kast, J. R. & Ts'o, P. O. P. (1981). Computer programming for nucleic acid studies. II. Total chemical shifts calculation of all protons of double stranded helices. Comp. Prog. Biomed. 13, 167184.CrossRefGoogle ScholarPubMed
Gorenstein, D. G. (1975). Dependence of 31P chemical shifts on oxygen-phosphorusoxygen bond angles in phosphate esters. J. Am. chem. Soc. 97, 898900.CrossRefGoogle Scholar
Gorenstein, D. (1977). A generalized gauche NMR effect in 13C, 19F and 31P chemical shifts and directly bonded coupling constants. Torsional angle and bond angle effects. J. Am. chem. Soc. 99, 22542258.CrossRefGoogle Scholar
Gorenstein, D. (1984). Phosphorus 31 NMR. Principles and Applications. New York, Academic Press.Google Scholar
Gorenstein, D. & Kar, O. (1975). 31P chemical shifts in phosphate diestermono-anions. Bond angle and torsional angle effects. Biochem. biophys. Res. Com. 65, 10731080.CrossRefGoogle ScholarPubMed
Gresh, N. & Pullman, B. (1979). A theoretical study of the interaction of ammonium and guanidinium ions with the phosphodiester linkage. Theor. chim. Acta 52, 6773.CrossRefGoogle Scholar
Griffey, R. H. & Poulter, C. D. (1983). Detection of the imino hydrogen bond in G-C pairs by 1H and 15N nuclear magnetic resonance spectroscopy. Tetrahedron Lett. 24, 40674070.CrossRefGoogle Scholar
Haasnoot, C. A. G. & Altona, C. (1979). A conformational study of nucleic acid phosphate ester bonds using phosphorus-31 nuclear magnetic resonance. Nucl. Acids Res. 6, 11351149.CrossRefGoogle ScholarPubMed
Haasnoot, C. A. G.Westerink, H. P., van der Marel, G. A. & van Boom, J. H. (1984). Discrimination between A-type and B-type conformations of double helical nucleic acid fragments in solution by means of two-dimensional nuclear Ovehauser experiments. J. Biomol. Struct. Dyn. 2, 345359.CrossRefGoogle ScholarPubMed
Hall, K.Cruz, P., Tinoco, I. JR, Jovin, T. M. & van de Sande, J. H. (1984). Z-RNA a left handed RNA double helix. Nature 311, 584586.CrossRefGoogle ScholarPubMed
Hall, G. G. & Hardisson, A. (1962). Ring currents and their effects in aromatic molecules. Proc. R. Soc. London A 268, 228338.Google Scholar
Hansen, A. E. & Bouman, T. D. (1985). Localized orbital&local origin method for calculation and analysis of NMR shieldings. Applications to 13C shielding tensors. J. chem. Phys. 82, 50355047.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(CGCGAATTCGCG) using two-dimensional nuclear magnetic resonance methods. J. molec. Biol. 171, 319336.CrossRefGoogle Scholar
Hawkes, G. E., Randall, E. W. & Hull, W. E. (1977). Natural abundance nitrogen-15 nuclear magnetic resonance spectroscopy. The pyrimidine and purine nucleosides. J. chem. Soc. Perkin Trans. II, 12681275.CrossRefGoogle Scholar
Holbrook, S. R., Sussman, J. L., Warrant, R. W. & Kim, S.-H. (1978). Crystal structure of yeast phenylalanine transfer RNA. II. Structural features and functional implications. J. molec. Biol. 123, 631660.CrossRefGoogle ScholarPubMed
Hruska, F. E. & Blonski, W. J. P. (1982). A 1H and 13C nuclear magnetic resonance study of nucleosides and methylated pyrimidine bases. Can. J. Chem. 60, 30263032.CrossRefGoogle Scholar
Iwahashi, H., Hiromu, S. & Kyogoku, Y. (1982). Detection of separated amino proton resonance signals of adenine derivatives at low temperature and its application to estimation of population of the adenine-uracil dimers in solution. Biochemistry 21, 631638.CrossRefGoogle ScholarPubMed
Iwahashi, H. & Kyogoku, Y. (1977). Detection of proton acceptor sites of hydrogen bonding between nucleic acid bases by the use of 13C magnetic resonance. J. Am. chem. Soc. 99, 77617765.CrossRefGoogle Scholar
Jardetzky, O. (1964). Proton magnetic resonance studies of nucleotide interactions. Biopolymers Symp. 1, 501514.Google Scholar
Johnson, C. E. & Bovey, F. A. (1958). Calculation of nuclear magnetic resonance spectra of aromatic hydrocarbons. J. chem. Phys. 29, 10121014.CrossRefGoogle Scholar
Jones, A. J., Grant, D. M., Winkley, M. W. & Robins, R. K. (1970). Carbon 13 magnetic resonance. XVII. Pyrimidine and purine nucleosides. J. Am. chem. Soc. 92, 4079740887.Google ScholarPubMed
Kan, L.-S., Borer, P. N. & Ts'o, P. O. P. (1975). Conformation and interaction of short double stranded helices. II. Proton magnetic resonance studies on the hydrogen bonded NH-N protons of ribosyl ApApGpCpUpU helix. Biochemistry 14, 48644869.CrossRefGoogle ScholarPubMed
Kan, L.-S., Cheng, D. M., Jayaraman, K., Leutzinger, E. E., Miller, P. S. & Ts'o, P. O. P. (1982). Proton nuclear magnetic resonance study of a self complementary decadeoxyrinucleotide CCAAGCTTGG. Biochemistry 21, 67236732.CrossRefGoogle ScholarPubMed
Kan, L.-S., Chandrasegaran, S., Pulford, S. M. & Miller, P. S. (1983). Detection of a guanine-adenine base pair in a decadeoxyribonucleotide by proton magnetic resonance spectroscopy. Proc. natn. Acad. Sci. USA 80, 42634265.CrossRefGoogle Scholar
Kan, L.-S. & Ts'o, P. O. P. (1977). 1H-NMR studies of transfer RNA. III. The observed and computed spectra of the hydrogen bonded NH resonances of baker's yeast transfer RNAPhe. Nucl. Acids Res. 4, 16331647.CrossRefGoogle Scholar
Karplus, M. & Pople, J. A. (1963). Theory of carbon NMR chemical shifts in conjugated molecules. J. chem. Phys. 38, 28032807.CrossRefGoogle Scholar
Katz, L. & Penman, S. (1966). Association by hydrogen bonding of free nucleosides in non-aqueous solution. J. molec. Biol. 15, 220231.CrossRefGoogle ScholarPubMed
Kennard, O. (1985). Structural studies of DNA fragments: the G. T wobble pair in A, B and Z DNA: the G.A base pair in B-DNA. J. biomol. Struct. Dyn. 3, 205226.CrossRefGoogle Scholar
Kohler, S. J.& Klein, M. P. (1977). Phosphorus-31 nuclear magnetic shielding tensors of L-O-serin phosphate and 3′-cytidine monophosphate. J. Am. chem. Soc. 99, 82908293.CrossRefGoogle Scholar
Kyogoku, Y., Watanabe, M., Kainosho, M. & Oshima, T. (1980). 15N-NMR study on ribonuclease T1-guanylic acid complex. Studia Biophys. 81, 123124.Google Scholar
Lancelot, G., Asseline, U., Thuong, N. T. & Helene, C. (1985). Proton and phosphorus nuclear magnetic resonance studies of an oligothymidilate covalently linked to an acridine derivative and its binding to complementary sequences. Biochemistry 24, 25212529.CrossRefGoogle Scholar
Lankhorst, P. P., Erkelens, C., Haasnoot, C. A. G. & Altona, C. (1983). Carbon 13 NMR in conformational analysis of nucleic acid fragments. Heteronuclear chemical shift correlation spectroscopy of RNA fragments. Nucl. Acids Res. 11, 72157230.CrossRefGoogle Scholar
Lee, C.-H., Ezra, F. S., Kondo, N. S., Sarma, R. H. & Danyluk, S. S. (1976). Conformational properties of dinucleoside monophosphates in solution: dipurines and dipyrimidines. Biochemistry 15, 36273638.CrossRefGoogle ScholarPubMed
Lee, C.-H. & Tinoco, I. JR (1977). Studies of the conformation of modified dinucleoside phosphates containing 1, N6-ethenoadenosine and 2′-O-methylcytidine by 360-MHz 1H nuclear magnetic resonance spectroscopy. Investigation of the solution conformation of dinucleoside phosphates. Biochemistry 16, 54035414.CrossRefGoogle Scholar
Lerner, D. B., Becktel, W. J., Everett, R., Goddman, M. & Kearns, D. R. (1984). Solvation effects on the 31P-NMR chemical shifts in infrared spectra of phosphate diesters. Biopolymers 23, 21572172.CrossRefGoogle ScholarPubMed
London, F. (1937). Théorie quantique des courants interatomiques dans les combinaisons aromatiques. J. Phys. Radium 8, 397409.CrossRefGoogle Scholar
Mantsch, H. H. & Smith, I. C. P. (1972). Fourier transform 13C-NMR spectra of polyuridylic acid, uridine and related nucleotides. Biochem. biophys. Res. Com. 46, 808815.CrossRefGoogle Scholar
Markowski, V., Sullivan, G. R. & Roberts, J. D. (1977). Nitrogen-15 nuclear magnetic resonance spectroscopy of some nucleosides and nucleotides. J. Am. chem. Soc. 99, 714718.CrossRefGoogle ScholarPubMed
Marshall, T. W. & Pople, J. A. (1958). Nuclear magnetic shielding of a hydrogen atom in an electric field. Molec. Phys. 1, 199202.CrossRefGoogle Scholar
McMichael, Rohlfing C., Allen, L. C. & Ditchfield, R. (1984). Proton and carbon 13 chemical shifts: comparison between theory and experiment. Chem. Phys. Lett. 87, 97ndash;150.Google Scholar
Mitra, C. K., Sarma, R. H., Giessner-Prettre, C. & Pullman, B. (1980). Solution structure of DNA: the method of nuclear magnetic resonance spectroscopy. Int. J. Quant. Chem. Quant. Biol. Symp. 7, 3966.Google Scholar
Mitra, C. K., Sarma, M. H. & Sarma, R. H. (1981). Plasticity of the DNA double helix. J. Am. chem. Soc. 103, 67276737.CrossRefGoogle Scholar
Moller, A., Nordheim, A., Kozlowski, S. A., Patel, D. J. & Rich, A. (1984). Bromination stabilizes Poly(dG-dC) in the Z-DNA form under low salt conditions. Biochemistry 23, 5462.CrossRefGoogle ScholarPubMed
Morokuma, K. (1971). Molecular orbitals of hydrogen bonds. III. C = 0…H−0 hydrogen bond in H2CO…H2O and H2CO…2H2O. J. chem. Phys. 55, 12361244.CrossRefGoogle Scholar
Musher, J. I. (1962). Linear variation of proton shielding with electric field. J. chem. Phys. 37, 3439.CrossRefGoogle Scholar
Newmark, R. A. & Cantor, C. R. (1968). Nuclear magnetic resonance study of the interactions of guanosine and cytidine in dimethyl sulfoxide. J. Am. chem. Soc. 90, 50105017.CrossRefGoogle ScholarPubMed
Patel, D. J. & Canuel, L. (1976). Nuclear magnetic resonance studies of the helix coil transition of poly(dA-dT) in aqueous solution. Proc. natn. Acad. Sci. USA 73, 674678.CrossRefGoogle ScholarPubMed
Patel, D. J. & Canuel, L. (1979). Helix coil transition of the self complementary dG-dG-dA-dA-dT-dT-dC-dC duplex. Eur. J. Biochem. 96, 267276.CrossRefGoogle ScholarPubMed
Patel, D. J., Canuel, L. L. & Pohl, F. M. (1979). ‘Alternating B-DNA’ conformation for the oligo(dG-dC) duplex in high-salt solution. Proc. natn. Acad. Sci. USA 76, 25082511.CrossRefGoogle ScholarPubMed
Patel, D. J., Kozlowski, S. A., Ikuta, S., Itakura, K., Bhatt, R. & Hare, D. R. (1983). NMR studies of DNA conformation and dynamics in solution. Cold Spring Harb. Symp. quant. Biol. 47, 197206.CrossRefGoogle ScholarPubMed
Patel, D. J., Kozlowski, S. A., Marky, L. A., Broka, C., Rice, J. A., Itakura, K. & Breslauer, K. J. (1982a). Premelting and melting transitions in the d(CGCGAATTCGCG) self-complementary duplex in solution. Biochemistry 21, 428436.CrossRefGoogle Scholar
Patel, D. J., Kozlowski, S., Marky, L. A., Rice, J. A., Broka, C., Dallas, J., Itakura, K. & Breslauer, K. J. (1982b). Structure, dynamics, and energetics of deoxyguanosine-thymidine wobble base pair formation in the self-complementary d(CGTGAATTCGCG) duplex in solution. Biochemistry 21, 437444.CrossRefGoogle Scholar
Patel, D. J. & Tonelli, A. E. (1975). Nuclear magnetic resonance investigation of the structure of the self complementary duplex of d ApTpGpCpApT in aqueous solution. Biochemistry 14, 39903996.CrossRefGoogle Scholar
Petersen, S. B. & Led, J. J. (1981). Watson-Crick pairing between guanosine and cytidine studied by 13C nuclear magnetic resonance spectroscopy. J. Am. chem. Soc. 103, 53085313.CrossRefGoogle Scholar
Pople, J. A. (1962a). Molecular orbital theory of diamagnetism. I. An approximate LCAO scheme. J. chem. Phys. 37, 5359.CrossRefGoogle Scholar
Pople, J. A. (1962b). Molecular orbital theory of diamagnetism. II. Calculation of Pascal constants for non cyclic molecules. J. chem. Phys. 37, 6066.CrossRefGoogle Scholar
Pople, J. A. (1962c). The theory of chemical shifts. Discuss. Faraday Soc. 34, 714.CrossRefGoogle Scholar
Poulter, C. D. & Livingston, C. L. (1979). 15N-2′, 3′, 5′-tri-O-benzoyluridine. Detection of hydrogen bonding in A-U base pairs by 15N-NMR. Tetrahedron Lett. 755758.CrossRefGoogle Scholar
Pullman, B., Pullman, A. & Berthod, H. (1978). SCF ab initio of the ‘through-water’ versus ‘direct’ boinding of the Na and the Mg2− cations to the phosphate anion. Int. J. Quant. Chem. Quant. Biol. Symp. 5, 7990.Google Scholar
Raszka, M. & Kaplan, N. O. (1972). Association by hydrogen bonding of mononucleotides in aqueous solution. Proc. natn. Acad. Sci. USA 69, 20252029.CrossRefGoogle ScholarPubMed
Rein, R., Shibata, M., Garduno-Juarez, R. & Kieber-Emmons, (1983). Structure of mispairs leading to substitution mutations. In Structure and Dynamics: Nucleic Acids and Proteins (ed. Clementi, E. and Sarma, R. H.), pp. 269288. New York: Adenine Press.Google Scholar
Ribas, Prado F. & Giessner-Prettre, C. (1981). Parameters for the calculation of the ring current and magnetic anisotropy contributions to magnetic shielding constants: nucleic acid bases and intercalating agents. J. molec. Struct. 76, 8192.Google Scholar
Ribas Prado, F., Giessner-Prettre, C. & Pullman, B. (1978). On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. III. Proton chemical shifts of 5′-nucleotides as a function of different conformational parameters. J. theor. Biol. 74, 259277.CrossRefGoogle Scholar
Ribas Prado, F., Giessner-Prettre, C. & Pullman, C. (1979b). Ab initio quantum mechanical calculations of the variation of the magnetic shielding constant of hydrogen and carbon 13 nuclei of dimethylphosphate anion as a function of molecular conformation: a model study for nucleic acid constituents. Int. J. Quant. Chem. Quant. Biol.Symp. 6, 491501.Google Scholar
Ribas Prado, F., Giessner-Prettre, C. & Pullman, B. (1981 a). Non-empirical calculations of the nuclear magnetic resonance spectra of imidazole and hydrated imidazole. Org. magn. Reson. 16, 103110.CrossRefGoogle Scholar
Ribas Prado, F., Giessner-Prettre, C., Pullman, B. & Daudey, J.-P. (1979a). Ab initio quantum mechanical calculations of the magnetic shielding tensor of phosphorus 31 of the phosphate group. J. Am. chem. Soc. 101, 17371742.CrossRefGoogle Scholar
Ribas Prado, F., Giessner-Prettre, C., Pullman, A., Hinton, J. F., Harpool, D. & Metz, K. R. (1981 b). Non Empirical Quantum Mechanical Calculations of the 1H, 13C, 15N and 17O Magnetic Shielding Constants and of the Spin-Spin Coupling Constants in Formamide, Hydrated Formamide and N-Methylformamide. Theor. chim. Acta 59, 5559.CrossRefGoogle Scholar
Robillard, G. T., Tarr, C. E., Vosman, F. & Berendsen, H. J. C. (1976). Similarity of the crystal and solution structure of yeast tRNAPhe. Nature 262, 363369.CrossRefGoogle ScholarPubMed
Rordorf, B. F., Kearns, D. R., Hawkins, E. & Chang, S. H. (1976). High-resolution NMR study of yeast and the native and denatured conformers of yeast . Biopolymers 15, 325326.CrossRefGoogle ScholarPubMed
Scheit, K. H. (1967). Detection of hydrogen bridges between inosine and other nucleosides by NMR spectroscopy. Angew. Chemie 79, 190191.CrossRefGoogle Scholar
Schindler, M. & Kutzelnigg, W. (1983). Theory of magnetic susceptibilities and NMR chemical shifts in terms of localized quantities. 3. Application to hydrocarbons and other organic molecules. J. Am. chem. Soc. 105, 13601370.CrossRefGoogle Scholar
Schwartz, H. M., Maccoss, M. & Danyluk, S. S. (1985). 17O-NMR of nucleosides. 3. Chemical shifts of substituted uridines and ribothymidines. Org. magn. Reson. 23, 885894.Google Scholar
Schweizer, M. P., Broom, A. D., Ts'o, P. O. P. & Hollis, D. P. (1968). Studies of inter and intramolecular interactions in mononucleotides by proton magnetic resonance. J. Am. chem. Soc. 90, 10421055.CrossRefGoogle ScholarPubMed
Schweizer, M. P., Chan, S. I. & Ts'o, P. O. P. (1965). Interaction and association of bases and nucleosides in aqueous solutions. IV. Proton magnetic resonance studies of the association of pyrimidine nucleosides and their interactions with purine. J. Am. chem. Soc. 87, 52415247.CrossRefGoogle ScholarPubMed
Schweizer, M. P. & Robins, R. K. (1973). NMR studies on the conformation of nucleosides and 3′, 5′-cyclic nucleotides. The Jerusalem Symp. Quant. Chem. Biochem. V. Conformation of biological molecules and polymers, pp. 329343.Google Scholar
Shindo, H. (1981). 13C-NMR study of the conformation and mobility of 145-base-pairs poly(dAdT). poly(dAdT) in solution. Eur. J. Biochem. 120, 309312.CrossRefGoogle Scholar
Shindo, H., Simpson, R. T. & Cohen, J. S. (1979). An alternating conformation characterizes the phosphodiester backbone of poly(dA-dT) in solution. J. biol. Chem. 254, 81258128.CrossRefGoogle ScholarPubMed
Shoup, R. R., Miles, H. T. & Becker, E. D. (1966). NMR evidence of specific basepairing between purines and pyrimidines. Biochem. biophys. Res. Com. 23, 194201.CrossRefGoogle ScholarPubMed
Shulman, R. G., Hilbers, C. W., Kearns, D. R., Reid, B. R. & Wong, Y. P. (1973) Ring current shifts in the 300 Mhz nuclear magnetic resonance spectra of six purified transfer RNA molecules. J. molec. Biol. 78, 5769.CrossRefGoogle ScholarPubMed
Stolarski, R., Kierdaszuk, B., Hagberg, C.-E. & Shugar, D. (1984). Hydroxylamine and methoxyamine mutagenesis: displacement of the tautomeric equilibrium of the promutagen N8-methoxyadenosine by complementary base pairing. Biochemistry 23, 29062913.CrossRefGoogle ScholarPubMed
Stone, M. P., Winkle, S. A. & Borer, P. N. (1986). 13C-NMR of ribosyl ApApA, ApApG and ApUpG. J. biomol. Struct. Dyn. 4, 767781.CrossRefGoogle Scholar
Stone, M. P., Winkle, S. A., McFarland, G., Yoo, M. G. & Borer, P. N. (1985). 13C-NMR of ribosyl A-A-A, A-A-G and A-U-G. Synthesis and assignment. Biophys. Chem. 23, 129138.CrossRefGoogle ScholarPubMed
Tran-Dinh, S. & Neumann, J. M. (1977). A 31P-NMR study of the interaction of Mg2+ ions with nucleosides diphosphates. Nucl. Acids Res. 4, 397403.CrossRefGoogle ScholarPubMed
Ts'o, P. O. P., Kondo, N. S., Schweizer, M. P. & Hollis, D. P. (1969). Studies of the conformation and interaction in dinucleoside mono- and diphosphates by proton magnetic resonance. Biochemistry 8, 9971029.CrossRefGoogle ScholarPubMed
Tutunjian, P., Tropp, J. & Waugh, J. (1983). 31P shielding tensor of deoxycitidine 5′ -monophosphate.J. Am. chem. Soc. 105, 48484849.CrossRefGoogle Scholar
Uesugi, S. & Ikehara, M. (1977). Carbon-13 magnetic resonance spectra of 8- substituted purine nucleosides. Characteristic shifts for the syn conformation. J. Am. chem. Soc. 99, 32503253.CrossRefGoogle ScholarPubMed
Uesugi, S., Ohkubo, M., Ohtsuka, E., Ikehara, M., Kobayashi, Y. & Kyogoku, Y. (1984). Synthesis and conformational studies of ribooligo-nucleotides which contain an alternating C-G sequence and show unusual circular dichroism spectra. Nucl. Acids Res. 12, 77937810.CrossRefGoogle ScholarPubMed
Veillard, A. (1962). Le déplacement chimique en réesonance magnétique nucléaire dans les hétérocycles aromatiques d'intérêt biochimique. J. chim. Phys. 59, 10561066.CrossRefGoogle Scholar
Vorlickova, M., Kypr, J. & Sklenar, V. (1983). Salt induced conformational transition of poly [d(A-T)]. poly [d(A-T)]. J. molec. Biol. 166, 8592.CrossRefGoogle Scholar
Wang, A. H.-J., Hakoshima, T., van der Marel, G., van Boom, J. H. & Rich, A. (1984). AT base pairs are less stable than GC base pairs in Z-DNA: the crystal structure of d(m6CGTAm5CG). Cell 37, 321331.CrossRefGoogle Scholar
Wang, S. M. & Li, N. C. (1968). Proton magnetic resonance studies of self-association and metal complexation of nucleosides in dimethyl sulfoxide. J. Am. chem. Soc. 90, 50695074.CrossRefGoogle ScholarPubMed
Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., van der Marel, G., van Boom, J. H. & Rich, A. (1981). Left-handed double helical DNA: variations in the backbone conformation. Science 211, 171176.CrossRefGoogle ScholarPubMed
Watanabe, M., Sugeta, H., Iwahashi, H., Kyogoku, Y. & Kainosho, M. (1981). Detection of proton-acceptor sites of hydrogen bonding in adenine-uracile base pairs by the use of 15N magnetic resonance. Eur. J. Chem. 117, 553558.CrossRefGoogle ScholarPubMed
Westerink, H. P., van der Marel, J. H., van Boom, J. H. & Haasnoot, C. A. G. (1984). Conformational analysis of c(CGCGCG) in aqueous solution: an A-type double helical conformation studied by two-dimensional nuclear Overhauser effect spectroscopy. Nucl. Acids Res. 12, 43234338.CrossRefGoogle Scholar
Wu, H.-Y. & Behe, M. J. (1985a). Methylated pyrimidines stabilize an alternating conformation of poly(dA-dU). poly(dA-dU). Biochemistry 24, 54995502.CrossRefGoogle ScholarPubMed
Wu, H.-Y. & Behe, M. J. (1985b). Salt induced transitions between multiple conformations of poly(rG-m5dC). poly(rG-5dC). Nucl. Acids Res. 13, 39313940.CrossRefGoogle ScholarPubMed