Abstract
From a chemist’s viewpoint, DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are polymers composed of nucleotide units (Fig. 3.1.1). (For standard textbooks on physical aspects of nucleic acid chemistry see [200–202].) The side chains in these polymers are purine and pyrimidine bases. The common bases found in DNA are guanine (G), adenine (A), cytosine (C), and thymine (T), while the common RNA bases are G, A, C and uracil (U). RNA also differs from DNA in that it bears a hydroxy group in the 2′ position. The five-membered furanose ring (ribose or deoxyribose) has a well-defined configuration by which we mean that the relative spatial arrangements of bonds in the l′, 2′, 3′ and 4′ positions are fixed. The sugar-base combination is called a nucleoside and the phosphates esters are called nucleotides. The linkage in DNA and RNA structures is always 3′–5′. Molecules with short segments of 2′–5′ linkages are known but they play a minor role in biology.
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Section 3.4
Gerlt, J. A., Younsblood, A. V.: The solution conformational preferences of the sugar and sugar phosphate constituents of RNA and DNA. J. Am. Chem. Soc. 102, 7433 (1980)
Ferrige, A. G., Lindon, J. C.: Application of resolution enhancement in FT NMR to the structural determination of doxy sugars. Spectrosc. Lett. 13, 339 (1980)
Section 3.5
Klimke, G., Luedemann, H. D., Townsend, L. B.: Further evidence for a S-syn correlation in the purine (beta) ribosides: the solution conformation of two tricyclic analogs of adenosine and guanosine. Z. Naturforsch., C, Biosci. 34C, 653 (1979)
Klimke, G., et al.: Ribose conformations of adenosine analogs modified at the 2’, 3’ or 5’ positions. Z. Naturforsch., C. Biosci. 34C, 1075 (1979)
Uzawa, J., Uramoto, M.: Assignment of indirect carbon-13-proton couplings in the carbon-13 NMR spectra of some purine and pyrimidine nucleosides and their analogs by long-range selective proton decoupling. Org. Mag. Res. 12, 612 (1979)
Blieszner, K. C., Horton, D., Markovs, R. A.: Acyclic-sugar purine nucleosides derived from D-glucose: sterochemical correlations in acyclic-sugar derivatives unequally substituted at C-1. Carbohydr. Res. 80, 241 (1980)
Stolarski, R., Dudycz, L., Shugar, D.: NMR studies on the syn-anti dynamic equilibrium in purine nucleosides and nucleotides. Eur. J. Biochem. 108, 111 (1980)
Stolarski, R., et al.: Comparison of theoretical and experimental approaches to determination of conformation of nucleosides about the glycosidic bond. Biochim. Biophys. Acta 610, 1 (1980)
Lipnick, R. L., Fissekis, J. D.: A comparative proton magnetic resonance conformational study of the tRNA “Wobble” nucleosides 5-carboxymethyl-, 5-carbo-methoxymethyl-, and 5-carbomoylmethyluridine. Can. J. Biochem. 58, 1355 (1980)
Guschlbauer, W.: Conformational analysis of ribonucleosides from proton-proton coupling constants. Biochim, Biophys. Acta 610, 47 (1980)
Kharasch, E. D., Novak, R. F.: Ring current effects in adriamycin-flavin mononucleotide complexation as observed by proton FT NMR spectroscopy. Biochem. Biophys. Res. Commun. 92, 1320 (1980)
Guschlbauer, W., Jankowski, K.: Nucleoside conformation is determined by the electronegativity of the sugar substituent. Nucleic Acids Res. 8, 1421 (1980)
Section 3.6
Bobruskin, I. D. et al.: Nuclear Magnetic Resonance study of the conformation of nucleotides, oligonucleotides, and their analogs in solution. Mol. Biol. (Moscow) 13, 1407 (1979)
Bobruskin, I. D., et al.: NMR study of the conformation state of nucleosides and nucleotides in aqueous solutions. Bioorg. Khim. 6, 1163 (1980)
Cadet, J., et al.: Conformational studies of.alpha.- and.beta.-pyrimidine. Biochim. Biophys. Acta 608, 435 (1980)
Chang, Ching-Jer, Lee, Chi-Gen.: Methylation and conformational analysis of purine ribonucleotides. J. Carbohydr., Nucleosides, Nucleotides 7, 93 (1980)
Hayashi, F., Akasaka, K., Hatano, H.: Conformation of adenosine 3’,5’-monophosphate in solution as studied by the NMR-desert method. H. Self-association and temperature-dependent glycosidic isomerization at pH 7. Biochim. Biophys. Acta 588, 181 (1979)
Cohn, M., Hu, A.: Isotopic oxygen-18 shifts in phosphorus-31 NMR of adenine nucleotides synthesized with oxygen-18 in various positions. J. Am. Chem. Soc. 102, 913 (1980)
Yarbrough, L. R., Bock, J. L.: Stacking interactions in fluorescent nucleotide analogs containing 1-aminoaphthalene-5-sulfonate at the phosphoryl terminus. J. Biol. Chem. 225, 9907 (1980)
Zolin, V. F., Koreneva, L. G., Lagodzinskaya, G. V.: Use of rare earth elements as probe for studying biologically active compounds. VIII. Study of the conformation of some nucleotides using a lanthanide shifting reagent and luminescence spectroscopy. Biofizika 24, 945 (1979)
Neidle, S., et al.: 9-beta: D-Arabinofuranosyl-8-n-butylaminoadenine, a C-8 substituted nucleoside in the anti conformation. Biochim. Biophys. Acta 565, 379 (1979)
Watanabe, K., et al.: CD and NMR studies on the conformational thermostability of 2-thioribothymidine found in the T.PSI.0 loop of thermophile tRNA. Biochem. Biophys. Res. Commun. 91, 671 (1979)
Evans, F. E., Wright, J. M.: Proton and phosphorus-31 nuclear magnetic resonance study on the stabilization of the anti conformation about the glycosyl bond of 8-alkylamino adenyl nucleotides. Biochemistry 19, 2113 (1980)
Kan, L., S. et al.: Proton nuclear magnetic resonance studies en dideoxyribonucleoside methylphosphonates. Biochemistry 19, 2122 (1980)
Haasnoot, C.A.G., et al.: Prediction of anti and gauche vicinal proton-proton coupling constants for hexapyranose rings using a generalised Karplus equation. Bull. Soc. Chim. Belg. 89, 125 (1980)
Egert, E., et al.: Influence of substituents at the 5 position on the structure of uridine. J. Am. Chem. Soc. 102, 3707 (1980)
Section 3.7
Lappi, D. A., Evans, F. E., Kaplan, N. O.: Reduced nicotinamide 8-(alkylamino) adenine di-nucleotides: enzyme-coenzyme interactions with different adenyl glycogyl bond conformations. Biochemistry 19, 3841 (1980)
Lee, Che-Hung, Tinoco, I. Jr.: Conformation studies of 13 trinucleoside diphosphates by 360 MHz PMR spectroscopy. A bulged base conformation. I. Base protons and H1’ protons. Biophys. Chem. 11, 283 (1980)
Cheng, D. M., et al.: Conformational flexibility of the 3’ acceptor end of transfer ribonucleic acid Biochemistry 19, 2491 (1980)
Bobruskin, I. D., Kirpichnikov, M. P., Florentev, V. L.: NMR study of the conformation of nucleotides, oligonucleotides and their analogs in solution. H. Syn-anti equilibrium of adenosine, 5’-AMP, 3’-CMP and 3’-CMP in solution. Mol. Biol. (Moscow) 13, 870 (1979)
Bobruskin, I. D., et al.: Nuclear magnetic resonance study of the conformational states of dinucleoside phosphates in aqueous solution. Biofizika 25, 745 (1980)
Sarma, R. H.: Spatial configuration of oligonucleotides in solution as reflected in nuclear resonance study. Nucleic Acid Geom, Dyn., Pergamon Press 1980, p. 143
Bobruskin, I. D., et al.: Nuclear magnetic resonance study of the conformation of nucleotides, oligonucleotides and their analogs in solution. IV. Syn-anti equilibrium in aqueous solution of 2’-deoxynucleosides and nucleotides. Mol. Biol. (Moscow) 14, 830 (1980)
Bobruskin, I. D., et al.: Nuclear magnetic resonance study of the conformation of nucleotides, oligonucleotides and their analogs in solution. III. Syn-anti equilibrium in a solution of cytidine and 2’-deoxycytidine. Mol. Biol. (Moscow) 13, 1407 (1979)
Sarma, R. H., Dhingra, M. M., Feldmann, R. J.: The diverse spatial configurations of DNA. Evidence for a vertically stabilized double helix. Sterodyn. Mol. Syst., Proc. Symp., Pergamon Press 1979, p. 251
Green, M. K., Kotowyez, G.: The Nature of the nicotinamide adenine dinucleotide phosphate (NADP) complex with manganese (II) ions and studied by proton and phosphorus magnetic resonance. Can. J. Chem. 457, 2434 (1979)
Olsthoorn, C. S., et al.: Conformational characteristics of the trinucloside diphosphate dApdApdA and its constituents from nuclear magnetic resonance and circular dichroism studies, Extrapolation to the stacked conformers. Eur. J. Biochem. 112, 95 (1980)
Everett, J. R., et al.: Nearest-neighbour and next-nearest-neighbour effects in the proton NMR spectra of the oligoribonucleotides ApGpX and CpApX. Biopolymers 19, 557 (1980)
Shindo, H. McGhee, J. D., Cohen, J. S.: Phosphorus-31 NMR studies of DNA in nucleosome core particles. Biopolymers 19, 523 (1980)
Ikehara, M., Uesugi, S., Shida, T.: Polynucleotides, LV. Synthesis and properties of dinucleoside monophosphates derived from adening 8,2’-S- and uracil 6,2’-O-cyclonucleosides. Further support for the left-handed stacking of oligonucleotides having high-anti base torision angles. Chem. Pharm. Bull. 28, 189 (1980)
Section 3.9
Shindo, H., et al.: Nonuniform backbone conformation of deoxyribonucleic acid indicated by phosphorus-31 nuclear magnetic resonance chemical shift anisotropy. Biochemistry 19, 518 (1980)
Temussi, P. A., et al.: Temperature dependence of phosphorus-31 NMR spectra of chicken erythrocyte nucleosomes. Physiol. Chem. Phys. 11, 445 (1979)
Hilbers, C. W.: Hydrogen-bonded proton exchange and its effect on NMR spectra of nucleic acids. Biol. Appl. Magn. Reson., Academic Press 1979, p. 1
Robillard, G. D., Reid, B. R.: Elucidation of nucleic acid structure by proton NMR. Biol. Appl. Magn. Reson., Academic Press 1979, p. 45
Patel, D. J.: Structure and dynamics of poly (dG-dC) in solution. Steroid diamine cntdot.nucleic acid complexes and generation of an “alternating B-DNA” conformation in high salt. Stereodyn. Mol. Syst., Proc. Symp., Pergamon Press 1979, p. 397
Section 3.10.
Hamill, W. D. Jr., Horton, W. J., David, M.: Nuclear magnetic resonance relaxation studies of carbon-13 labeled uracil in transfer ribonucleic acid. J. Am. Chem. Soc. 102, 5454 (1980)
Buckingham, R. H., Kearns, D. R.: Low field nuclear magnetic resonance studies of the structure of UGA suppressor tryptophan tRNA from Escherichia Coli: normal and photocrosslinked species. Biochimie 62, 491 (1980)
Schweizer, M. P., et al.: Carbon-13 NMR studies on (4–13C)-uracil-labeled Escherichia coli transfer RNA Val. Nucleic Acids Res. 8, 2075 (1980)
Lipnick, R. L., Fissekis, J. D.: Carbon-13 NMR spectra of the tRNA “wobble” nucleosides 5carboxymethyl-, 5-carbomethoxymethyl-, and 5-carbomoylmethyluridine. J. Heterocyl, Chem. 17, 195 (1980)
Bolton, P. H., James, T. L.: Conformational mobility of deoxyribonucleic acid, transfer ribonucleic acid, and poly (adenylic acid) as monitored by carbon-13 nuclear magnetic resonance relaxation. Biochemistry 19, 1388 (1980)
Luoma, G. A., et al.: Melting of Saccharomyces cerevisiae 5S ribonucleic acid: Ultra absorption, circular dichroism, and 360-MHz proton nuclear magnetic resonance spectroscopy. Biochemistry 19, 5456 (1980)
Reid, B. R., Hurd, R. E.: High-resolution NMR studies on tRNA structure in solution. Cold Spring Harbor Monogr. Ser. 79, 9A (Transfer RNA: Struct. Prop., Recognition), pp. 177–190
Schmidt, P. G., Tompson, J. G., Agris, P. F.: Tranfer RNA structure by carbon-13 NMR: C2 of adenine, uracil and cytosine. Nucleic Acids Res. 8, 643 (1980)
Marshall, A. G., Smith, J. L.: Raman and 19F1H nuclear Overhauser evidence for a rigid solution information of Escherichia coli 5-fluorouracil 5S ribonucleic acid. Biochemistry 19, 5955 (1980)
Johnston, P. D., Redfield, A. G.: Proton FT NMR studies of tRNA structure and dynamics. Cold Spring Harbor Monogr. Ser. 79, 9A (Transfer RNA: Struct., Prop. Recognition), p. 191
Section 3.11
Chen, D. M., et al.: B1 eomycin-A2 complexes with poly (dA-dT): a proton nuclear magnetic resonance study of the nonexchangeable hydrogens. Biochem. Biophys. Res. Commun. 92, 197 (1980)
Cozzone, P., Toniolo, C., Jardetzky, O.: NMR study of the main components of culpeine and their possible interaction with nucleic acids. FEBS Lett. 110, 21 (1980)
Fritzsche, H., et al.: On the interaction of caffeine with nucleic acids. III and IV. Studies of the caffeine-DNA interaction by infrared and ultraviolet linear dichroism, proton and deuteron nuclear magnetic resonance. Biophys. Chem. 11, 121 (1980) and 11, 109 (1980)
Krugh, T. R., Nuss, M. E.: Nuclear magnetic resonance studies of drug-nucleic acid complexes. Biol. Appl. Magn. Reson., Academic Press 1979, p. 113
Nuss, M. E., et al.: An NMR study of the interaction of daunomycin with dinucleotides and dinucleoside phosphates. Biochim. Biophys. Acta 609, 136 (1980)
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© 1982 Springer-Verlag Berlin Heidelberg
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Govil, G., Hosur, R.V. (1982). Nucleosides, Nucleotides and Nucleic Acids. In: Conformation of Biological Molecules. NMR Basic Principles and Progress, vol 20. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-68097-7_3
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DOI: https://doi.org/10.1007/978-3-642-68097-7_3
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