Stereoelectronic Effects in Nucleosides and Nucleotides

  • Momcilo Miljkovic


An excellent review of this subject was published in 2005 by Chattopadhyaya et al. [1].


Lone Pair Steric Repulsion Anomeric Effect Conformational Equilibrium CH2OH Group 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Thibaudeau C, Acharya P, Chattopadhyaya J (2005) Stereoelectronic effects in nucleosides and nucleotides and their structural implications, 2nd edn. Department of Bioorganic Chemistry, Biomedical Center, Upsala University Press, UpsalaGoogle Scholar
  2. 2.
    Taira K, Uebayasi M, Maeda H, Furukawa K (1990) Energetics of RNA cleavage: implications for the mechanism of action of ribozymes. Protein Eng 3:691–701Google Scholar
  3. 3.
    Storer JW, Uchimaru T, Tanabe K, Uebayasi M, Nishikawa S, Taira K (1991) Existence of a marginally stable intermediate during the base-catalyzed methanolysis of methylene phosphate and ab initio studies of the monohydration of the pentacoordinated oxyphosphorane intermediate. J Am Chem Soc 113:5216–5219Google Scholar
  4. 4.
    Zhou D-M, Taira K (1998) The hydrolysis of RNA: from theoretical calculations to the hammerhead ribozyme-mediated cleavage of RNA. Chem Rev 98:991–1026Google Scholar
  5. 5.
    Bizzozero SA, Dutler H (1981) Stereochemical aspects of peptide hydrolysis catalyzed by serine proteases of the chymotrypsin type. Bioorgan Chem 10:46–62Google Scholar
  6. 6.
    Post CB, Karplus M (1986) Does lysozyme follow the lysozyme pathway? An alternative based on dynamic, structural, and stereoelectronic considerations. J Am Chem Soc 108:1317Google Scholar
  7. 7.
    Taira K (1987) Stereoelectronic control in the hydrolysis of RNA by imidazole. Bull Chem Soc Japan 60:1903Google Scholar
  8. 8.
    Koole LH, Buck HM, Nyilas A, Chattopadhyaya J (1987) Structural properties of modified deoxyadenosine structures in solution. Impact of the gauche and anomeric effects on the furanose conformation. Can J Chem 65:2089–2094Google Scholar
  9. 9.
    Koole LH, Buck HM, Bazin H, Chattopadhyaya J (1987) Conformational studies of 3′-C-methyl and 2′-C-methyl analogs of cordycepin. Tetrahedron 43:2989–2997Google Scholar
  10. 10.
    Koole LH, Moody HM, Buck HM, Groullier A, Essadiq H, Vial J-M, Chattopadhyaya J (1988) Synthesis and conformation of 1-(3′-C-methyl-2′-deoxy-β-D-xylofuranosyl)uracil and 9-(3′-C-methyl-2′-deoxy-β-D-xylofuranosyl) adenine; two novel sugar-methylated nucleoside analogs. Recl Trav Chim Pays-Bas 107:343–346Google Scholar
  11. 11.
    Plavec J, Koole LH, Sandström A, Chattopadhyaya J (1991) A mild and general method for the synthesis of 2-substituted-5-hydroxypyrimidines. Tetrahedron 47:7363–7365Google Scholar
  12. 12.
    Plavec J, Buet V, Groullier A, Koole L, Chattopadhyaya J (1991) Structural studies on 1-(1-deoxy-β-D-psicofuranosyl)thymine. Tetrahedron 47:5847–5856Google Scholar
  13. 13.
    Plavec J, Koole LH, Chattopadhyaya J (1992) Structural analysis of 2′,3′-dideoxyinosine, 2′,3′-dideoxyadenosine, 2′,3′-dideoxyguanosine, and 2′,3′-dideoxycytidine by 500-MHz proton NMR spectroscopy and ab initio molecular orbital calculations. J Biochem Biophys Methods 25:253–272Google Scholar
  14. 14.
    Plavec J, Tong W, Chattopadhyaya J (1993) How do the gauche and anomeric effects drive the pseudorotational equilibrium of the pentofuranose moiety of nucleosides? J Am Chem Soc 115:9734–9746Google Scholar
  15. 15.
    Plavec J, Garg N, Chattopadhyaya J (1993) How does the steric effect drive the sugar conformation in 3′-C-branched nucleosides. J Chem Soc Chem Commun (1993) :1011–1014Google Scholar
  16. 16.
    Plavec J, Fabre-Buet V, Uteza V, Grouiller A, Chattopadhyaya J (1993) Conformational studies on some C1′-branched β-D-nucleosides by proton-NMR spectroscopy and molecular mechanics calculations. J Biochem Biophys Methods 26:317Google Scholar
  17. 17.
    Plavec J, Thibaudeau C, Viswanadham G, Sund C, Chattopadhyaya J (1994) How does the 3′-phosphate drive the sugar conformation in DNA? J Chem Soc Chem Commun (1994):781–783Google Scholar
  18. 18.
    Thibaudeau C, Plavec J, Watanabe KA, Chattopadhyaya J (1994) How do the aglycons drive the pseudorotational equilibrium of the pentofuranose moiety in C-nucleosides? J Chem Soc Chem Commun (1994):537–540Google Scholar
  19. 19.
    Thibaudeau C, Plavec J, Chattopadhyaya J (1994) Quantitation of the anomeric effect in adenosine and guanosine by comparison of the thermodynamics of the pseudorotational equilibrium of the pentofuranose moiety in N- and C-nucleosides. J Am Chem Soc 116:8033–8037Google Scholar
  20. 20.
    Thibaudeau C, Plavec J, Garg N, Papchikhin A, Chattopadhyaya J (1994) How does the electronegativity of the substituent indicate the strength of the gauche effect? J Am Chem Soc 116:4038–4043Google Scholar
  21. 21.
    Plavec J, Thibaudeau C, Chattopadhyaya J (1994) How does the 2′-hydroxy group drive the pseudorotational equilibrium in nucleoside and nucleotide by the tuning of the 3′-gauche effect? J Am Chem Soc 116:6558–6560Google Scholar
  22. 22.
    Plavec J, Thibaudeau C, Viswanadham G, Sund C, Sandström A, Chattopadhyaya J (1995) The interaction of the 2′-OH group with the vicinal phosphate in ribonucleoside 3′-(ethylphosphate) drives the sugar phosphate backbone into unique (S, ε) conformational state. Tetrahedron 51:11775–11792Google Scholar
  23. 23.
    Plavec J, Thibaudeau C, Chattopadhyaya J (1996) How do the energetics of the stereoelectronic gauche and anomeric effects modulate the conformation of nucleosides and nucleotides? Pure Appl Chem 68:2137–2144Google Scholar
  24. 24.
    Thibaudeau C, Plavec J, Chattopadhyaya J (1996) Quantitation of the pD dependent thermodynamics of N.dblarw. S pseudorotational equilibrium of the pentofuranose moiety in nucleosides gives a direct measurement of the strength of the tunable an omeric effect and the pKa of the nucleobase. J Org Chem 61:266–286Google Scholar
  25. 25.
    Chattopadyaya J (1996) The nature of intramolecular stereoelectronic forces in nucleosides and nucleotides. Nucleic Acids Res Symp Ser 35:111–112Google Scholar
  26. 26.
    Luyten I, Thibaudeau C, Sandström A, Chattopadhyaya J (1997) The tunable transmission of the aromatic character of the aglycon through the anomeric effect in C-nucleosides drives-its own sugar conformation: a thermodynamic study. Tetrahedron 53:6433–6464Google Scholar
  27. 27.
    Luyten I, Thibaudeau C, Chattopadhyaya J (1997) The strength of the anomeric effect in adenosine, guanosine and their 2′-deoxy counterparts is medium-dependent. J Org Chem 62:8800–8808Google Scholar
  28. 28.
    Luyten I, Thibaudeau C, Chattopadhyaya J (1997) The determination of the ionization constants of C-nucleosides. Tetrahedron 53:6903Google Scholar
  29. 29.
    Thibaudeau C, Chattopadhyaya J (1997) Nucleosides Nucleotides 16:523Google Scholar
  30. 30.
    Thibaudeau C, Földesi A, Chattopadhyaya J (1997) The first experimental evidence for a larger medium-dependent flexibility of natural β-D-nucleosides compared to the α-D-nucleosides. Tetrahedron 53:14043–14072Google Scholar
  31. 31.
    Thibaudeau C, Földesi A, Chattopadhyaya J (1998) The quantitation of the competing energetics of the stereoelectronic and steric effects of the 3′-OH and the aglycon in the α- versus β-D- and L-2′-deoxyribonucleosides by 1H NMR. Tetrahedron 54:1867–1900Google Scholar
  32. 32.
    Thibaudeau C, Chattopadhyaya J (1998) The information transmission from the nucleobase drives the sugar-phosphate backbone conformation in the nucleotide wire. Nucleosides Nucleotides 17:1589–1603Google Scholar
  33. 33.
    Thibaudeau C, Plavec J, Chattopadhyaya J (1998) A new generalized Karplus-type equation relating vicinal proton-fluorine coupling constants to H-C-C-F torsion angles. J Org Chem 63:4967–4984Google Scholar
  34. 34.
    Luyten I, Matulic-Adamic J, Biegelman L, Chattopadhyaya J (1998) The electronic nature of the aglycon dictates the drive of pseudorotational equilibrium of the pentofuranose moiety in C-nucleosides. Nucleosides Nucleotides 17:1605–1611Google Scholar
  35. 35.
    Thibaudeau C, Kumar A, Bekiroglu S, Matsuda A, Marquez VE, Chattopadhyaya J (1998) NMR conformation of (-)-β-D-aristeromycin and its 2′-deoxy and 3′-deoxy counterparts in aqueous solution. J Org Chem 63:5447–5462Google Scholar
  36. 36.
    Thibaudeau C, Nishizono N, Sumita Y, Matsuda A, Chattopadhyaya J (1999) Determination of the group electronegativity of CF3 group in 3′-O-CF3-thymidine by 1H-NMR. Nucleosides Nucleotides 18:1035–1053Google Scholar
  37. 37.
    Acharya P, Nawrot B, Thibaudeau C, Chattopadhyaya J (1999) The strength of the 3′-gauche effect dictates the structure 3′-O-anthraniloyladenosine and its 5′-phosphate, two analogs of the 3′-end of aminoacyl-tRNA. J Chem Soc Perkin Trans II (1999) :1531–1536Google Scholar
  38. 38.
    Acharya P, Trifonova A, Thibaudeau C, Földesi A, Chattopadhyaya J (1999) The transmission of the electronic character of guanine-9-yl the sugar-phosphate backbone torsions in guanosine 3′,5′-biphosphate. Angew Chem Int Ed 38:3645–3650Google Scholar
  39. 39.
    Velikian I, Acharya P, Trifonova A, Földesi A, Chattopadhyaya J (2000) The RNA molecular wire: the pH-dependent change of the electronic character of adenin-9-yl is transmitted to drive the sugar and phosphate torsions in adenosine 3′,5′-biphosphate. J Phys Org Chem 13:300–305Google Scholar
  40. 40.
    Polak M, Plavec J, Trifonova A, Földesi A, Chattopadhyaya J (1999) The change in the electronic character upon cisplatin binding to guanine nucleotide is transmitted to drive the conformation of the local sugar-phosphate backbone – a quantitative study. J Chem Soc Perkin I (1999) :2835–2843Google Scholar
  41. 41.
    Griffey RH, Lesnik E, Freier S, Sanghvi YS, Teng K, Kawasaki A, Guinosso C, Wheeler P, Mohan V, Cook PD (1994) In: Sanghvi YS, Cook PD (eds) Carbohydrate modifications in antisense research, new twists on nucleic acids; structural properties of modified nucleosides incorporated into oligonucleotides, vol 580. American Chemical Society, Washington, DC, p 212Google Scholar
  42. 42.
    Freier SM, Altmann K-H (1997) The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA:RNA duplexes. Nucleic Acids Res 25:4429–4443Google Scholar
  43. 43.
    Tereshko V, Gryaznov S, Egli M (1998) Consequences of replacing the DNA 3′-oxygen by an amino group: high-resolution crystal structure of a fully modified N3 → P5′ phosphoramidate DNA dodecamer duplex. J Am Chem Soc 120:269–283Google Scholar
  44. 44.
    Berger I, Tereshko V, Ikeda H, Marquez VE, Egli M (1998) Crystal structures of B-DNA with incorporated 2′-deoxy-2′fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability. Nucleic Acids Res 26:2473–2480Google Scholar
  45. 45.
    Ikeda H, Fernandez R, Wilk A, Barchi JJ Jr, Huang X, Marquez VE (1998) The effect of two antipodal fluorine-induced sugar puckers on the conformation and stability of the Dickerson-Drew dodecamer duplex[d(CGCGAATTCGCG)]2. Nucleic Acids Res 26:2237–2244Google Scholar
  46. 46.
    Angyal SJ (1984) The composition of reducing sugars in solution. Adv Carbohydr Chem Biochem (Tipson RS, Horton D (ed) Academic Press, London) 42:15–68Google Scholar
  47. 47.
    Squillacote M, Sheridan OL, Chapman OL, Anet FAL (1975) Spectroscopic detection of the twist-boat conformation of cyclohexane. Direct measurement of the free energy difference between the chair and the twist-boat. J Am Chem Soc 97:3244–3246Google Scholar
  48. 48.
    Anderson JE (1974) Top Curr Chem 45:139Google Scholar
  49. 49.
    Kilpatrick JE, Pitzer KS, Spitzer R (1947) The thermodynamics and molecular structure of cyclopentane. J Am Chem Soc 69:2483Google Scholar
  50. 50.
    Strauss HL (1983) Pseudorotation: a large amplitude molecular motion. Ann Rev Phys Chem 34:301–328Google Scholar
  51. 51.
    Carreira LA, Jiang GJ, Person WB, Willis JN (1972) Spectroscopic determination of the barrier to planarity in cyclopentane. J Chem Phys 56:1440–1443Google Scholar
  52. 52.
    Hall LD, Steiner PR, Pedersen C (1970) Specifically fluorinated carbohydrates. VI. Pentofuranosyl fluorides. Can J Chem 48:1155–1165Google Scholar
  53. 53.
    Altona C, Sundaralingam M (1972) Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation. J Am Chem Soc 94:8205–8212Google Scholar
  54. 54.
    Westhof E, Sundaralingam M (1980) Interrelationship between the pseudorotation parameters P and Tm and the geometry of the furanose ring. J Am Chem Soc 102:1493Google Scholar
  55. 55.
    Sasisekharan V (1973) Jerus Symp Quant Chem Biochem 5:247Google Scholar
  56. 56.
    Saenger W (1988) Principles of nucleic acid structure. Springer, BerlinGoogle Scholar
  57. 57.
    Saenger W (1988) Principles of nucleic acid structure. Springer, Berlin, pp. 9396Google Scholar
  58. 58.
    Lai TF, Marsh RE (1972) Crystal structure of adenosine. Acta Cryst B28:1982–1989Google Scholar
  59. 59.
    Shikata K, Ueki T, Mitsui T (1973) Crystal and molecular structure of adenosine hydrochloride. Acta Cryst 29:31–38Google Scholar
  60. 60.
    Olson WK, Sussman JL (1982) How flexible is the furanose ring? 1. A comparison of experimental and theoretical studies. J Am Chem Soc 104:270–278Google Scholar
  61. 61.
    Olson WK (1982) How flexible is furanose ring? An updated potential energy estimate. J Am Chem Soc 104:278–286Google Scholar
  62. 62.
    Pearlman DA, Kim S-H (1985) Conformational studies of nucleic acids. II. The conformational energetics of commonly occurring nucleosides. J Biomol Struct Dyn 3:99Google Scholar
  63. 63.
    Jalluri RK, Yuh H, Taylor EW (1993) O-C-N anomeric effect in nucleosides. A major factor underlying the experimentally observed eastern barrier to pseudorotation. In: Thatcher GRJ (ed) The anomeric effects and associated stereoelectronic effects, vol 539. American Chemical Society, Washington, DC, pp 277–293Google Scholar
  64. 64.
    Sweigart DA (1973) Lone pair orbital in group VI and VII hydrides. J Chem Educ 50:322Google Scholar
  65. 65.
    David S, Eisenstein O, Hehre WJ, Salem L, Hoffman R (1973) Superjacent orbital control. Interpretation of the anomeric effect. J Am Chem Soc 95:3806–3807Google Scholar
  66. 66.
    Laing M (1987) No rabbit ears on water. The structure of the water molecule: what should we tell the students? J Chem Educ 64:124–128Google Scholar
  67. 67.
    Brundle CR, Turner DW (1968) High resolution molecular photoelectron spectroscopy. II. Water and deuterium oxide. Proc R Soc Lond A A307:27–36Google Scholar
  68. 68.
    Cossé-Barbi A, Dubois JE (1987) Anomeric orbital and steric control in static conformations and systems dynamics: rotations of methoxy groups in 2,2-dimethoxypropane and similar crystallographic COCOC fragments. J Am Chem Soc 109:1503–1511Google Scholar
  69. 69.
    Cossé-Barbi A, Watson DG, Dubois JE (1989) Anomeric effect in carbohydrates: non-equivalence of endocyclic oxygen lone pairs. Tetrahedron Lett 30:163–166Google Scholar
  70. 70.
    Romers C, Altona C, Buys HR, Havinga E (1969) In: Eliel EL, Allinger NL (eds) Topics in stereochemistry, vol 4. Willey Science, New York, p 39Google Scholar
  71. 71.
    de Leeuw HPM, Haasnoot CAG, 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. Full description of nucleoside molecular geometries in terms of four parameters. Isr J Chem 20:108–126Google Scholar
  72. 72.
    Allen FH, Davies JE, Galloy JJ, Johnson O, Kennard O, MacRae CF, Mitchell EM, Mitchell GF, Watson DG (1991) The development of versions 3 and 4 of the Cambridge Structural Database System. J Chem Inf Comput Sci 31:187–204Google Scholar
  73. 73.
    Lo A, Shefter E, Cochran TG (1975) Analysis of N-glycosyl bond length in crystal structures of nucleosides and nucleotides. J Pharm Sci 64:1707–1710Google Scholar
  74. 74.
    Juaristi E, Cuevas G (1992) Recent studies on the anomeric effect. Tetrahedron 48:5019–5087Google Scholar
  75. 75.
    Thatcher GRJ (1993) In: Thatcher GRJ (ed) Anomeric effect and associated stereoelectronic effects. Scope and controversy, vol 539. American Chemical Society, Washington, DC, pp 6–25Google Scholar
  76. 76.
    Fox JJ, Sugar D (1952) Spectrometric studies of nucleic acid derivatives and related compounds as a function of pH. II. Natural and synthetic pyrimidine nucleosides. Biochim Biophys Acta 9:369–384Google Scholar
  77. 77.
    Tran-Dinh S, Thiéry J, Guschlbauer J-J (1972) Nucleoside conformations. VIII. Conformation of guanosine 2′-phosphate in aqueous solution by proton magnetic resonance spectroscopy. Biochim Biophys Acta 281:289–298Google Scholar
  78. 78.
    Sarma RH, Mynott RJ (1973) Conformation of pyridine nucleotides studied by phosphorus-31 and hydrogen-1 Fourier transform nuclear magnetic resonance spectroscopy. I. Oxidized and reduced mononucleotides. J Am Chem Soc 95:1641–1649Google Scholar
  79. 79.
    Remin M, Shugar D (1973) Conformational analysis of cytidine 1-β-D-(arabinofuranosyl)cytosine and their O′-methyl derivatives by proton magnetic resonance spectroscopy. J Am Chem Soc 95:8146–8156Google Scholar
  80. 80.
    Altona C, Sundaralingam S (1973) Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants. J Am Chem Soc 95:2333–2344Google Scholar
  81. 81.
    Tran-Dinh S, Guschlbauer W (1975) Nucleoside conformations. 19. Temperature and pH effects on the conformation of guanosine phosphates. Nucleic Acids Res 3:873–886Google Scholar
  82. 82.
    Hruska FE, Wood DJ, Singh H (1977) Effect of temperature and protonation upon the conformation of 2′-O-methyladenosine. Correlation of conformational parameters in purine nucleosides. Biochim Biophys Acta 474:129–140Google Scholar
  83. 83.
    Jalluri RK, Yuh YH, Taylor EW (1993) O-C-N anomeric effect in nucleosides. A major factor underlying the experimentally observed eastern barrier to pseudorotation. In: Thatcher GRJ (ed) The anomeric effect and associated stereoelectronic effects, vol 539. American Chemical Society, Washington, DC, pp 277–293Google Scholar
  84. 84.
    Seela F, Becher G, Rosemeyer H, Reuter H, Kastner G, Mikhailopulo I (1999) The high-anti conformation of 7-halogenated 8-aza-7-deaza-2′-deoxyguanosines. A study of the influence of modified bases on the sugar structure of nucleosides. Helv Chim Acta 82:105–124Google Scholar
  85. 85.
    Hillen W, Gassen HG (1978) 5-substituents in the uridine moiety and their effect on the conformation of ApU-type dinucleoside phosphates. Biochim Biophys Acta 518:7–16Google Scholar
  86. 86.
    Egert E, Lindner HJ, Hillen W, Böhm MC (1980) Influence of substituents at the 5 position on the structure of uridine. J Am Chem Soc 102:3707–3713Google Scholar
  87. 87.
    Uhl W, Reiner J, Gassen HG (1983) On the conformation of 5-substituted uridines as studied by proton magnetic resonance. Nucleic Acids Res 11:1167–1180Google Scholar
  88. 88.
    O’Leary DJ, Kishi Y (1994) Preferred conformation of C-glycosides. 13. A comparison of the conformational behavior of several C-, N-, and O-furanosides. J Org Chem 59:6629–6636Google Scholar
  89. 89.
    Ekiel I, Remin M, Darzynkiewicz E, Shugar D (1979) Correlations of conformational parameters and equilibrium conformational states in a variety of β-D-arabinonucleosides and their analogs. Biochim Biophys Acta 562:177–191Google Scholar
  90. 90.
    Yamamoto Y, Yokoyama S, Miyazawa T, Watanabe K, Higuchi S (1983) FEBS Lett 157:95Google Scholar
  91. 91.
    Allore BD, Queen A, Blonski WJ, Hruska FE (1983) A kinetic and nuclear magnetic resonance study of methylated pyrimidine nucleosides. Can J Chem 61:2397–2402Google Scholar
  92. 92.
    Birnbaum GI, Blonski WJP, Heuska FE (1983) Structure and conformation of anticodon nucleoside 5-methoxyuridine in the solid state and in solution. Can J Chem 61:2299–2304Google Scholar
  93. 93.
    Cadet J, Ducolomb R, Taieb C (1975) NMR at 250 MHz of 6-methyl-2′-deoxyuridine. Preferential syn-configuration in aqueous solution. Tetrahedron Lett 40:3455–3458Google Scholar
  94. 94.
    Birnbaum GI, Hruska FE, Niemczura WP (1980) A pyrimidine nucleoside constrained in the syn form. Structure and conformation of 6-methyl-2′-deoxyuridine. J Am Chem Soc 102:5586–5590Google Scholar
  95. 95.
    Bergström DF, Zhang P, Toma PH, Andrews PC, Nichols R (1995) Synthesis, structure, and deoxyribonucleic acid sequencing with a universal nucleoside: 1-(2′-deoxy-β-D-ribofuranosyl)-3-nitropyrrole. J Am Chem Soc 117:1201–1209Google Scholar
  96. 96.
    Swarna Latha Y, Yathindra N (1992) Stereochemical studies on nucleic acid analogs. I. Conformations of α-nucleosides and α-nucleotides: interconversion of sugar puckers via O4′-exo. Biopolymers 32:249–269Google Scholar
  97. 97.
    Post ML, Birnbaum GI, Huber CP, Shugar D (1977) α-Nucleosides in biological systems. Crystal structure and conformation of α-cytidine. Biochim Biophys Acta 479:133–142Google Scholar
  98. 98.
    Sundaralingam M (1971) Stereochemistry of nucleic acids and their constituents. XVIII. Conformational analysis of α nucleosides by X-ray crystallography. J Am Chem Soc 93:6644–6647Google Scholar
  99. 99.
    Rohrer DC, Sundaralingam M (1970) Stereochemistry of nucleic acids and their constituents. XII. Crystal and molecular structure of α-D-amino-2′-deoxyadenosine monohydrate. J Am Chem Soc 92:4956–4962Google Scholar
  100. 100.
    Remin M, Ekiel I, Shugar D (1975) Proton-magnetic-resonance study of the solution conformation of the α and β anomers of 5-ethyl-2′-deoxyuridine. Eur J Biochem 53:197–206Google Scholar
  101. 101.
    Seto H, Otake N, Yonehara H (1972) Tetrahedron Lett 38:3991Google Scholar
  102. 102.
    Ruzic-Toros Z (1979) [Crystal structure of]5,6-dimethyl-1-(α-D-ribofuranosyl)benzimidazole. Acta Cryst B35:1277–1280Google Scholar
  103. 103.
    Crowfoot Hodgkin D, Lindsey J, Sparks RA, Trueblood KN, White JG (1962) Structure of vitamin B12. V. Structure of the air-dried crystals of vitamin B12. Proc R Soc A266:494Google Scholar
  104. 104.
    Brink-Shoemaker C, Cruickshank DWJ, Crowfoot Hodgkin D, Kamper MJ, Pilling D (1964) Structure of vitamin B12. VI. Structure of crystals of vitamin B12 grown from and immersed in water. Proc R Soc Lond A A278:1–26Google Scholar
  105. 105.
    Hawkinson SW, Coulter CL, Greaves ML (1979) Structure of vitamin B12. VIII. Crystal structure of vitamin B12-5′ phosphate. Proc Roy Soc A318:143Google Scholar
  106. 106.
    Savage HFJ, Lindley PF, Finney JL, Timmins PA (1987) High-resolution neutron and X-ray refinement of vitamin B12 coenzyme, C72H100CoN18O17P.17H2O. Acta Cryst B43:280–295Google Scholar
  107. 107.
    Lenhert PG (1968) Structure of vitamin B12. VII. X-ray analysis of the vitamin B12 coenzyme. Proc R Soc Lond A A303:45–84Google Scholar
  108. 108.
    Hamor TA, O’Leary MK, Walker RT (1977) The crystal and molecular structure of α-5-acetyl-2′-deoxyuridine. Acta Cryst B33:1218–1223Google Scholar
  109. 109.
    Shefter E, Kotick MP, Bardos J (1967) Crystal and molecular structure of 5-[1(2-deoxy-α-D-erythro-pentofuranosyl)acyl]disulfide. J Pharm Sci 56:1293–1299Google Scholar
  110. 110.
    Ide H, Shimzu H, Kimura Y, Sakamoto S, Makino K, Glackin M, Wallace SS, Nakamuta H, Sasaki M, Sugimoto N (1995) Influence of α-deoxyadenosine on the stability and structure of DNA. Thermodynamic and molecular mechanics studies. Biochemistry 34:6947–6955Google Scholar
  111. 111.
    Gutowski GE, Chaney MO, Jones ND, Hamill RL, Davis FA, Miller RD (1973) Pyrazomycin B: isolation and characterization of an –C-nucleoside antibiotic related to pyrazomycin. Biochim Biophys Res Commun 51:312–317Google Scholar
  112. 112.
    Armstrong VW, Dattagupta JK, Eckstein F, Saenger W (1976) The base catalyzed anomerization of β-5-formyluridine; crystal and molecular structure of α-5-formyluridine. Nucleic Acids Res 3:1791–1810Google Scholar
  113. 113.
    Cline SJ, Hodgson DJ (1979) The crystal and molecular structure of 9-α-D-arabinofuranosyladenine. Biochim Biophys Acta 563:540–544Google Scholar
  114. 114.
    Post ML, Huber CP, Birnbaum GI, Shugar D (1981) Crystal structures and conformations of 1-α-D-xylofuranosylcytosine and its protonated form (hydrogen chloride salt). Can J Chem 59:238–245Google Scholar
  115. 115.
    Piper IM, MacLean DB, Faggiani R, Lock CJL, Szarek WA (1985) Configurational and conformational studies on condensation products of biogenic amines with 2,5-anhydro-D-mannose. Can J Chem 63:2915–2921Google Scholar
  116. 116.
    Hoffman RA, van Wijk J, Leeflang BR, Kamerling JP, Altona C, Vliegenthart JFG (1992) Conformational analysis of the α-L-arabinofuranosides present in wheat arabinoxylans from proton-proton coupling constants. J Am Chem Soc 114:3710–3714Google Scholar
  117. 117.
    Serianni A, Barker R (1984) [13C]-Enriched tetroses and tetrofuranosides: an evaluation of the relationship between NMR parameters and furanosyl ring conformation. J Org Chem 49:3292–3300Google Scholar
  118. 118.
    Serianni AS, Chipman DM (1987) Furanose ring conformation: the application of ab initio molecular orbital calculations to the structure and dynamics of erythrofuranose and threofuranose rings. J Am Chem Soc 109:5297–5303Google Scholar
  119. 119.
    Kline PC, Serianni AS (1990) 13C-enriched ribonucleosides: synthesis and application of 13C-1H and 13C-13C spin-coupling constants to asses furanose and N-glycoside bond conformations. J Am Chem Soc 112:7373, 7381Google Scholar
  120. 120.
    Raap J, van Boom JH, van Lieshoiut HC, Haasnoot CAG (1988) J Am Chem Soc 110:2736–7381Google Scholar
  121. 121.
    Ellervik U, Magnussonm G (1994) Anomeric effect in furanosides. Experimental evidence from conformationally restricted compounds. J Am Chem Soc 116:2340–2347Google Scholar
  122. 122.
    Griffey RH, Lesnik E, Freier S, Sanghvi YS, Teng K, Kawasaki A, Guinoso C, Wheeler P, Mohan V, Cook PD (1994) In: Sanghvi VS, Cook PD (eds) Carbohydrate modifications in antisense research, new twist on nucleic acids; structural properties of modified nucleosides incorporated into oligonucleotides, vol 580. American Chemical Society, Washington, DC, p 212Google Scholar
  123. 123.
    Teng K, Cool PD (1994) Nucleic acid mimics. Synthesis of ethylene glycol- and propoxy-linked thymidyl-tetrahydrofuranylthymine dimers via a Vorbruggen-type glycosylation reaction. J Org Chem 59:278–280Google Scholar
  124. 124.
    Cyr N, Perlin AS (1979) The conformations of furanosides. A carbon-13 nuclear magnetic resonance study. Can J Chem 57:2504–2511Google Scholar
  125. 125.
    Saenger W (1988) Principles of nucleic acids structure. Springer, BerlinGoogle Scholar
  126. 126.
    Izatt RM, Christensen JJ, Ryttiing JH (1971) Sites and thermodynamic quantities associated with proton and metal ion interaction with ribonucleic acid, deoxyribonucleic acid, and their constituent bases, nucleosides, and nucleotides. Chem Rev 71:439–482Google Scholar
  127. 127.
    Garcia B, Palacios JC (1988) Protonation study of biological bases of DNA. Ber Bunsenges Phys Chem 92:696–700Google Scholar
  128. 128.
    Taylor R, Kennard O (1982) The molecular structures of nucleosides and nucleotides. Part 1. The influence of protonation on the geometries of nucleic acid constituents. J Mol Struct 78:1–28Google Scholar
  129. 129.
    Jardetzky CD, Jardetzky O (1960) Investigation of the structure of purines, pyrimidines, ribose nucleosides and nucleotides by proton magnetic resonance.II. J Am Chem Soc 82:222–229Google Scholar
  130. 130.
    Angell CL (1961) An infrared spectroscopic investigation of nucleic acid constituents. J Chem Soc (1961) :504–515Google Scholar
  131. 131.
    Tsuboi M, Kyogoku Y, Shimanouchi T (1962) Infrared absorption spectra of protonated and deprotonated nucleosides. Biochim Biophys Acta 55:1–12Google Scholar
  132. 132.
    Kartritzky AR, Wariing AJ (1962) Tautomeric azines. Tautomerism of 1-methyluracil and 5-bromo-1-methyluracil. J Chem Soc (1962) :1540–1544Google Scholar
  133. 133.
    Lord RC, Thomas GJJ (1967) Raman studies of nucleic acids. II. Aqueous purine and pyrimidine mixtures. Biochim Biophys Acta 142:1–11Google Scholar
  134. 134.
    Clauwaert J, Stockx J (1968) Interactions of polynucleotides and their components. I. Dissociation constants of the bases and their derivatives. Z Naturforsch 23B:25–30Google Scholar
  135. 135.
    Wagner R, von Philipsborn W (1970) Protonation of amino and hydroxypyrimidines. NMR-spectra and structures of mono and dications. Helv Chim Acta 53:299–320Google Scholar
  136. 136.
    Christensen JJ, Rytting H, Izatt RM (1970) Thermodynamic pK, ΔH.deg, ΔS.deg, and ΔCp.deg values for proton dissociation from several purines and their nucleosides in aqueous solution. Biochemistry 9:4907–4913Google Scholar
  137. 137.
    Poulter CD, Anderson RB (1972) Direct observation of uracil dication and related derivatives. Tetrahedron Lett 36:3823–3826Google Scholar
  138. 138.
    Dunn DB, Hall RH (1975) In: Fassman GD (ed) Handbook of biochemistry and molecular biology, vol 1. CRC Press, Cleveland, p 65Google Scholar
  139. 139.
    Le Doan T, Perrouault L, Praseuth D, Habhoub N, Decout J-L, Thouong NT, Lhomme J, Hélène C (1987) Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an oligo-[α]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res 15:7749–7760Google Scholar
  140. 140.
    Moser HE, Dervan PB (1987) Sequence-specific cleavage of double helical DNA by triple helix formation. Science 238:645Google Scholar
  141. 141.
    Povsic TJ, Dervan PB (1989) Triple helix formation by oligonucleotides on DNA extended to the physiological pH range. J Am Chem Soc 111:3059–3061Google Scholar
  142. 142.
    Xodo LE, Manzini G, Quadrifoglio F, van der Marel GA, van Boom JH (1991) Effect of 5-methylcytosine on the stability of triple-stranded DNA – a thermodynamic study. Nucleic Acids Res 19:5625–5631Google Scholar
  143. 143.
    Brown T, Leonard GA, Booth ED, Kneale G (1990) Influence of pH on the conformation and stability of mismatch base-pairs in DNA. J Mol Biol 212:437Google Scholar
  144. 144.
    Boulard Y, Cognet JAH, Gabarro-Arpa J, LeBret M, Sowers LC, Fazakerley GV (1992) The pH dependent configurations of the C′A mispair in DNA. Nucleic Acid Res 20:1933–1941Google Scholar
  145. 145.
    Wang C, Gao H, Gaffney BL, Jones RA (1991) Nitrogen-15 labeled oligodeoxynucleotides. 3. Protonation of the adenine N1 in the A′C and A′G mispairs of the duplexes {d[CG(15N1)AGAATTCCCG]}2 and {d[CGGGAATTC(15N1)ACG]}2. J Am Chem Soc 113:5486–5488Google Scholar
  146. 146.
    Macaya RF, Gilbert DE, Malek S, Sinsheimer JS, Feigon J (1991) Structure and stability of X′G′C mismatches in the third strand of intramolecular triplexes. Science 254:270–273Google Scholar
  147. 147.
    Gao X, Patel DJ (1988) G(syn)′A(anti) mismatch formation in DNA dodecamers at acidic pH: pH-dependent conformational transition of G′A mispairs detected by proton NMR. J Am Chem Soc 110:5178–5182Google Scholar
  148. 148.
    Dolinnaya NG, Fresco JR (1992) Single stranded nucleic acid helical secondary structure stabilized by ionic bonds: d(A+-G)10. Proc Natl Acad Sci U S A 89:9242–9246Google Scholar
  149. 149.
    Dolinnaya NG, Braswell EH, Fosella JA, Klump H, Fresco JR (1993) Molecular and thermodynamic properties of d(A+-G)10, a single-stranded nucleic acid helix without paired or stacked bases. Biochemistry 32:10263–10270Google Scholar

Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Momcilo Miljkovic
    • 1
  1. 1.Pennsylvania State UniversityHersheyUSA

Personalised recommendations