DFT study of the interaction of cytidine and 2′-deoxycytidine with Li+, Na+, and K+: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond

Carbohydrate Research

Volumn 344, Issue 6, 2009, Pages 771-778

  Tehrani, Zahra Aliakbar ^a   Fattahi, Alireza ^a   Pourjavadi, Ali ^a  

^a SHARIF UNIVERSITY OF TECHNOLOGY   (Iran)

Author keywords

2 Deoxyribonucleoside; DFT study; Metal complexation; N Glycosidic bond; Ribonucleoside

Indexed keywords

ATOMIC NUMBERS; BASIS SETS; BINDING STRENGTHS; BOND DISTANCES; COMPUTATIONAL STUDIES; CONFORMATIONAL BEHAVIORS; COORDINATION MODES; CYTIDINE; DENSITY FUNCTIONAL THEORY CALCULATIONS; DFT STUDY; GAS-PHASE; GLYCOSYL; LINEAR CORRELATIONS; METAL BINDINGS; METAL CATIONIZATION; METAL CATIONS; METAL COMPLEXATION; METAL ION; N-GLYCOSIDIC BOND; PHASE ANGLES; POSITIVE CHARGES; PSEUDOROTATION; RIBONUCLEOSIDE; SUGAR RING CONFORMATIONS; SUGAR RINGS; SUGAR UNITS; TORSION ANGLES;

ATOMS; CONFORMATIONS; COORDINATION REACTIONS; DENSITY FUNCTIONAL THEORY; METAL IONS; NUCLEIC ACIDS; NUCLEOTIDES; PROBABILITY DENSITY FUNCTION; SUGAR (SUCROSE); SUGARS; TRACE ANALYSIS;

METALS;

CYTIDINE; DEOXYCYTIDINE; LITHIUM; NUCLEOSIDE; POTASSIUM; SODIUM;

ARTICLE; CHEMICAL BOND; CHEMICAL INTERACTION; CONFORMATION; DENSITY FUNCTIONAL THEORY; MATHEMATICAL COMPUTING; METAL BINDING; MOLECULAR STABILITY; NUCLEIC ACID ANALYSIS; PRIORITY JOURNAL;

CATIONS; COMPUTERS, MOLECULAR; CYTIDINE; DEOXYCYTIDINE; GLYCOSYLATION; LITHIUM; MOLECULAR STRUCTURE; POTASSIUM; RIBONUCLEOSIDES; SODIUM;

EID: 63549110269     PISSN: 00086215     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.carres.2009.02.007     Document Type: Article

References (60)

1. Stivers J.T., and Jiang Y.L. Chem. Rev. 103 (2003) 2729-2759
2. Loeb L.A., and Preston B.D. Annu. Rev. Genet. 20 (1986) 201-230
3. Schyman P., Danielsson J., Pinak M., and Laaksonen A. J. Phys. Chem. A. 109 (2005) 1713-1719
4. Fromme J.C., Banerjee A., and Verdine G.L. Curr. Opin. Struct. Biol. 14 (2004) 43-49
5. Versees W., and Steyaert J. Curr. Opin. Struct. Biol. 13 (2003) 731-738
6. Obrien P.J., and Ellenberger T. Biochemistry. 42 (2003) 12418-12429
7. Scharer O.D. Angew. Chem., Int. Ed. 42 (2003) 2946-2974
8. Dinner A.R., Blackburn G.M., and Karplus M. Nature 413 (2001) 752-755
9. Lindahl T., and Nyberg B. Biochemistry 11 (1972) 3610-3618
10. Lönnberg H., and Lehikoinen P. Nucleic Acids Res. 10 (1982) 4339-4349
11. Clarke M.J., and Morrissey P.E. Inorg. Chim. Acta 80 (1983) L69-L70
12. Remaud G., Zhou X.X., Chattopadhyaya J., Oivanen M., and Lönnberg H. Tetrahedron 43 (1987) 4453-4461
13. Arpalahti J., Käppi R., Hovinen J., Lönnberg H., and Chattopadhyaya J. Tetrahedron 45 (1989) 3945-3954
14. Kumar A.M., and Nayak R. Biochem. Biophys. Res. Commun. 173 (1990) 731-735
15. Laayoun A., Décout J.L., and Lhomme J. Tetrahedron Lett. 35 (1994) 4989-4990
16. Lindahl T. Nature 362 (1993) 709-715
17. Bianchet M.A., Seiple L.A., Jiang Y.L., Ichikawa Y., Amzel L.M., and Stivers J.T. Biochemistry 42 (2003) 12455-12460
18. Cavalieri E.L., Vauthier E.C., Cosse-Barbi A., and Fliszar S. Theor. Chem. Acc. 104 (2000) 235-239
19. Baik M.H., Friesner R.A., and Lippard S.J. J. Am. Chem. Soc. 124 (2002) 4495-4503
20. Hotokka M., and Lönnberg H. J. Mol. Struct. (Theochem) 363 (1996) 191-201
21. Cysewski P., Bira D., and Bialkowski K. J. Mol. Struct. (Theochem) 678 (2004) 77-81
22. Kebarle P., and Peschke M. Anal. Chim. Acta 406 (2000) 11-35
23. Sigel H., Massoud S.S., and Corfu N.A. J. Am. Chem. Soc. 116 (1994) 2958-2971
24. Sajadi S.A.A., Song B., Gregan F., and Sigel H. Inorg. Chem. 38 (1999) 439-448
25. Eichhorn G.L. Adv. Inorg. Biochem. 3 (1981) 1-46
26. Martin R.B. Acc. Chem. Res. 18 (1985) 32-38
27. Sigel H. Chem. Soc. Rev. 22 (1993) 255-267
28. Yamauchi O., Odani A., Masuda H., Sigel H., and Sigel A. In: Sigel H. (Ed). Interactions of Metal Ions with Nucleotides, Nucleic Acids, and Their Constituents Metal Ions in Biological Systems Vol. 32 (1996), Marcel Dekker, New York 207-270
29. In: Sigel A., and Sigel H. (Eds). Probing of Nucleic Acids by Metal Ion Complexes of Small Molecules Metal Ions in Biological Systems Vol. 33 (1996), Marcel Dekker, New York
30. Nakano S.I., Fujimoto M., Hara H., and Sugimoto N. Nucleic Acids Res. 27 (1999) 2957-2965
31. Brautigan C.A., and Steitz T.A. Curr. Opin. Struct. Biol. 8 (1998) 54-63
32. El-Deiry W., Downey K., and So A. Proc. Natl. Acad. Sci. U.S.A. 81 (1984) 7378-7382
33. Orgel A., and Orgel L. J. Mol. Biol. 14 (1965) 453-457
34. Beckman R., Mildvan A., and Loeb L. Biochemistry 24 (1985) 5810-5817
35. Saenger W. Principles of Nucleic Acid Structure (1984), Springer, New York
36. Cheng X., Wu Z., and Fenselau C. J. Am. Chem. Soc. 115 (1993) 4844-4848
37. Loeb L.A., and Zakour A.R. In: Spiro T.G. (Ed). Nucleic Acids Metal Ion Interactions (1980), John Wiley & Sons, New York 115-144
38. Cerda B.A., and Wesdemiotis C. J. Am. Chem. Soc. 118 (1996) 11884-11892
39. Wu Z., and Fenselau C. Rapid Commun. Mass Spectrom. 8 (1994) 777-780
40. Armentrout P.B. J. Am. Soc. Mass Spectrom. 11 (2000) 371-379
41. Mertz E., and Krishtalik L.J. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 2081-2086
42. Dewar M.J.S., and Storch D.M. Proc. Natl. Acad. Sci. U.S.A. 82 (1985) 2225-2229
43. Petrushka J., Sowers L.C., and Goodman M.F. Proc. Natl. Acad. Sci. U.S.A. 83 (1986) 1559-1562
44. Kool E.T. Annu. Rev. Biophys. Biomol. Struct. 30 (2001) 1-22
45. Sychrovsky V., Müller N., Schneider B., Smrecki V., Spirko V., Sponer J., and Trantirek L. J. Am. Chem. Soc. 127 (2005) 14663-14667
46. spartan '06V102'; Wavefunction: Irvine, CA.
47. Becke A.D. J. Chem. Phys. 98 (1993) 5648-5652
48. Lee C., Yang W., and Parr R.G. Phys. Rev. B 37 (1988) 785-789
49. Zhu W., Luo X., Puah M.C., Tan X., Shen J., Gu J., Chen K., and Jiang H. J. Phys. Chem. A 108 (2004) 4008-4018
50. Altona C., and Sundaralingam M. J. Am. Chem. Soc. 94 (1972) 8205-8212
51. Almenningen A., Seipk H.M., and Willadsen T. Acta Chem. Scand. 23 (1969) 2748-2754
52. Engerholm G.G., Luntz A.C., Gwinn W.D., and Harris D.O. J. Chem. Phys. 50 (1969) 2446-2457
53. Trueblood K.N. Diffraction Studies of Molecular Motion in Crystals. In: Domenicano A.I., and Hargittai I. (Eds). Accurate Molecular Structure. Their Determination and Importance (1992), Oxford University Press, Oxford 469-492
54. Bernstein J. Effect of Crystal Environment on Molecular Structure. In: Domenicano A.I., and Hargittai I. (Eds). Accurate Molecular Structure. Their Determination and Importance (1992), Oxford University Press, Oxford 469-497
55. Furberg S., Petersen C.S., and Romming C. Acta Crystallogr 18 (1965) 313-320
56. Wahl M.C., and Sundaralingam M. Trends Biochem. Sci. 22 (1997) 97-102
57. Auffinger P., and Westhof E. J. Mol. Biol. 274 (1997) 54-63
58. Gu Y., Kar T., and Scheiner S. J. Am. Chem. Soc. 121 (1999) 9411-9422
59. Sponer J., Burda J.V., Leszczynski J., and Hobza P. J. Biomol. Struct. Dyn. 16 (1999) 139-146
60. Fattahi A., and Tavasoli E. J. Phys. Org. Chem. 21 (2008) 112-118