Cross-modulation of physicochemical character of aglycones in dinucleoside (3′→5′) monophosphates by the nearest neighbor interaction in the stacked state

Journal of the American Chemical Society

Volumn 124, Issue 46, 2002, Pages 13722-13730

  Acharya, S ^a   Acharya, P ^a   Foldesi A ^a   Chattopadhyaya, J ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

INTRAMOLECULAR STACKING;

BIOSYNTHESIS; DIMERS; ENZYMES; HYDROGEN BONDS; NUCLEIC ACIDS; PH EFFECTS; PHOSPHATES;

PHYSICAL CHEMISTRY;

DINUCLEOSIDE PHOSPHATE; NUCLEIC ACID BASE; OLIGONUCLEOTIDE; POLYNUCLEOTIDE;

ACIDITY; ALKALINITY; ARTICLE; CHEMICAL BOND; HYDROGEN BOND; MICROENVIRONMENT; MOLECULAR INTERACTION; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; PH MEASUREMENT; PKA; PROTEIN INTERACTION; PROTEIN SYNTHESIS; PROTON NUCLEAR MAGNETIC RESONANCE; SEQUENCE ANALYSIS;

CARBOHYDRATE CONFORMATION; DINUCLEOSIDE PHOSPHATES; ELECTROSTATICS; FLAVONOIDS; HYDROGEN-ION CONCENTRATION; KINETICS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; THERMODYNAMICS;

EID: 0037146042     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja026831h     Document Type: Article

References (45)

1. Jeffrey, G. A.; Saenger, W. Hydrogen Boding in Biological Systems; Springer-Verlag: Berlin, 1991.
2. Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: Berlin, 1988.
3. Cech, T. R. Annu. Rev. Biochem. 1990, 59, 543.
4. (a) Thibaudeau, C.; Plavec, J.; Chattopadhyaya, J. J. Org. Chem. 1996, 61, 266.
5. a of constituent heterocyclic nucleobases by the quantitation of the pD-dependent energetics of the two-state N ⇆ S pseudorotational equilibrium.
6. Acharya, P.; Trifonova, A.; Thibaudeau, C.; Földesi, A.; Chattopadhyaya, J. Angew. Chem. Int. Ed. 1999, 38, 3645.
7. Thibaudeau, C.; Chattopadhyaya, J. Stereoelectronic Effects in Nucleosides and Nucleotides and Their Structural Implications; Department of Bioorganic Chemistry, Uppsala University Press (jyoti@boc.uu.se): Uppsala, Sweden, 1999; ISBN 91-506-1351-0, and references therein.
8. Burkard, M. E.; Kierzek, R.; Turner, D. H. J. Mol. Biol. 1999, 290, 967, and references therein.
9. Bommarito, S.; Peyret, N.; SantaLucia, J. Jr. Nucleic Acid Res. 2000, 28, 1929.
10. Ossipov, D.; Zamaaratski, E.; Chattopadhyaya, J. Nucleosides Nucleotides 1998, 17 (9-11), 1613.
11. Maltseva, T. V.; Agback, P.; Repkova, M. N.; Venyaminova, A. G.; Ivanova, E. M.; Sandstr6m, A.; Zarytova, V. F.; Chattopadhyaya, J. Nucleic Acid Res. 1994, 22, 5590.
12. Ossipov, D.; Pradeepkumar, P. I.; Holmer, M.; Chattopadhyaya, J. J. Am. Chem. Soc. 2001, 123, 3551.
13. Hunter, C. A. J. Mol. Biol. 1993, 230, 1025, and references therein.
14. The importance of stacking has been identified in DNA polymerase activity and in efficiency of DNA synthesis. For review: Kool, E. T. Annu. Rev. Biophys. Biomol. Struct. 2001, 30, 1, and references therein.
15. The interaction of the aromatic rings depends on the stacking geometry: edge-to-face stacked, (ii) offset stacked, and (iii) face-to-face stacked. The offset stacked arrangement minimizes π-electron repulsion and maximizes the interactions in the σ-framework. For review: Hunter, C. A.; Lawson, K. R.; Perkins, J.; Urch, C. J. J. Chem. Soc. Perkin Trans. 2 2001, 651.
16. Jennings, W. B.; Farrell, B. M.; Malone, J. F. Acc. Chem. Res. 2001, 34, 885.
17. The experimental evidence showed that the magnitude of offset stacked interactions can be dictated by the geometry of the stacked components, which, in turn, is influenced by the nature of ring substituents. Rashkin, M. J.; Waters, M. L. J. Am. Chem. Soc. 2002, 124, 1860, and refs 1, 2, and 8 therein.
18. Altona, C. in Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactios; Sundaralingam, M. Rao, S. T. Eds.; University Park Press: Baltimore, MD, 1975; p 613.
19. Lee, C.-H.; Ezra, F. S.; Kondo, N. S.; Sarma, R. H.; Danyluk, S. Biochemistry 1976, 15, 3627.
20. Topal, M. D.; Warshaw, M. M. Biopolymers 1976, 15, 1775.
21. Kolondny, N. H.; Neville, A. C.; Coleman, D. L.; Zamecnik, P. C. Biopolymers 1977, 16, 259.
22. Cox, R. A. A Biochem. J. 1966, 100, 148.
23. Schmidt, A.; Kindermann, M. K.; Vainotalo, P.; Nieger, M. J. Org. Chem. 2000, 64, 9499.
24. Chan, S. I.; Nelson, J. H. J. Am. Chem. Soc. 1969, 91, 168.
25. a Prediction for Organic Acids and Bases; Chapman and Hall: New York, 1981.
26. Sharp, K. A.; Honig, B. Annu. Rev. Biophys. Chem. 1990, 19, 301.
27. 30-36
28. - is the most staked among all pyrimidine-pyrimidine dimers (compare the ΔΔG° in Figure 4D).
29. -1. Moreover, these values are well-correlated with free energy stabilization of stacking at helix termini in larger RNA and are consistent with our present studies (Figure 4D) too.
30. Patel, D. J.; Suri, A. K. Rev. Mol. Biotechnol. 2000, 74, 39.
31. Legault, P.; Pardi, A. J. Am. Chem. Soc. 1997, 119, 6621 and references therein.
32. Ravindranathan, S.; Butcher, S. E.; Feigon, J. Biochemistry, 2000, 39, 16026.
33. Drohat, A. C.; Stivers, J. T. Biochemistry 2000, 39, 11865.
34. Nakano, S.; Chadalavada, D. M.; Bevilacqua, P. C. Science 2000, 287, 1493, and references therein.
35. Xiong, L.; Polacek, N.; Sander, P.; Böttger, E. C.; Mankin, A. RNA 2001, 7, 1365.
36. Ryder, S. P.; Oyelere, A. K.; Padilla, J. L.; Klostermeier, D.; Millar, D. P.; Strobel, S. A. RNA 2001, 7, 1454, and references therein.
37. Narlikar, G. J.; Herschlag, D. Annu. Rev. Biochem. 1997, 66, 19, and references therein.
38. Ramakrishnan, V. Cell 2002, 69, 557.
39. Leninger, A. L.; Nelson, D. L.; Cox, M. M. Principles of Biochemistry 2nd Ed.; Worth Publishers Inc.: New York. 1993.
40. Grinstaff, M. W. Angew. Chem. Int. Ed. 1999, 38, 3629.
41. Giese, B. Acc. Chem. Res. 2000, 33, 631.
42. Guerra, C. F.; Bickelhaupt, F. M. Angew. Chem. Int. Ed. 1999, 38, 2942.
43. Felemez, M.; Bernard, P.; Schlewer, G.; Spiess, B. J. Am. Chem. Soc. 2000, 122, 3156.
44. -1) in interaction with HOMO [-0.3996 au] of the indole ring. It has been found that in these stacked pairs, the indole ring more strongly interacts with the pyrimidine rather than imidazole part of the adeninium ring. Ishida, T.; Shibata, M.; Fuji, K.; Inoue, M. Biochemistry 1983, 22, 3571.
45. Xu, D.; Norlund, T. M. Biophys. J. 2000, 78, 1042.