Experimental measurement of aromatic stacking affinities in the context of duplex DNA

Journal of the American Chemical Society

Volumn 118, Issue 34, 1996, Pages 8182-8183

  Guckian, Kevin M ^a   Schweitzer, Barbara A ^a   Ren, Rex X F ^a   Sheils, Charles J ^a   Paris, Pamela L ^a   Tahmassebi, Deborah C ^a   Kool, Eric T ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA DETERMINATION; DNA STRUCTURE; THERMODYNAMICS;

EID: 0029830638     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja961733f     Document Type: Article

References (32)

1. See, for example: Yu, M. H.; Weissman, J. S.; Kim, P. S. J. Mol. Biol. 1996, 249, 388-397.
2. Werner, M. H.; Gronenborn, A. M.; Clore, G. M. Science 1996, 271, 778-784.
3. See, for example: (a) Breslauer, K. J.; Frank, R.; Blocker, H; Marky, L. A. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 3746-3750. (b) SantaLucia, J.; Allawi, H. T.; Seneviratne. P. A. Biochemistry 1996, 35, 3555-3562.
4. See, for example: (a) Breslauer, K. J.; Frank, R.; Blocker, H; Marky, L. A. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 3746-3750. (b) SantaLucia, J.; Allawi, H. T.; Seneviratne. P. A. Biochemistry 1996, 35, 3555-3562.
5. Petersheim, M.; Turner, D. H. Biochemistry 1983, 22, 256-263.
6. (a) Jernigan, R. L.; Sarai. A.; Ting, K.-L.; Nussinov, R. J. Biomol. Struct. Dyn. 1986, 4, 41-48.
7. (b) Hunter, C. A. J. Mol. Biol. 1993, 230, 1025-1054.
8. (c) Maroun, R. C.; Olson, W. K. Biopolymers 1988, 27, 561-584.
9. (d) Ornstein, R. L.; Rein, R.; Breen. D. L.; Macelroy, R. D. Bioplymers 1978, 17, 2341-2360.
10. (e) Friedman, R. A.; Honig, B. Biopolymers 1992, 32, 145-159.
11. (f) Maroun, R. C.; Olson, W. K. Biopolymers 1988,27, 585-603.
12. (g) Sarai, A.; Mazur, J.; Nussinov, R.; Jernigan, R. L. Biochemistry 1988, 27, 8498-8502.
13. For a review of helical structure (stacking) in single-stranded, heterogeneous polymeric DNA, see: Felsenfeld, G.; Miles, H. T. Annu. Rev. Biochem. 1967, 36, 407.
14. Such studies have been carried out by Turner et al. with the natural bases in RNA (ref 4 and Turner, D. H.; Sugimoto, N. Annu. Rev. Biophys. Biophys. Chem. 1988, 17, 167-192), but there are no such single-base stacking studies reported in DNA.
15. Senior, M.; Jones, R. A.; Breslauer, K. J. Biochemistry 1988, 27, 3879-3885.
16. Schweitzer, B. A.; Kool, E. T. J. Org. Chem. 1994, 59, 7238-7242.
17. Moran, S.; Ren, R. X.-F.; Sheils, C. J.; Kool, E. T. Nucleic Acids Res. 1996, 24, 2044-2052.
18. Ren, X.-F.; Schweitzer, B. A.; Sheils, C. J.; Kool, E. T. Angew. Chem. 1996, 108, 834-837; Angew. Chem., Int. Ed. Engl. 1996, 35, 743-746.
19. Ren, X.-F.; Schweitzer, B. A.; Sheils, C. J.; Kool, E. T. Angew. Chem. 1996, 108, 834-837; Angew. Chem., Int. Ed. Engl. 1996, 35, 743-746.
20. Chaudhuri, N. C.; Ren, R. X.-F.; Kool, E. T. Synlett, in press.
21. Millican, T. A.; Mock, G. A.; Chauncey, M. A.;Patel, T. P.; Eaton, M. A. W.; Gunning, J.; Cutbush, S. D., Neidle, S.; Mann, J. Nucleic Acids Res. 1984, 12, 7435.
22. 1. .
23. (a) Petti, M. A.; Sheppodd, T. J.; Barrans, R. E., Jr.; Dougherty, D. A. J. Am. Chem. Soc. 1988, 110, 6825.
24. (b) Cowart, M. D.; Sucholeiki, I.; Bukownik, R. R.; Wilcox, C. S. J. Am. Chem. Soc. 1988, 110, 6204.
25. (c) Ferguson, S. B.; Sanford, E. M.; Seward, E. M.; Diederich, F. J. Am. Chem. Soc. 1991, 113, 5410-5419.
26. (d) Smithrud, D. B.; Wyman, T. B.; Diederich, F. J. Am. Chem. Soc. 1991, 113, 5420-5426.
27. (a) Leonard, N. J. Acc. Chem. Res. 1979, 12, 423-429.
28. (b) Rotello, V. M.; Viani, E. A.; Deslongchamps, G.; Murray, B. A.; Rebek, J. J. Am. Chem. Soc. 1993, 115, 797-798.
29. (c) Newcomb, L. F.; Gellman, S. H. J. Am. Chem. Soc. 1994, 116, 4993-4994.
30. (a) Warshaw, M. M.; Tinoco, I., Jr. J. Mol. Boil. 1966, 20, 29-38.
31. (b) Ts'o, P. O. P.; Melvin, J. S.; Olson, A. C. J. Am. Chem. Soc. 1963, 85, 1289.
32. Proton NMR spectra of oligonucleotide trimers with 6-8 at the center position show strong upfield shifts in neighboring bases (see supporting information) and thus provide evidence of stacking with nearest neighbors even in single-stranded DNA.