Factors contributing to aromatic stacking in water: Evaluation in the context of DNA

Journal of the American Chemical Society

Volumn 122, Issue 10, 2000, Pages 2213-2222

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

^a UNIVERSITY OF ROCHESTER   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; BENZENE; BENZENE DERIVATIVE; CYTOSINE; DOUBLE STRANDED DNA; GUANINE; INDOLE DERIVATIVE; NAPHTHALENE; PHENANTHRENE; PYRENE; PYRROLE; THYMINE; TOLUENE DERIVATIVE; WATER;

ARTICLE; DIPOLE; DISPERSION; DNA DETERMINATION; DNA STRUCTURE; ELECTRIC POTENTIAL; GEOMETRY; HYDROPHOBICITY; SURFACE PROPERTY; THERMODYNAMICS;

EID: 0034654495     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja9934854     Document Type: Article

References (65)

1. Pimentel, G. C.; McClellan, A. L. The Hydrogen Bond; W. H. Freeman: San Francisco, 1960; pp 206-225.
2. Gould, I. R.; Kollman, P. R. J. Am. Chem. Soc. 1994, 116, 2493-2499.
3. Cantor, C. R.; Schimmel, P. R. Biophysical Chemistry Part III: The Behavior of Biological Macromolecules; W. H. Freeman: San Francisco, 1980; Vol. 3, pp 1117-1133.
4. Petersheim, M.; Turner, D. H. Biochemistry 1983, 22, 256-263.
5. Turner, D. H.; Sugimoto, N.; Freier, S. M. Annu. Rev. Biophys. Biophys. Chem. 1988, 17, 167-192.
6. Senior, M.; Jones, R. A.; Breslauer, K. J. Biochemistry 1988, 27, 3879-85.
7. Doktycz, M. J.; Paner, T. M.; Amaratunga, M.; Benight, A. S. Biopolymers 1990, 30, 829-845.
8. Senior, M. M.; Jones, R. A.; Breslauer, K. J. Proc. Natl. Acad. Sci. U.S.A. 1988, 85, 6242-6246.
9. Ren, X.-F.; Schweitzer, B. A.; Sheils, C. J.; Kool, E. T. Angew. Chem., Intl. Ed. Engl. 1996, 35, 743-746.
10. Yoshizawa, S.; Kawai, G.; Watanabe, K.; Miura, K.; Hirao, I. Biochemistry 1997, 36, 6, 4761-4767.
11. Calladine, C. R. J. Mol. Biol. 1982, 161, 343-352.
12. Sarai, A.; Mazur, J.; Nussinov, R.; Jernigan, R. L. Biochemistry 1988, 27, 8498-8502.
13. Ornstein, R. L.; Rein, R.; Breen, D. L.; Macelroy, R. D. Biopolymers 1978, 17, 2341-2360.
14. Jorgensen, W. L.; Severance, D. L. J. Am. Chem. Soc. 1990, 112, 4768-4774.
15. Maroun, R. C.; Olson, W. K. Biopolymers 1988, 27, 561-584.
16. Friedman, R. A.; Honig, B. Biopolymers 1992, 32, 145-159.
17. Hunter, C. A. J. Mol. Biol. 1993, 230, 1025-1054.
18. Norberg, J.; Nilsson, L. J. Am. Chem. Soc. 1995, 117, 10832-10840.
19. Friedman, R. A.; Honig, B. Biophys. J. 1995, 69, 1528-1535.
20. Sponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 5590-5596.
21. Felsenfeld, G.; Miles, H. T. Annu. Rev. Biochem. 1967, 36, 407.
22. Colocci, N.; Distefano, M. D.; Dervan, P. B. J. Am. Chem. Soc. 1993, 115, 4468-4473.
23. Warshaw, M. M.; Tinoco, I., Jr. J. Mol. Biol. 1966, 20, 29-38.
24. Farquhar, E. L.; Downing, M.; Gill, S. J. Biochemistry 1968, 7, 1224-1225.
25. Browne, D. T.; Eisinger, J.; Leonard, N. J. J. Am. Chem. Soc. 1968, 90, 7302-7323.
26. Ts'o, P. O. P.; Kondo, N. S.; Robins, R. K.; Broom, A. D. J. Am. Chem. Soc. 1969, 91, 5625-5631.
27. Solie, T. N.; Schellman, J. A. J. Mol. Biol. 1968, 33, 61-77.
28. Mutai, K.; Gruber, B. A.; Leonard, N. J. J. Am. Chem. Soc. 1975, 97, 4095-4104.
29. Leonard, N. J. Acc. Chem. Res. 1979, 12, 423-429.
30. Lowe, M. J.; Schellman, M. J. J. Mol. Biol. 1972, 65, 91-109.
31. Albergo, D. D.; Turner, D. H. Biochemistry 1981, 20, 1413-1418.
32. Hickey, D. R.; Turner, D. H. Biochemistry 1985, 24, 2086-94.
33. Rotello, V. M.; Viani, E. A.; Deslongchamps, G.; Murray, B. A.; Rebek, J. J. Am. Chem. Soc. 1993, 115, 797-798.
34. (a) Newcomb, L. F.; Gellman, S. H. J. Am. Chem. Soc. 1994, 116, 4993-4994.
35. (b) Gellman, S. H.; Haque, T. S.; Newcomb, L. F. Biophys. J. 1996, 71, 3523-3526.
36. Gardner, R. R.; Christianson, L. A.; Gellman, S. H. J. Am. Chem. Soc. 1997, 119, 5041-5042.
37. Petti, M. A.; Shepodd, T. J.; Barrans, R. E.; Dougherty, D. A. J. Am. Chem. Soc. 1988, 110, 6825-6840.
38. Cozzi, F.; Cinquini, M.; Annuziata, R.; Siegel, J. S. J. Am. Chem. Soc. 1993, 115, 5330-5331.
39. Chaudhuri, N. C.; Kool, E. T. Tetrahedron Lett. 1995, 36, 1795-1798.
40. Ren, R. X. F.; Chaudhuri, N. C.; Paris, P. L.; Rumney, S.; Kool, E. T. J. Am. Chem. Soc. 1996, 118, 7671-7678.
41. Moran, S.; Ren, R. X.; Sheils, C. J.; Rumney, S. t.; Kool, E. T. Nucleic Acids Res. 1996, 24, 2044-2052.
42. Durland, R. H.; Rao, T. S.; Bodepudi, V.; Seth, D. M.; Jayaraman, K.; Revankar, G. R. Nucleic Acids Res. 1995, 23, 647-53.
43. Schweitzer, B. A.; Kool, E. T. J. Am. Chem. Soc. 1995, 117, 1863-1872.
44. It should be noted that such thermal denaturation experiments ignore the possible contribution of heat capacity changes, which are significant in some instances. See, for example: (a) Chalikian, T. V.; Volker, J.; Plum, G. E.; Breslauer K. J. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7853-7858. (b) Holbrook, J. A.; Capp, M. W.; Saecker, R. M.; Record, M. T., Jr. Biochemistry 1999, 38, 8409-8422.
45. It should be noted that such thermal denaturation experiments ignore the possible contribution of heat capacity changes, which are significant in some instances. See, for example: (a) Chalikian, T. V.; Volker, J.; Plum, G. E.; Breslauer K. J. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7853-7858. (b) Holbrook, J. A.; Capp, M. W.; Saecker, R. M.; Record, M. T., Jr. Biochemistry 1999, 38, 8409-8422.
46. Ghose, A. K.; Crippen, G. M. J. Comput. Chem. 1986, 7, 565-577.
47. Nowick, J. S.; Chen, J. S.; Noronha, G. J. Am. Chem. Soc. 1993, 115, 7636-7644.
48. Schweitzer, B. A.; Kool, E. T. J. Org. Chem. 1995, 60, 8326.
49. Schweitzer, B. A.; Kool, E. T. J. Org. Chem. 1994, 59, 7238-7242.
50. Loakes, D.; Brown, D. M. Nucleic Acids Res. 1994, 22, 4039-43.
51. Loakes, D.; Hill, F.; Brown, D. M.; Salisbury, S. A. J. Mol. Biol. 1997, 270, 426-435.
52. Guckian, K. M.; Schweitzer, B. A.; Ren, R. X.-F.; Sheils, C. J.; Paris, P. A.; Tahmassebi, D. C.; Kool, E. T. J. Am. Chem. Soc. 1996, 118, 8182-8183.
53. Sharp, K. A.; Nicholls, A.; Fine, R. F.; Honig, B. Science 1991, 252, 106-9.
54. Petruska, J.; Goodman, M. F. J. Biol. Chem. 1995, 270, 746-50.
55. Doktycz, M. J.; Paner, T. M.; Amaratunga, M.; Benight, A. S. Biophys. J. 1990, 57, A451-A451.
56. Sugimoto, N.; Matsumura, A.; Hasegawa, K.; Sasaki, M. Nucleic Acids Symp. Ser. 1991, 25, 51-52.
57. Breslauer, K. J.; Frank, R.; Blocker, H.; Marky, L. A. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 3746-50.
58. SantaLucia, J.; Allawi, H. T.; Seneviratne, A. Biochemistry 1996, 35, 3555-3562.
59. (a) Hunter, C. A. Chem. Soc. Rev. 1994, 101-118.
60. (b) Jorgensen, W. L.; Severance, D. L. J. Am. Chem. Soc. 1990, 112, 4768-4774.
61. Kim, J. L.; Nikolov, D. B.; Burley, S. K. Nature 1993, 365, 520-7.
62. Nikolov, D. B.; Burley, S. K. Nat. Struct. Biol. 1994, 1, 621-3 7.
63. Kim, Y.; Geiger, J. H.; Hahn, S.; Sigler, P. B. Nature 1993, 365, 512-20.
64. Inoue, H.; Imura, A.; Ohtsuka, E. Nucleic Acids Res. 1985, 13, 7119-28.
65. Lin, K.-Y.; Jones, R. J.; Matteucci, M. J. Am. Chem. Soc. 1995, 117, 3873-3874.