Cytosine catalysis of nitrosative guanine deamination and interstrand cross-link formation

Journal of the American Chemical Society

Volumn 127, Issue 20, 2005, Pages 7346-7358

  Glaser, Rainer ^a   Wu, Hong ^a   Lewis, Michael ^a  

^a UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINATION; BINDING ENERGY; CARBOXYLIC ACIDS; CATALYSIS; CROSSLINKING; ELECTRONIC STRUCTURE; ISOMERS; PH EFFECTS; POTENTIAL ENERGY;

CYTOSINE CATALYSIS; DEPROTONATION; NITROSATIVE GUANINE; OLIGONUCLEOTIDES;

NITROGEN COMPOUNDS;

BETAINE; CYTOSINE; GUANINE; NUCLEIC ACID BASE; OLIGONUCLEOTIDE;

ANISOTROPY; ARTICLE; CATALYSIS; CROSS LINKING; CYCLIZATION; DEAMINATION; DNA DAMAGE; NITROSATION; PROTON TRANSPORT; RING CLOSING METATHESIS; STRUCTURE ANALYSIS;

CARBODIIMIDES; CATALYSIS; CYTOSINE; DEAMINATION; DIAZONIUM COMPOUNDS; DNA; GUANINE; IMIDAZOLES; MODELS, MOLECULAR; RIBONUCLEOSIDES; THERMODYNAMICS;

EID: 19744377792     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja0501159     Document Type: Article

References (110)

1. Burrows, C. J.; Muller, J. G. Chem. Rev. 1998, 98, 1109.
2. Wakabayashi, K. In Mutation and the Environment. Proceedings of the Fifth International Conference on Environmental Mutations. Cleveland, OH, July 10-15, 1989; Albertini, R. J., Ed.; Wiley-Liss: New York, 1990; Part E, pp 107-116.
3. Wood, R. D.; Mitchell, M.; Sgouros, J.; Lindahl, T. Science 2001, 291, 1284.
4. Schärer, O. D. Angew. Chem., Int. Ed. 2003, 42, 2946.
5. (a) Tannenbaum, S. R.; Tamir, S.; Rojas-Walker, T. D.; Wishnok, J. S. In Nitrosamines and Related N-Nitroso Compounds: Chemistry and Biochemistry; Loeppky, R. N., Michejda, C. J., Eds.; ACS Symposium Series 553; American Chemical Society: Washington, DC, 1994; p 120.
6. (b) Caulfield, J. L.; Wishnok, J. S.; Tannenbaum, S. R. J. Biol. Chem. 1998, 273, 12689.
7. (c) Nagano, T.; Takizawa, H.; Hirobe, M. Tetrahedron Lett. 1995, 36, 8239.
8. Strecker, A. Liebigs Ann. Chem. 1861, 118, 151.
9. Kossel, A. Z. Physiol. Chem. 1884, 18, 404.
10. (a) Shapiro, R.; Dubelman, S.; Feinberg, A. M.; Grain, P. F.; McCloskey, J. A. J. Am. Chem. Soc. 1977, 99, 302.
11. (b) Dubelman, S.; Shapiro, R. Nucleic Acids Res. 1977, 4, 1815.
12. (a) Kirchner, J. J.; Hopkins, P. B. J. Am. Chem. Soc. 1991, 113, 4681.
13. (b) Kirchner, J. J.; Sigurdsson, S. T.; Hopkins, P. B. J. Am. Chem. Soc. 1992, 114, 4021.
14. (a) Harwood, E. A.; Hopkins, P. B.; Sigurdsson, S. T. J. Org. Chem. 2000, 65, 2959.
15. (b) Harwood, E. A.; Sigurdsson, S. T.; Edfeldt, N. B. F.; Reid, B. R.; Hopkins, P. B. J. Am. Chem. Soc. 1999, 121, 5081.
16. Riccardis, F. D.; Johnson, F. Org. Lett. 2000, 2, 293.
17. (a) Suzuki, T.; Yamaoka, R.; Nishi, M.; Ide, H.; Makino, K. J. Am. Chem. Soc. 1996, 118, 2515.
18. (b) Suzuki, T.; Yamada, M.; Furukawa, H.; Kanaori, K.; Tajima, K.; Makino, K. Nucleic Acids Symp. Ser. 1997, 37, 239.
19. (c) Suzuki, T.; Kanaori, K.; Tajima, K.; Makino, K. Nucleic Acids Symp. Ser. 1997, 37, 313.
20. (d) Suzuki, T.; Ide, H.; Yamada, M.; Endo, N.; Kanaori, K.; Tajima, K.; Morii, T.; Makino, K. Nucleic Acids Res. 2000, 28, 544.
21. (e) Suzuki, T.; Yamada, M.; Ide, H.; Kanaori, K.; Tajima, K.; Morii, T.; Makino, K. Chem. Res. Toxicol. 2000, 13, 227.
22. (f) Suzuki, T.; Yamada, M.; Nakamura, T.; Ide, H.; Kanaori, K.; Tajima, K.; Morii, T.; Makino, K. Chem. Res. Toxicol. 2000, 13, 1223.
23. Marnett, L. J. Chem. Res. Toxicol. 1996, 9, 807.
24. (a) Davis, K. L.; Martin, E.; Turko, I. V.; Murad, F. Annu. Rev. Pharmacol. Toxicol. 2001, 41, 203.
25. (b) Jackson, A. L.; Loeb, L. A. Mutat. Res. 2001, 477, 7.
26. Tamir, S.; Tannenbaum, S. R. Biochim. Biophys. Acta 1996, 1288, F31.
27. Keefer, L. K., et al. Science 1991, 254, 1001.
28. Nguyen, T.; Brunson, D.; Crespi, C. L.; Penman, B. W.; Wishnok, J. S.; Tannenbaum, S. R. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 3030.
29. (a) Lucas, L. T.; Gatehouse, D.; Shuker, D. E. G. J. Biol. Chem. 1999. 274, 18319.
30. (b) Lucas L. T.; Gatehouse, D.; Jones, G. D. D.; Shuker, D. E. G. Chem. Res. Toxicol. 2001, 14, 158.
31. Dong, M.; Wang, C.; Deen, W. M.; Dedon, P. C. Chem. Res. Toxicol. 2003, 16, 1044.
32. Zollinger, H. Diazo Chemistry I; VCH Publications: New York, 1994.
33. Glaser, R.; Son, M.-S. J. Am. Chem. Soc. 1996, 118, 10942.
34. Glaser, R.; Rayat, S.; Lewis, M.; Son, M.-S.; Meyer, S. J. Am. Chem. Soc. 1999, 121, 6108.
35. Rayat, S.; Glaser, R. J. Org. Chem. 2003, 68, 9882.
36. Rayat, S.; Wu, Z.; Glaser, R. Chem. Res. Toxicol. 2004, 17, 1157.
37. Rayat, S.; Majumdar, P.; Tipton, P.; Glaser, R. J. Am. Chem. Soc. 2004, 126, 9960.
38. Qian, M.; Glaser, R. J. Am. Chem. Soc. 2004, 126, 2274.
39. Qian, M.; Glaser, R. J. Am. Chem. Soc. 2005, 127, 880.
40. Edfeldt, N. B. F.; Harwood, E. A.; Sigurdsson, S. T.; Hopkins, P. B.; Reid, B. R. Nucleic Acids Res. 2004, 32, 2785.
41. Glaser, R.; Lewis, M. Org. Lett. 1999, 1, 273.
42. (a) Becke, A. D. J. Chem. Phys. 1993, 98, 5648.
43. (b) Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1998, 37, 785.
44. (c) Miehlich, B.; Savin, A.; Stoll, H.; Preuss, H. Chem. Phys. Lett. 1989, 157, 200.
45. St. Amant, A. In Reviews in Computational Chemistry; Lipkowitz, K. B., Boyd, D. B., Eds.; VCH Publisher: New York, 1996; Vol. 7, p 217.
46. (a) Florian, J.; Johnson, B. G. J. Phys. Chem. 1994, 98, 3681.
47. (b) Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623.
48. (c) Wang, J.; Eriksson, L. A.; Boyd, R. J.; Shi, Z.; Johnson, B. G. J. Phys. Chem. 1994, 98, 1844.
49. (a) Kristyan, S.; Pulay, P. Chem. Phys. Lett. 1994, 229, 175.
50. (b) Hobza, P.; Sponer, J.; Reschel, T. J. Comput. Chem. 1995, 16, 1315.
51. (c) Papai, I.; Jancso, G. J. Phys. Chem. A 2000, 104, 2132.
52. Møller, C.; Plesset, M. S. Phys. Rev. 1934, 46, 618.
53. Frisch, M. J., et al. Gaussian 03; Gaussian, Inc.: Pittsburgh, PA, 2003.
54. Peng, C.; Ayala, P. Y.; Schlegel, H. B.; Frisch, M. J. J. Comput. Chem. 1996, 17, 49.
55. (a) Foster, J. P.; Weinhold, F. J. Am. Chem. Soc. 1980, 102, 7211.
56. (b) Reed, A. E.; Weinhold, F. J. Chem. Phys. 1983, 78, 4066.
57. (c) Reed, A. E.; Curtiss, L. A.; Weinhold, F. Chem. Rev. 1988, 88, 899.
58. (a) Gorb, L.; Podolyan, Y.; Dziekonski, P.; Sokalski, W. A.; Leszczynski, J. J. Am. Chem. Soc. 2004, 126, 10119.
59. (b) Florian, J.; Leszczynski, J. J. Am. Chem. Soc. 1996, 118, 3010.
60. (a) Li, X.; Cai, Z.; Sevilla, M. D. J. Phys. Chem. B 2001, 105, 10115.
61. (b) Hutter, M.; Clark, T. J. Am. Chem. Soc. 1996, 118, 7574.
62. Kobayashi, K.; Tagawa, S. J. Am. Chem. Soc. 2003, 125, 10213.
63. (a) Bell, R. P. The Proton in Chemistry; Cornell University Press: Ithaca, NY, 1973.
64. (b) Proton Transfer in Hydrogen-Bonded Systems; Bountis, T., Ed.; NATO ASI Series 291; Plenum Press: New York, 1992.
65. (c) Jeffrey, G. A.; Saenger, W. Hydrogen Bonding in Biological Structures; Springer-Verlag: Berlin. 1991.
66. (d) Benderskii, V. A.; Makarov, D. E.; Wight, C. A. Chemical Dynamics at Law Temperature; Advances in Chemical Physics 88; Wiley & Sons: New York, 1994.
67. (e) Bell, R. P. The Tunnel Effect in Chemistry; Chapman and Hall: London, 1980.
68. Lewis, M. Ph.D. Dissertation, University of Missouri-Columbia, 2001.
69. IUPAC Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology etc. http://www.chem.qmw.ac.uk/iupac/ (accessed December 10, 2004).
70. (a) Fan, J.; Wang, Y.; Ueng, C. H. J. Phys. Chem. 1993, 97, 8193 and references therein.
71. (b) Dhawan, R.; Dghaym, R. D.; Arndtsen, B. A. J. Am. Chem. Soc. 2003, 125, 1474 and references therein.
72. Ollis, W. D.; Stanlbrth, S. P.; Ramsden, C. A. Tetrahedron 1985, 41, 2239.
73. Diazocyclohexa-2,4-dienone: Lowe-Ma, C. K.; Nissan, R. A.; Wilson, W. S.; Houk, K. N.; Wang, X. J. Chem. Res., Synop. 1988, 7, 214.
74. (a) Glaser, R.; Horan, C. J. J. Org. Chem. 1995, 60, 7518.
75. (b) Glaser, R.; Horan, C. J.; Zollinger, H. Angew. Chem., Int. Ed. Engl. 1997, 36, 2210.
76. (c) Glaser, R.; Horan, C. J.; Lewis, M.; Zollinger, H. J. Org. Chem. 1999, 64, 902.
77. Glaser, R.; Choy, G. S.-C. J. Am. Chem. Soc. 1993, 115, 2340.
78. Yanson, I. K.; Teplitsky, A. B.; Sukhodub, L. F. Biopolymers 1979, 18, 1149.
79. Sponer, J.; Leszczynski, J.; Hobza, P. J. Phys. Chem. 1996, 100, 1965.
80. Brameld, K.; Dasgupta, S.; Goddard, W. A. J. Phys. Chem. B 1997, 101, 4851.
81. Florian, J.; Sponer, J.; Warshel, A. J. Phys. Chem. B 1999, 103, 884.
82. Lias, S. G.; Liebmann, J. F.; Levin, R. D. J. Phys. Chem. Ref. Data 1984, 13, 695.
83. Greco, F.; Liguori, A.; Sindona, G.; Uccella, N. J. Am. Chem. Soc. 1990, 112, 9092.
84. (a) Taylor, R.; Kennard, O. J. Mol. Struct. 1982, 78, 1.
85. (b) Wilson, M. S.; McCloskey, J. A. J. Am. Chem. Soc. 1975, 97, 1975.
86. (c) Izatt, R. M.; Christensen, J. J.; Rytting, J. H. Chem. Rev. 1971, 71, 439.
87. (a) Podolyan, Y.; Gorb, L.; Leszczynski, J. J. Phys. Chem. A 2000, 104, 7346.
88. (b) Russo, N.; Toscano, M.; Grand, A.; Jolibois, F. J. Comput. Chem. 1998, 19, 989.
89. (c) Gorb, L.; Leszczynski, J. Int. J. Quantum Chem. 1998, 70, 855.
90. (d) Colominas, C.; Luque, F. J.; Orozco, M. J. Am. Chem. Soc. 1996, 118, 6811.
91. Maier, G.; Endres, J. Chem.-Eur. J. 1999, 5, 1590.
92. (a) Cook, R. J.; Mislow, K. J. Am. Chem. Soc. 1971, 93, 6703.
93. (b) Moriarty, R. M.; Yeh, C.-L.; Ramey, K. C.; Whitehurst, P. W. J. Am. Chem. Soc. 1970, 92, 6360.
94. Compare: Kleinpeter, E.; Klod, S.; Rudorf, W.-D. J. Org. Chem. 2004, 69, 4317.
95. (a) Zhou, C.; Birney, D. M. J. Am. Chem. Soc. 2002, 124, 5231.
96. (b) Birney, D. M. J. Am. Chem. Soc. 2000, 122, 10917.
97. (c) Birney, D. M.; Ham, S.; Unruh, G. R. J. Am. Chem. Soc. 1997, 119, 4509.
98. (a) Kirchner, J. J.; Hopkins, P. B. J. Am. Chem. Soc. 1991, 113, 4681.
99. (b) Kirchner, J. J.; Sigurdsson, S. T.; Hopkins, P. B. J. Am. Chem. Soc. 1992, 114, 4021.
100. Elcock, A. H.; Lyne, P. D.; Mulholland, A. J.; Handra, A.; Richards, W. G. J. Am. Chem. Soc. 1995, 117, 4706.
101. (a) Ford, G. P. J. Am. Chem. Soc. 1986, 108, 5104.
102. (b) Ford, G. P.; Scribner, J. D. J. Am. Chem. Soc. 1983, 105, 349.
103. van Duin, A. C. T.; Dasgupta, S.; Lorant, F.; Goddard, W. A. J. Phys. Chem. A 2001, 105, 9396.
104. Collyer, S. M.; McMahon, T. B. J. Phys. Chem. 1983, 87, 909.
105. This intrinsic difference is too large to be made up by multiple hydration: (a) Cunningham, A. J.; Payzant, J. D.; Kebarle, P. J. Am. Chem. Soc. 1972, 94, 7627.
106. (b) Kebarle, P.; Searles, S. K.; Zolla, A.; Scarborough, I.; Arshid, M. J. Am. Chem. Soc. 1967, 89, 6393.
107. Wu, Z.; Glaser, R. J. Am. Chem. Soc. 2004, 126, 10632.
108. Glaser, R.; Lewis, M.; Wu, Z. J. Phys. Chem. A 2002, 106, 7950.
109. Lewis, M.; Glaser, R. Chem.-Eur. J. 2002, 8, 1934.
110. (b) Lewis, M.; Glaser, R. J. Am. Chem. Soc. 1998, 120, 8541.