Kinetic Analysis of Diamine-Catalyzed RNA Hydrolysis

Journal of Organic Chemistry

Volumn 62, Issue 7, 1997, Pages 2155-2160

  Komiyama, Makoto ^a   Yoshinari, Koichi ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b Ministry of International Trade and Industry   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001015862     PISSN: 00223263     EISSN: None     Source Type: Journal    
DOI: 10.1021/jo961935u     Document Type: Article

References (44)

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17. For the hydrolysis of model phosphoesters, (a) Komiyama, M.; Yoshinari, K. J. Chem. Soc., Chem. Commun. 1989, 1880. (b) Wall, M.; Hynes, R. C.; Chin, J. Angew. Chem. Int. Ed. Engl. 1993, 32, 1633, (c) Smith, J.; Ariga, K.; Anslyn, E. V. J. Am. Chem. Soc. 1993, 115, 362. (d) Tsuboi, A.; Bruice, T. C. J. Am. Chem. Soc. 1994, 116, 11614 and references therein.
18. For the hydrolysis of model phosphoesters, (a) Komiyama, M.; Yoshinari, K. J. Chem. Soc., Chem. Commun. 1989, 1880. (b) Wall, M.; Hynes, R. C.; Chin, J. Angew. Chem. Int. Ed. Engl. 1993, 32, 1633, (c) Smith, J.; Ariga, K.; Anslyn, E. V. J. Am. Chem. Soc. 1993, 115, 362. (d) Tsuboi, A.; Bruice, T. C. J. Am. Chem. Soc. 1994, 116, 11614 and references therein.
19. For the hydrolysis of model phosphoesters, (a) Komiyama, M.; Yoshinari, K. J. Chem. Soc., Chem. Commun. 1989, 1880. (b) Wall, M.; Hynes, R. C.; Chin, J. Angew. Chem. Int. Ed. Engl. 1993, 32, 1633, (c) Smith, J.; Ariga, K.; Anslyn, E. V. J. Am. Chem. Soc. 1993, 115, 362. (d) Tsuboi, A.; Bruice, T. C. J. Am. Chem. Soc. 1994, 116, 11614 and references therein.
20. For the hydrolysis of model phosphoesters, (a) Komiyama, M.; Yoshinari, K. J. Chem. Soc., Chem. Commun. 1989, 1880. (b) Wall, M.; Hynes, R. C.; Chin, J. Angew. Chem. Int. Ed. Engl. 1993, 32, 1633, (c) Smith, J.; Ariga, K.; Anslyn, E. V. J. Am. Chem. Soc. 1993, 115, 362. (d) Tsuboi, A.; Bruice, T. C. J. Am. Chem. Soc. 1994, 116, 11614 and references therein.
21. For nonenzymatic hydrolysis of DNA: (a) Basile, L. A.; Raphael, A. L.; Barton, J. K. J. Am. Chem. Soc. 1987, 109, 7550. (b) Matsumoto, Y.; Komiyama, M. Nucleic Acids, Symp. Ser. 1992, 27, 33. (c) Komiyama, M.; Takeda, N.; Uchida, H.; Takahashi, Y.; Shiiba, T.; Kodama, T.; Yashiro, M. J. Chem. Soc., Perkin Trans. 2 1995, 269. (d) Takasaki, B. K.; Chin, J. J. Am. Chem. Soc. 1995, 116, 1121. (e) Schnaith, L. M. T.; Hanson, R. S.; Que, L., Jr. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 569.
22. For nonenzymatic hydrolysis of DNA: (a) Basile, L. A.; Raphael, A. L.; Barton, J. K. J. Am. Chem. Soc. 1987, 109, 7550. (b) Matsumoto, Y.; Komiyama, M. Nucleic Acids, Symp. Ser. 1992, 27, 33. (c) Komiyama, M.; Takeda, N.; Uchida, H.; Takahashi, Y.; Shiiba, T.; Kodama, T.; Yashiro, M. J. Chem. Soc., Perkin Trans. 2 1995, 269. (d) Takasaki, B. K.; Chin, J. J. Am. Chem. Soc. 1995, 116, 1121. (e) Schnaith, L. M. T.; Hanson, R. S.; Que, L., Jr. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 569.
23. For nonenzymatic hydrolysis of DNA: (a) Basile, L. A.; Raphael, A. L.; Barton, J. K. J. Am. Chem. Soc. 1987, 109, 7550. (b) Matsumoto, Y.; Komiyama, M. Nucleic Acids, Symp. Ser. 1992, 27, 33. (c) Komiyama, M.; Takeda, N.; Uchida, H.; Takahashi, Y.; Shiiba, T.; Kodama, T.; Yashiro, M. J. Chem. Soc., Perkin Trans. 2 1995, 269. (d) Takasaki, B. K.; Chin, J. J. Am. Chem. Soc. 1995, 116, 1121. (e) Schnaith, L. M. T.; Hanson, R. S.; Que, L., Jr. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 569.
24. For nonenzymatic hydrolysis of DNA: (a) Basile, L. A.; Raphael, A. L.; Barton, J. K. J. Am. Chem. Soc. 1987, 109, 7550. (b) Matsumoto, Y.; Komiyama, M. Nucleic Acids, Symp. Ser. 1992, 27, 33. (c) Komiyama, M.; Takeda, N.; Uchida, H.; Takahashi, Y.; Shiiba, T.; Kodama, T.; Yashiro, M. J. Chem. Soc., Perkin Trans. 2 1995, 269. (d) Takasaki, B. K.; Chin, J. J. Am. Chem. Soc. 1995, 116, 1121. (e) Schnaith, L. M. T.; Hanson, R. S.; Que, L., Jr. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 569.
25. For nonenzymatic hydrolysis of DNA: (a) Basile, L. A.; Raphael, A. L.; Barton, J. K. J. Am. Chem. Soc. 1987, 109, 7550. (b) Matsumoto, Y.; Komiyama, M. Nucleic Acids, Symp. Ser. 1992, 27, 33. (c) Komiyama, M.; Takeda, N.; Uchida, H.; Takahashi, Y.; Shiiba, T.; Kodama, T.; Yashiro, M. J. Chem. Soc., Perkin Trans. 2 1995, 269. (d) Takasaki, B. K.; Chin, J. J. Am. Chem. Soc. 1995, 116, 1121. (e) Schnaith, L. M. T.; Hanson, R. S.; Que, L., Jr. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 569.
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33. Dugas, H.; Penney, C. Bioorganic Chemistry; Springer-Verlag: New York, 1981.
34. 0, indicating that the reactions do not involve significant complexation between the RNA and N-2-N. A deviation due to a polyion complex formation was observed only below pH 7 (see ref 2b).
35. Jencks, W. P. Catalysis in Chemistry and Enzymology; Dover Publications, Inc: New York, 1969; pp 173-175.
36. a's for the first protonation are the same with the second protonation of N-2-N and N-3-N.
37. The intramolecular nucleophilic attack by the 2′-OH in ApA hydrolysis is replaced with the intermolecular one by water in A>p hydrolysis. Thus, the activation entropy term is more critical in A>p hydrolysis. Only N-2-N, which has a minimal conformational freedom, shows the intramolecular cooperation there.
38. The negative deviations of these monocations from the straight lines are probably ascribed to conformational effects. When the ammonium ions in these molecules electrostatically interact with the negatively charged phosphates of RNA, their neutral amino residues, which function as the general base catalysts, cannot be placed at the most appropriate position for the catalysis.
39. The preference might be ascribed to smaller steric hindrance.
40. a's for the second protonation are rather smaller than the value for N-2-N (6.8).
41. Dalby, K. N.; Kirby, A. J.; Hollfelder, F. J. Chem. Soc., Perkin Trans. 2 1993, 1269.
42. Bender, M. L.; Bergeron, R.; Komiyama, M. The Bioorganic Chemistry of Enzymatic Catalyses; John & Wiley Sons: New York, 1984; Chap. 5.
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44. Glasoe, P. K.; Long, F. A. J. Phys. Chem. 1960, 64, 188.