Hydrolysis of DNA and RNA by lanthanide ions: Mechanistic studies leading to new applications

Chemical Communications

Volumn , Issue 16, 1999, Pages 1443-1451

  Komiyama, Makoto ^a   Takeda, Naoya ^a   Shigekawa, Hidemi ^b  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF TSUKUBA   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; LANTHANIDE; METAL ION; NUCLEIC ACID; RESTRICTION ENDONUCLEASE; RNA;

CATALYSIS; HYDROLYSIS; KINETICS; REVIEW; SPECTROSCOPY;

EID: 0033592217     PISSN: 13597345     EISSN: None     Source Type: Journal    
DOI: 10.1039/a901621j     Document Type: Review

References (59)

1. Recent reviews: M. Komiyama and J. Sumaoka, Curr. Opin. Chem. Biol., 1998, 2, 751; M. Oivanen, S. Kuusela and H. Lönnberg, Chem. Rev., 1998, 98, 961; B. N. Trawick, A. T. Daniher and J. K. Bashkin, Chem. Rev., 1998, 98, 939; G. Pratviel, J. Bernadou and B. Meunier, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1998, vol. 45, p. 251; D. M. Perreault and E. V. Anslyn, Angew. Chem., Int. Ed. Engl., 1997, 36, 432; J. Chin, Curr. Opin. Chem. Biol., 1997, 1, 514; E. Kimura and T. Koike, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1997, vol. 44, p. 229 and references cited therein.
2. Recent reviews: M. Komiyama and J. Sumaoka, Curr. Opin. Chem. Biol., 1998, 2, 751; M. Oivanen, S. Kuusela and H. Lönnberg, Chem. Rev., 1998, 98, 961; B. N. Trawick, A. T. Daniher and J. K. Bashkin, Chem. Rev., 1998, 98, 939; G. Pratviel, J. Bernadou and B. Meunier, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1998, vol. 45, p. 251; D. M. Perreault and E. V. Anslyn, Angew. Chem., Int. Ed. Engl., 1997, 36, 432; J. Chin, Curr. Opin. Chem. Biol., 1997, 1, 514; E. Kimura and T. Koike, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1997, vol. 44, p. 229 and references cited therein.
3. Recent reviews: M. Komiyama and J. Sumaoka, Curr. Opin. Chem. Biol., 1998, 2, 751; M. Oivanen, S. Kuusela and H. Lönnberg, Chem. Rev., 1998, 98, 961; B. N. Trawick, A. T. Daniher and J. K. Bashkin, Chem. Rev., 1998, 98, 939; G. Pratviel, J. Bernadou and B. Meunier, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1998, vol. 45, p. 251; D. M. Perreault and E. V. Anslyn, Angew. Chem., Int. Ed. Engl., 1997, 36, 432; J. Chin, Curr. Opin. Chem. Biol., 1997, 1, 514; E. Kimura and T. Koike, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1997, vol. 44, p. 229 and references cited therein.
4. Recent reviews: M. Komiyama and J. Sumaoka, Curr. Opin. Chem. Biol., 1998, 2, 751; M. Oivanen, S. Kuusela and H. Lönnberg, Chem. Rev., 1998, 98, 961; B. N. Trawick, A. T. Daniher and J. K. Bashkin, Chem. Rev., 1998, 98, 939; G. Pratviel, J. Bernadou and B. Meunier, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1998, vol. 45, p. 251; D. M. Perreault and E. V. Anslyn, Angew. Chem., Int. Ed. Engl., 1997, 36, 432; J. Chin, Curr. Opin. Chem. Biol., 1997, 1, 514; E. Kimura and T. Koike, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1997, vol. 44, p. 229 and references cited therein.
5. Recent reviews: M. Komiyama and J. Sumaoka, Curr. Opin. Chem. Biol., 1998, 2, 751; M. Oivanen, S. Kuusela and H. Lönnberg, Chem. Rev., 1998, 98, 961; B. N. Trawick, A. T. Daniher and J. K. Bashkin, Chem. Rev., 1998, 98, 939; G. Pratviel, J. Bernadou and B. Meunier, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1998, vol. 45, p. 251; D. M. Perreault and E. V. Anslyn, Angew. Chem., Int. Ed. Engl., 1997, 36, 432; J. Chin, Curr. Opin. Chem. Biol., 1997, 1, 514; E. Kimura and T. Koike, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1997, vol. 44, p. 229 and references cited therein.
6. Recent reviews: M. Komiyama and J. Sumaoka, Curr. Opin. Chem. Biol., 1998, 2, 751; M. Oivanen, S. Kuusela and H. Lönnberg, Chem. Rev., 1998, 98, 961; B. N. Trawick, A. T. Daniher and J. K. Bashkin, Chem. Rev., 1998, 98, 939; G. Pratviel, J. Bernadou and B. Meunier, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1998, vol. 45, p. 251; D. M. Perreault and E. V. Anslyn, Angew. Chem., Int. Ed. Engl., 1997, 36, 432; J. Chin, Curr. Opin. Chem. Biol., 1997, 1, 514; E. Kimura and T. Koike, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1997, vol. 44, p. 229 and references cited therein.
7. Recent reviews: M. Komiyama and J. Sumaoka, Curr. Opin. Chem. Biol., 1998, 2, 751; M. Oivanen, S. Kuusela and H. Lönnberg, Chem. Rev., 1998, 98, 961; B. N. Trawick, A. T. Daniher and J. K. Bashkin, Chem. Rev., 1998, 98, 939; G. Pratviel, J. Bernadou and B. Meunier, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1998, vol. 45, p. 251; D. M. Perreault and E. V. Anslyn, Angew. Chem., Int. Ed. Engl., 1997, 36, 432; J. Chin, Curr. Opin. Chem. Biol., 1997, 1, 514; E. Kimura and T. Koike, in Advances in Inorganic Chemistry, ed. A. G. Sykes, Academic Press, San Diego, 1997, vol. 44, p. 229 and references cited therein.
8. 5 sites.
9. The half-life of the phosphodiester linkage in DNA at pH 7 and 30 °C is estimated to be 200 million years. Although the linkage in RNA is much more reactive than that in DNA, its half-life is still 1000 years or so.
10. Supercoiled DNA, which is activated by strain and other factors, was reportedly cleaved via the hydrolytic pathway: L. A. Basile, A. L. Raphael and J. K. Barton, J. Am. Chem. Soc., 1987, 109, 7550; L. M. T. Schnaith, R. S. Hanson and L. Que, Jr., Proc. Natl. Acad. Sci. U.S.A., 1994, 91, 569; S. Hashimoto and Y. Nakamura, J. Chem. Soc., Perkin Trans. 1, 1996, 2623; R. Hettich and H.-J. Schneider, J. Am. Chem. Soc., 1997, 119, 5638.
11. Supercoiled DNA, which is activated by strain and other factors, was reportedly cleaved via the hydrolytic pathway: L. A. Basile, A. L. Raphael and J. K. Barton, J. Am. Chem. Soc., 1987, 109, 7550; L. M. T. Schnaith, R. S. Hanson and L. Que, Jr., Proc. Natl. Acad. Sci. U.S.A., 1994, 91, 569; S. Hashimoto and Y. Nakamura, J. Chem. Soc., Perkin Trans. 1, 1996, 2623; R. Hettich and H.-J. Schneider, J. Am. Chem. Soc., 1997, 119, 5638.
12. Supercoiled DNA, which is activated by strain and other factors, was reportedly cleaved via the hydrolytic pathway: L. A. Basile, A. L. Raphael and J. K. Barton, J. Am. Chem. Soc., 1987, 109, 7550; L. M. T. Schnaith, R. S. Hanson and L. Que, Jr., Proc. Natl. Acad. Sci. U.S.A., 1994, 91, 569; S. Hashimoto and Y. Nakamura, J. Chem. Soc., Perkin Trans. 1, 1996, 2623; R. Hettich and H.-J. Schneider, J. Am. Chem. Soc., 1997, 119, 5638.
13. Supercoiled DNA, which is activated by strain and other factors, was reportedly cleaved via the hydrolytic pathway: L. A. Basile, A. L. Raphael and J. K. Barton, J. Am. Chem. Soc., 1987, 109, 7550; L. M. T. Schnaith, R. S. Hanson and L. Que, Jr., Proc. Natl. Acad. Sci. U.S.A., 1994, 91, 569; S. Hashimoto and Y. Nakamura, J. Chem. Soc., Perkin Trans. 1, 1996, 2623; R. Hettich and H.-J. Schneider, J. Am. Chem. Soc., 1997, 119, 5638.
14. DNA hydrolysis: Y. Matsumoto and M. Komiyama, Nucleic Acids Symp. Ser., 1992, 27, 33; M. Komiyama, K. Matsumura, K. Yonezawa and Y. Matsumoto, Chem. Express, 1993, 8, 85; T. Shiiba, K. Yonezawa, N. Takeda, Y. Matsumoto, M. Yashiro and M. Komiyama, J. Mol. Catal., 1993, 84, L21.
15. DNA hydrolysis: Y. Matsumoto and M. Komiyama, Nucleic Acids Symp. Ser., 1992, 27, 33; M. Komiyama, K. Matsumura, K. Yonezawa and Y. Matsumoto, Chem. Express, 1993, 8, 85; T. Shiiba, K. Yonezawa, N. Takeda, Y. Matsumoto, M. Yashiro and M. Komiyama, J. Mol. Catal., 1993, 84, L21.
16. DNA hydrolysis: Y. Matsumoto and M. Komiyama, Nucleic Acids Symp. Ser., 1992, 27, 33; M. Komiyama, K. Matsumura, K. Yonezawa and Y. Matsumoto, Chem. Express, 1993, 8, 85; T. Shiiba, K. Yonezawa, N. Takeda, Y. Matsumoto, M. Yashiro and M. Komiyama, J. Mol. Catal., 1993, 84, L21.
17. RNA hydrolysis: K. Matsumura and M. Komiyama, J. Chem. Soc., Chem. Commun., 1992, 640; J. R. Morrow, L. A. Buttrey, V. M. Shelton and K. A. Berback, J. Am. Chem. Soc., 1992, 114, 1903; J. R. Morrow and V. M. Shelton, New J. Chem., 1994, 18, 371; R. Breslow and D.-L. Huang, Proc. Natl. Acad. Sci. U.S.A., 1991, 88, 4080.
18. RNA hydrolysis: K. Matsumura and M. Komiyama, J. Chem. Soc., Chem. Commun., 1992, 640; J. R. Morrow, L. A. Buttrey, V. M. Shelton and K. A. Berback, J. Am. Chem. Soc., 1992, 114, 1903; J. R. Morrow and V. M. Shelton, New J. Chem., 1994, 18, 371; R. Breslow and D.-L. Huang, Proc. Natl. Acad. Sci. U.S.A., 1991, 88, 4080.
19. RNA hydrolysis: K. Matsumura and M. Komiyama, J. Chem. Soc., Chem. Commun., 1992, 640; J. R. Morrow, L. A. Buttrey, V. M. Shelton and K. A. Berback, J. Am. Chem. Soc., 1992, 114, 1903; J. R. Morrow and V. M. Shelton, New J. Chem., 1994, 18, 371; R. Breslow and D.-L. Huang, Proc. Natl. Acad. Sci. U.S.A., 1991, 88, 4080.
20. RNA hydrolysis: K. Matsumura and M. Komiyama, J. Chem. Soc., Chem. Commun., 1992, 640; J. R. Morrow, L. A. Buttrey, V. M. Shelton and K. A. Berback, J. Am. Chem. Soc., 1992, 114, 1903; J. R. Morrow and V. M. Shelton, New J. Chem., 1994, 18, 371; R. Breslow and D.-L. Huang, Proc. Natl. Acad. Sci. U.S.A., 1991, 88, 4080.
21. On the hydrolysis of various activated phosphoesters, see ref. 1.
22. (a) M. Komiyama, T. Shiiba, T. Kodama, N. Takeda, J. Sumaoka and M. Yashiro, Chem. Lett., 1994, 1025;
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26. Sequence-selective DNA scission: M. Komiyama, T. Shiiba, Y. Takahashi, N. Takeda, K. Matsumura and T. Kodama, Supramol. Chem., 1994, 4, 31; M. Komiyama, N. Takeda, T. Shiiba, Y. Takahashi, Y. Matsumoto and M. Yashiro, Nucleosides Nucleotides, 1994, 13, 1297; M. Komiyama, J. Biochem., 1995, 118, 665.
27. Sequence-selective DNA scission: M. Komiyama, T. Shiiba, Y. Takahashi, N. Takeda, K. Matsumura and T. Kodama, Supramol. Chem., 1994, 4, 31; M. Komiyama, N. Takeda, T. Shiiba, Y. Takahashi, Y. Matsumoto and M. Yashiro, Nucleosides Nucleotides, 1994, 13, 1297; M. Komiyama, J. Biochem., 1995, 118, 665.
28. Sequence-selective DNA scission: M. Komiyama, T. Shiiba, Y. Takahashi, N. Takeda, K. Matsumura and T. Kodama, Supramol. Chem., 1994, 4, 31; M. Komiyama, N. Takeda, T. Shiiba, Y. Takahashi, Y. Matsumoto and M. Yashiro, Nucleosides Nucleotides, 1994, 13, 1297; M. Komiyama, J. Biochem., 1995, 118, 665.
29. Sequence-selective RNA scission: K. Matsumura, M. Endo and M. Komiyama, J. Chem. Soc., Chem. Commun., 1994, 2019; J. Hall, D. Hüsken and R. Häner, Nucleosides Nucleotides, 1997, 16, 1357; D. Magda, M. Wright, S. Crofts, A. Lin and J. L. Sessler, J. Am. Chem. Soc., 1997, 119, 6947.
30. Sequence-selective RNA scission: K. Matsumura, M. Endo and M. Komiyama, J. Chem. Soc., Chem. Commun., 1994, 2019; J. Hall, D. Hüsken and R. Häner, Nucleosides Nucleotides, 1997, 16, 1357; D. Magda, M. Wright, S. Crofts, A. Lin and J. L. Sessler, J. Am. Chem. Soc., 1997, 119, 6947.
31. Sequence-selective RNA scission: K. Matsumura, M. Endo and M. Komiyama, J. Chem. Soc., Chem. Commun., 1994, 2019; J. Hall, D. Hüsken and R. Häner, Nucleosides Nucleotides, 1997, 16, 1357; D. Magda, M. Wright, S. Crofts, A. Lin and J. L. Sessler, J. Am. Chem. Soc., 1997, 119, 6947.
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33. N. Takeda, Y. Okada and M. Komiyama, unpublished results.
34. 3, the P-S bond and P-O(5′) bond are exclusively cleaved.
35. IV-saccharide complexes was reported: A. Kajimura, J. Sumaoka and M. Komiyama, Carbohydr. Res., 1998, 309, 345.
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37. J. Sumaoka, N. Takeda, Y. Okada, H. Takahashi, H. Shigekawa and M. Komiyama, Nucleic Acids Symp. Ser., 1998, 39, 137.
38. J. Sumaoka, K. Furuki and M. Komiyama, unpublished results.
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42. The EXAFS and XANES measurements were carried out on samples frozen in liquid nitrogen.
43. 3 are non-magnetic, but show 4f-derived emission in their resonant photoemission spectra. Apparently, the 4f character is delocalized by the hybridization. The number of 4f electrons should be between 0 and 1 depending on the amount of the charge-transfer: A. Fujimori, Phys. Rev. B, 1983, 28, 4489; A. Bianconi, H. Marcelli, R. Dexpert, A. Karnatak, T. J. Kotani and J. Petiau, Phys. Rev. B, 1987, 35, 806 and references cited therein.
44. 3 are non-magnetic, but show 4f-derived emission in their resonant photoemission spectra. Apparently, the 4f character is delocalized by the hybridization. The number of 4f electrons should be between 0 and 1 depending on the amount of the charge-transfer: A. Fujimori, Phys. Rev. B, 1983, 28, 4489; A. Bianconi, H. Marcelli, R. Dexpert, A. Karnatak, T. J. Kotani and J. Petiau, Phys. Rev. B, 1987, 35, 806 and references cited therein.
45. III combination is the most active catalyst for DNA hydrolysis ever reported.
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55. a is close to the reaction pH (see M. L. Bender, R. J. Bergeron and M. Komiyama, The Bioorganic Chemistry of Enzymatic Catalysis, Wiley, New York, 1984, ch. 6.
56. Some of the complexes in ref. 4 were proposed to be active for the hydrolysis of non-supercoiled DNA.
57. M. Yashiro, A. Ishikubo and M. Komiyama, J. Chem. Soc., Chem. Commun., 1995, 1793.
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