Enzymatic manipulation of the fragments obtained by cerium(IV)-induced DNA scission: Characterization of hydrolytic termini

Chemistry - A European Journal

Volumn 4, Issue 2, 1998, Pages 205-209

  Sumaoka, Jun ^a   Azuma, Yasushi ^a   Komiyama, Makoto ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Cerium; DNA cleavage; Hydrolyses; Hydrolysis; Phosphodiester

Indexed keywords

CERIUM; DNA FRAGMENT; ENZYMIC HYDROLYSIS; MOLECULAR INTERACTION;

EID: 0031965687     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1521-3765(19980210)4:2<205::aid-chem205>3.0.co;2-d     Document Type: Article

References (79)

1. a) E. Kimura, T. Koike, in Advances in Inorganic Chemistry, Vol. 44 (Ed.: A. G. Sykes), Academic Press, New York, 1997, pp. 229-261;
2. b) R. Breslow, Acc. Chem. Res. 1995, 28, 146-153;
3. M. Komiyama, J. Biochem. 1995, 118, 665-670.
4. a) J. R. Morrow, L. A. Buttrey, V. M. Shelton, K. A. Berback, J. Am. Chem. Soc. 1992, 114, 1903-1905;
5. b) J. R. Morrow, V. M. Shelton, New J. Chem. 1994, 78, 371-375.
6. a) R. Breslow, D.-L. Huang, Proc. Natl. Acad. Sci. USA. 1991, 88, 4080-4083;
7. b) W. H. Chapman, Jr., R. Breslow, J. Am. Chem. Soc. 1995, 117, 5462-5469.
8. a) Y. Matsumoto, M. Komiyama, J. Chem. Soc. Chem. Commun. 1990, 1050-1051;
9. b) M. Komiyama, K. Matsumura, Y. Matsumoto, idid. 1992, 640-641;
10. M. Komiyama, J. Kamitani, J. Sumaoka, H. Asanuma, Chem. Lett. 1996, 869-870;
11. M. Irisawa, N. Takeda, M. Komiyama, Chem. Commun. 1996, 1221-1222;
12. e) M. Yashiro, A. Ishikubo, M. Komiyama, J. Chem. Soc. Chem. Commun. 1995, 1793-1794;
13. f) M. Yashiro, A. Ishikubo, M. Komiyama, J. Biochem. 1996, 120, 1067-1068.
14. a) M. J. Young, J. Chin, J. Am. Chem. Soc. 1995, 117, 10577-10578;
15. b) P. Hurst, B. K. Takasaki, J. Chin, ibid. 1996, 118, 9982-9983;
16. B. Linkletter, J. Chin, Angew. Chem. 1995, 107, 529-531; Angew. Chem. Int. Ed. Engl. 1995, 34, 472-474.
17. B. Linkletter, J. Chin, Angew. Chem. 1995, 107, 529-531; Angew. Chem. Int. Ed. Engl. 1995, 34, 472-474.
18. S. Kuusela, A. Guzaev, H. Lönnberg, J. Chem. Soc. Perkin Trans. 2 1996, 1895-1899.
19. a) K. Matsumura, M. Endo, M. Komiyama, J. Chem. Soc. Chem. Commun. 1994, 2019-2020;
20. b) J. K. Bashkin, E. I. Frolova, U. S. Sampath, J. Am. Chem. Soc. 1994, 116, 5981-5982;
21. D. Magda, R. A. Miller, J. L. Sessler, B. E. Iverson, ibid. 1994, 116, 7439-7440;
22. J. Hall, D. Hüsken, R. Häner, Nucleic Acids Res. 1996, 24, 3522-3526.
23. a) J. Chin, X. Zou, Can. J. Chem. 1987, 65, 1882-1884;
24. b) J. Sumaoka, M. Yashiro, M. Komiyama, J. Chem. Soc. Chem. Commun. 1992, 1707-1708;
25. J. Sumaoka, S. Miyama, M. Komiyama, ibid. 1994, 1755-1756;
26. R. Wijesekera, P. Hendry, A. M. Sargeson, Aust. J. Chem. 1992, 45, 1187-1190;
27. e) M. Komiyama, J. Sumaoka, K. Yonezawa, Y. Matsumoto, M. Yashiro, J. Chem. Soc. Perkin Trans. 2 1997, 75-78.
28. K. Matsumura, M. Komiyama, J. Inorg. Biochem. 1994, 55, 153-156.
29. a) T. H. Fife, M. P. Pujari, J. Am. Chem. Soc. 1988, 110, 7790-7797;
30. b) D. R. Jones, L. F. Lindoy, A. M. Sargeson, ibid. 1984, 106, 7807-7819;
31. S. J. Oh, K. H. Song, J. W. Park, J. Chem. Soc. Chem. Commun. 1995, 575-576;
32. T. Koike, M. Inoue, E. Kimura, M. Shiro, J. Am. Chem. Soc. 1996, 118, 3091-3099;
33. e) G. Rawji, M. Hediger, R. M. Milburn, Inorg. Chim. Acta 1983, 79, 247-248;
34. f) J. S. Seo, N.-D. Sung, R. C. Hynes, J. Chin, Inorg. Chem. 1996, 35, 7472-7473.
35. a) P. Hendry, A. M. Sargeson, J. Am. Chem. Soc. 1989, 111, 2521-2527;
36. b) T. Koike, E. Kimura, ibid. 1991, 113, 8935-9841;
37. D. H. Vance, A. W. Czarnik, ibid. 1993, 115, 12165-12166;
38. H.-J. Schneider, J. Rammo, R. Hettich, Angew. Chem. 1993, 105, 1773-1776; Angew. Chem. Int. Ed. Engl. 1993, 32, 1716-1719;
39. H.-J. Schneider, J. Rammo, R. Hettich, Angew. Chem. 1993, 105, 1773-1776; Angew. Chem. Int. Ed. Engl. 1993, 32, 1716-1719;
40. e) R. Breslow, B. Zhang, J. Am. Chem. Soc. 1994, 116, 7893-7894;
41. f) K. A. Browne, T. C. Bruice, ibid. 1992, 114, 4951-4958;
42. g) A. Tsubouchi, T. C. Bruice, ibid. 1994, 116, 11614-11615;
43. h) R. A. Moss, B. D. Park, P. Scrimin, G. Ghirlanda, J. Chem. Soc. Chem. Commun. 1995, 1627-1628;
44. E. Kövári, J. Heitker, R. Kramer, ibid. 1995, 1205-1206;
45. j) E. Kövári, R. Krämer, J. Am. Chem. Soc. 1996, 118, 12704-12709;
46. k) J. R. Morrow, W. C. Trogler, Inorg. Chem. 1988, 27, 3387-3394;
47. S. Amin, D. A. Voss, Jr., W. D. Horrocks, Jr., J. R. Morrow, ibid. 1996, 35, 7466-7467;
48. M. J. Young, D. Wahnon, R. C. Hynes, J. Chin, J. Am. Chem. Soc. 1995, 117, 9441-9447;
49. n) B. K. Takasaki, J. Chin, ibid. 1995, 117, 8582-8585;
50. o) N. H. Williams, J. Chin, Chem. Commun. 1996, 131-132;
51. p) K. A. Deal, J. N. Burstyn, Inorg. Chem. 1996, 35, 2792-2798.
52. a) R. W. Hay, N. Govan, J. Chem. Soc. Chem. Commun. 1990, 714-715;
53. b) S. J. Oh, C. W. Yoon, J. W. Park, J. Chem. Soc. Perkin Trans. 2 1996, 329-331;
54. J. R. Morrow, W. C. Trogler, Inorg. Chem. 1989, 28, 2330-2333;
55. S. H. Gellman, R. Petter, R. Breslow, J. Am. Chem. Soc. 1986, 108, 2388-2394.
56. a) L. A. Basile, A. L. Raphael, J. K. Barton, J. Am. Chem. Soc. 1987, 109, 7550-7551;
57. b) L. M. T. Schnaith, R. S. Hanson, L. Que, Jr., Proc. Natl. Acad. Sci. USA. 1994, 91, 569-573;
58. N. E. Dixon, R. J. Geue, J. N. Lambert, S. Moghaddas, D. A. Pearce, A. M. Sargeson, Chem. Commun. 1996, 1287-1288;
59. E. L. Hegg, J. N. Burstyn, Inorg. Chem. 1996, 35, 7474-7481;
60. e) T. Ihara, H. Shimura, K. Ohmori, H. Tsuji, J. Takeuchi, M. Takagi, Chem. Lett. 1996, 687-688.
61. a) Y. Matsumoto, M. Komiyama, Nucleic Acids Symp. Ser. 1992, 27, 33-34;
62. b) T. Shiiba, K. Yonezawa, N. Takeda, Y. Matsumoto, M. Yashiro, M. Komiyama, J. Mol. Catal. 1993, 84, L21-L25;
63. M. Komiyama, Y. Matsumoto, T. Shiiba, N. Hayashi, K. Watanabe, Polym. J. 1993, 25, 1211-1214.
64. a) M. Komiyama, N. Takeda, Y. Takahashi, H. Uchida, T. Shiiba, T. Kodama, M. Yashiro, J. Chem. Soc. Perkin Trans. 2 1995, 269-274;
65. b) M. Komiyama, T. Shiiba, T. Kodama, N. Takeda, J. Sumaoka, M. Yashiro, J. Biochem. 1994, 115, 809-810.
66. Lanthanide complexes for the scission of supercoiled plasmid DNA were reported: a) J. Rammo, R. Hettich, A. Roigk, H.-J. Schneider, Chem. Commun. 1996, 105-107;
67. b) S. Hashimoto, Y. Nakamura, J. Chem. Soc. Perkin Trans. 1 1996, 2623-2628.
68. B. K. Takasaki, J. Chin, J. Am. Chem. Soc. 1994, 116, 1121-1122.
69. Oxidative cleavage of DNA has been also developed and elegantly applied in versatile ways: a) P. B. Dervan, Science 1986, 232, 464-471; b) D. S. Sigman, Acc. Chem. Res. 1986, 19, 180-186, and references therein.
70. Oxidative cleavage of DNA has been also developed and elegantly applied in versatile ways: a) P. B. Dervan, Science 1986, 232, 464-471; b) D. S. Sigman, Acc. Chem. Res. 1986, 19, 180-186, and references therein.
71. IV the ratio of the slower fragment to the faster one was nearly 1:1.
72. The ratio of the slower fragment to the faster one in the product is governed mainly by the following three factors: i) the amounts of the phosphodiester linkage and the terminal monophosphate in the reaction mixture, ii) the ratio of the rate constants of their hydrolysis, and iii) the manner of the scission of the phosphodiester linkage (P-O(3′) cleavage vs. P-O(5′) cleavage) in the DNA oligomer. Evaluation of these parameters from the time-course of the product distribution was unsuccessful.
73. 32P-labeling monophosphates were gradually removed by the enzyme, making a quantitative analysis difficult.
74. Structures of the termini for the oxidative DNA cleavage depend mainly on the kind of protons that are abstracted by the radical-like species, ref. [18]. At least half of the termini involve the moieties derived from the deoxyribose cleavage. Although a natural monophosphate terminus is in some cases produced, an unnatural terminus is simultaneously formed and thus the argument presented by us here still holds.
75. IV] in ref. [15].
76. IV.
77. IV-induced DNA scission see: H. Shigekawa, H. Ikawa, R. Yoshizaki, Y. Iijima, J. Sumaoka, M. Komiyama, Appl. Phys. Lett. 1996, 68, 1433-1435, and references therein.
78. M. Komiyama, T. Shiiba, Y. Takahashi, N. Takeda, K. Matsumura, T. Kodama, Supramol. Chem. 1994, 4, 31-34.
79. The intermediates (d(pAp) and pdA), which are formed by the hydrolysis of the internal phosphodiester linkage, are rapidly converted to the final product dA and not accumulated in the mixtures.