Effect of metal ions and sequence of deoxyribozymes on their RNA cleavage activity

Abstract

Catalytic DNA is a promising class of nucleic acid enzyme for possible use as a therapeutic agent and is also interesting in comparison with catalytic RNAs. In this study, we investigated the effect of metal ions and sequence on an original deoxyribozyme, d(GCCTGGCAG₁G₂C₃T₄A₅G₆C₇T₈A₉C₁₀A₁₁A₁₂C₁₃G₁₄A₁₅GTCCCT), which binds to an RNA substrate, r(AGGGACA↓UGCCAGGC), cleaving the RNA substrate at one site indicated by the arrow. The results show that the ability of metal ions to promote the RNA cleavage reaction by the original deoxyribozyme is Mn²⁺ > Mg²⁺ >Ca²⁺ ⪢ Ba²⁺. This result is very similar to the previous tendency observed in the case of a hammerhead ribozyme. Thus, these results suggest that RNA cleavage by the deoxyribozyme dependence on metal ions for catalysis is similar to that with ribozymes. On the other hand, a nucleotide deletion from the active domain of the original deoxyribozyme results in a novel deoxyribozyme with high Ca²⁺-dependency, a situation which is not observed with the original deoxyribozyme or hammerhead ribozymes.

References

1. T. R. Cech, in The RNA World, ed. G. Atokins, Cold Spring Harbor Laboratory Press, Plainview, New York, 1993, p. 239.
2. T. Pan, D. M. Long and O. C. Uhlenbeck, in The RNA World, ed. G. Atokins, Cold Spring Harbor Laboratory Press, Plainview, New York, 1993, p. 271.
3. H. W. Pley, K. M. Flaherty and D. B. Mckay, Nature, 1994, 372, 68.
4. W. G. Scott, J. T. Finch and A. Klug, Cell, 1995, 81, 991.
5. W. G. Scott, J. B. Murray, J. R. P. Arnold, B. L. Stoddard and A. Klug, Science, 1996, 274, 2065.
6. J. H. Cate, A. R. Gooding, E. Podell, K. Zhou, B. L. Golden, C. E. Kundrot, T. R. Cech and J. A. Doudna, Science, 1996, 273, 1696.
7. J. H. Cate, A. R. Gooding, E. Podell, K. Zhou, B. L. Golden, A. A. Szewczak, C. E. Kundrot, T. R. Cech and J. A. Doudna, Science, 1996, 273, 1678.
8. J. H. Cate, R. L. Hanna and J. A. Doudna, Nature Struct. Biol., 1997, 4, 553.
9. P. Legault and A. Pardi, J. Am. Chem. Soc., 1997, 119, 6621.
10. N. Sugimoto, R. Kierzek, S. M. Freier and D. H. Turner, Biochemistry, 1986, 25, 5755.
11. J. SantaLucia, R. Kierzek and D. H. Turner, J. Am. Chem. Soc., 1991, 113, 4313.
12. J. SantaLucia, R. Kierzek and D. H. Turner, Biochemistry, 1991, 30, 8242.
13. V. P. Antao, S. Y. Lai and I. Tinoco, Nucleic Acids Res., 1991, 19, 5901.
14. B. L. Golden, A. R. Gooding, E. R. Podell and T. R. Cech, Science, 1998, 282, 259.
15. D. L. Abramovitz, R. A. Friedman and A. M. Pyle, Science, 1996, 271, 1410.
16. Y. Chen, X. Li and P. Gegenheimer, Biochemistry, 1997, 36, 2425.
17. H. Fauzi, J. Kawakami, F. Nishikawa and S. Nishikawa, Nucleic Acids Res., 1997, 25, 3124.
18. D.-M. Zhou and K. Taira, Chem. Rev., 1998, 98, 991.
19. Y. Komatsu, I. Kanzaki, M. Shirai and E. Ohtsuka, Biochemistry, 1997, 36, 9935.
20. T. Pan and O. C. Uhlenbeck, Nature, 1992, 358, 560.
21. N. Sugimoto and T. Ohmichi, FEBS Lett., 1996, 393, 97.
22. K. T. Stage-Zimmermann and O. C. Uhlenbeck, RNA, 1998, 4, 875.
23. N. Sugimoto, R. Kierzek and D. H. Turner, Biochemistry, 1988, 27, 6384.
24. A. M. Pyle, Science, 1993, 261, 709.
25. S. C. Dahm and O. C. Uhlenbeck, Biochemistry, 1991, 30, 9464.
26. S. C. Dahm, W. B. Derrick and O. C. Uhlenbeck, Biochemistry, 1993, 32, 13040.
27. R. G. Kimelis and L. W. Mclaughlin, Biochemistry, 1996, 35, 5308.
28. T. Ohmichi and N. Sugimoto, Biochemistry, 1997, 36, 3514.
29. N. Carmi, L. Shultz and R. P. Breaker, Chem. Biol., 1996, 3, 1039.
30. N. Carmi, S. R. Balkhi and R. P. Breaker, Proc. Natl. Acad. Sci. USA, 1998, 95, 2233.
31. R. P. Breaker and G. F. Joyce, Chem. Biol., 1994, 1, 223.
32. S. W. Santoro and G. F. Joyce, Proc. Natl. Acad. Sci. USA, 1997, 94, 4262.
33. Y. Li and D. Sen, Nature Struct. Biol., 1996, 3, 743.
34. N. Sugimoto, T. Toda and T. Ohmichi, Chem. Commun., 1998, 15, 1533.
35. T. Kuwabara, M. Warashina, T. Tanabe, K. Tani, S. Asano and K. Taira, Nucleic Acids Res., 1997, 25, 3074.
36. N. Ota, M. Warashina, K. Hirano, K. Hatanaka and K. Taira, Nucleic Acids Res., 1998, 26, 3385.
37. N. Sugimoto, S. Nakano, M. Katoh, A. Matsumura, H. Nakamuta, T. Ohmichi, M. Yoneyama and M. Sasaki, Biochemistry, 1995, 34, 11211.
38. T. Campbell and T. R. Cech, RNA, 1995, 1, 598.
39. E. G. Richards, in Handbook of Biochemistry and Molecular Biology: Nucleic Acids, ed. G. D. Fasman, CRC Press, Cleveland, OH, 1975, vol. 1, p. 597.
40. P. Hendry, M. J. McCall and T. J. Lockett, in Methods in Molecular Biology, ed. P. C. Turner, Humana Press Inc., Towana, NJ, 1997, vol. 74, p. 221.
41. T. Kuwabara, S. V. Amontov, M. Warashina, J. Ohkawa and K. Taira, Nucleic Acids Res., 1996, 24, 2302.
42. T. Ohmichi, Y. Okumoto and N. Sugimoto, Nucleic Acids Res., 1998, 26, 5655.
43. H. T. Allawi and J. SantaLucia Jr., Biochemistry, 1998, 37, 2170.
44. H. T. Allawi and J. SantaLucia Jr., Biochemistry, 1997, 36, 10581.
45. S. Sawata, T. Shimayama, M. Komiyama, P. K. Kumar, S. Nishikawa and K. Taira, Nucleic Acids Res., 1993, 21, 5656.
46. S. W. Santro and G. F. Joyce, Biochemistry, 1998, 37, 13330.
47. A. M. Pyle, J. A. McSwiggen and T. R. Cech, Proc. Natl. Acad. Sci. USA, 1991, 87, 8187.
48. T. S. McConnell, D. Herschlag and T. R. Cech, Biochemistry, 1997, 36, 8293.
49. A. L. Feig, G. E. Ammons and O. C. Uhlenbeck, RNA, 1998, 4, 1251.
50. C. A. Grosshans and T. R. Cech, Biochemistry, 1989, 28, 6888.
51. W. D. Celander and T. R. Cech, Science, 1991, 251, 401.
52. M. Lehman and G. F. Joyce, Nature, 1993, 361, 182.