A further investigation and reappraisal of the thio effect in the cleavage reaction catalyzed by a hammerhead ribozyme

Nucleic Acids Research

Volumn 28, Issue 8, 2000, Pages 1730-1742

  Yoshinari, Koichi ^a,b   Taira, Kazunari ^a,c  

^a NATL INST FOR ADV INTERDISC RES   (Japan)

^b NATL INST BIOSCI HUM TECHNOL   (Japan)

^c UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CADMIUM; CALCIUM ION; MAGNESIUM ION; RIBOZYME; SULFUR;

ARTICLE; CONTROLLED STUDY; ENZYME KINETICS; ENZYME MECHANISM; ENZYME SPECIFICITY; ENZYME SUBSTRATE; PRIORITY JOURNAL; RNA CLEAVAGE;

EID: 0034655950     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/28.8.1730     Document Type: Article

References (65)

1. Uhlenbeck, O.C. (1987) Nature, 328, 596-600.
2. Haseloff, J. and Gerlach, W.L. (1988) Nature, 334, 585-591.
3. Symons, R.H. (1989) Trends Biochem. Sci., 14, 445-450.
4. Symons, R.H. (1992) Annu. Rev. Biochem., 61, 641-671.
5. Bratty, J., Chartrand, P., Ferbeyre, G. and Cedergren, R. (1993) Biochim. Biophys. Acta, 1216, 345-359.
6. Pyle, A.M. (1993) Science, 261, 709-714.
7. Yarus, M. (1993) FASEB J., 7, 31-39.
8. Dahm, S.C., Derrick, W.B. and Uhlenbech, O.C. (1993) Biochemistry, 32, 13040-13045.
9. Uebayashi, M., Uchimaru, T., Koguma, T., Sawata, S., Shimayama, T. and Taira, K. (1994) J. Org. Chem., 59, 7414-7420.
10. Sawata, S., Komiyama, M. and Taira, K. (1995) J. Am. Chem. Soc., 117, 2357-2358.
11. Pontius, B.W., Lott, W.B. and von Hippel, P.H. (1997) Proc. Natl Acad. Sci. USA, 94, 2290-2294.
12. Zhou, D.-M., Zhang, L.-H. and Taira, K. (1997) Proc. Natl Acad. Sci. USA, 94, 14343-14348.
13. Birikh, K.R., Heaton, P.A. and Eckstein, F. (1997) Eur. J. Biochem., 245, 1-16.
14. Lott, W.B., Pontius, B.W. and von Hippel, P.H. (1998) Proc. Natl Acad. Sci. USA, 95, 542-547.
15. Zhou, D.-M. and Taira, K. (1998) Chem. Rev., 98, 991-1026.
16. Lilley, D.M.J. (1999) Curr. Opin. Struct. Biol., 9, 330-338.
17. Wang, S., Karbstein, K., Peracchi, A., Beigelman, L. and Herschlag, D. (1999) Biochemistry, 38, 14363-14378.
18. Murray, J.B., Seyhan, A.A., Walter, N.G., Burk, J.M. and Scott, W.G. (1998) Chem. Biol., 5, 587-595.
19. Dahm, S.C. and Uhlenbeck, O.C. (1991) Biochemistry, 30, 9464-9469.
20. van Tol, H., Buzayan, J.M., Feldstein, P.A., Eckstein, F. and Bruening, G., (1990) Nucleic Acids Res., 18, 1971-1975.
21. Slim, G. and Gait, M.J. (1991) Nucleic Acids Res., 19, 1183-1188.
22. Koizumi, M. and Ohtsuka, E. (1991) Biochemistry, 30, 5145-5150.
23. Scott, E.C. and Uhlenbeck, O.C. (1999) Nucleic Acids Res., 27, 479-484.
24. Pearson, R.G. (1968) J. Chem. Educ., 45, 581-587.
25. Pearson, R.G. (1968) J. Chem. Educ., 45, 643-648.
26. Piccirilli, J.A., Vyle, J.S., Caruthers, M.H. and Cech, T.R. (1993) Nature, 361, 85-88.
27. Podar, M., Perlman, P.S. and Padgett, R.A. (1995) Mol. Cell. Biol., 15, 4466-4478.
28. Weinstein, L.B., Jones, B.C.N.M., Cosstick, R. and Cech, T.R. (1997) Nature, 388, 805-808.
29. Sontheimer, E.J., Sun, S. and Piccirilli, J.A. (1997) Nature, 388, 801-805.
30. Sontheimer, E.J., Gorden, P.M. and Piccirilli, J.A. (1999) Genes Dev., 13. 1729-1741.
31. Warnecke, J.M., Sontheimer, E.J., Piccirilli, J.A. and Hartmann, R.K. (2000) Nucleic Acids Res., 28, 720-727.
32. Zhou, D.-M., Kumar, P.K.R., Zhang, L.-H. and Taira, K. (1996) J. Am. Chem. Soc., 118, 8969-8970.
33. Zhou, D.-M., He, Q.-C., Zhou, J.-M. and Taira, K. (1998) FEBS Lett., 431, 154-160.
34. Pecoraro, V.L., Hermes, J.D. and Cleland, W.W. (1984) Biochemistry, 23, 5262-5271.
35. Sigel, R.K.O., Song, B. and Sige, J.H. (1997) J. Am. Chem. Soc., 119, 744-755.
36. Brautigam, C.A., Sun, S., Piccirilli, J.A. and Steitz, T.A. (1999) Biochemistry, 38, 696-704.
37. Pley, H.W., Flaherty, K.M. and McKay, D.B. (1994) Nature, 372, 68-74.
38. Scott, W.G., Finch, J.T. and Klug, A. (1995) Cell, 81, 991-1002.
39. Murray, J.B., Terwey, D.P., Maloney, L., Karpeisky, A., Usman, N., Beigelman, L. and Scott, W.G. (1998) Cell, 92, 665.
40. Ruffner, D.E. and Uhlenbeck, O.C. (1990) Nucleic Acids Res., 18, 6025-6029.
41. Ruffner, D.E., Stormo, G.D. and Uhlenbeck, O.C. (1990) Biochemistry, 29, 10695-10702.
42. Tuschl, T. and Eckstein, F. (1993) Proc. Natl Acad. Sci. USA, 90, 6991-6994.
43. Peracchi. A., Beigelman, L., Scott, E.C., Uhlenbeck, O.C. and Herschlag, D. (1997) J. Biol. Chem., 272, 26822-26826.
44. Takagi, Y. and Taira, K. (1995) FEBS Lett., 361, 273-276.
45. Zhou, D.-M., Usman, N., Wincott, F.E., Matulic-Adamic, J., Orita, M., Zhang, L.-H., Komiyama, M., Kumar, P.K.R. and Taira, K. (1996) J. Am. Chem. Soc., 118, 5862-5866.
46. Orita, M., Vinayak, R., Warashina, M., Chiba, A., Kaniwa, H., Nishikawa, F., Nishikawa, S. and Taira, K. (1996) J. Biol. Chem., 271, 9447-9454.
47. Warashina, M., Takagi, Y., Sawata, S., Zhou, D.M., Kuwabara, T. and Taira, K. (1997) J. Org. Chem., 62, 9138-9147.
48. Pan, T., Long, D.M. and Uhlenbeck, O.C. (1993) In Gesteland, R.F. and Atkins, J.F. (eds), The RNA World. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 271-302.
49. Ora, M., Oivanen, M. and Lönnberg, H. (1997) J. Org. Chem., 62, 3246-3253.
50. Ora, M., Peltomäki, M., Oivanen, M. and Lönnberg, H. (1998) J. Org. Chem., 63, 2939-2947.
51. Oivanen, M., Kuusela, S. and Lönnberg, H. (1998) Chem. Rev., 98, 961-990.
52. Sieitz, T.A. and Steiz, J.A. (1993) Proc. Natl Acad. Sci. USA, 90, 6498-6502.
53. Hermann, T., Auffinger, P., Scott, W.G. and Westhof, E. (1997) Nucleic Acids Res., 27, 3421-3427.
54. Cunningham, L.A., Li, J. and Lu, Y. (1998) J. Am. Chem. Soc., 122, 4518-4519.
55. Warnecke, J.M., Fürste, J.P., Hardt, W.-D., Erdmann, V.A. and Hartmann, R.K. (1996) Proc. Natl Acad. Sci. USA, 93, 8924-8928.
56. Warnecke, J.M., Green, C.J. and Hartmann, R.K. (1997) Nucl. Nucl., 16, 721-725.
57. Warnecke, J.M., Held, R., Busch, S. and Hartmann, R.K. (1999) J. Mol. Biol., 290, 433-445.
58. Brautigam, C.A. and Steitz, T.A. (1998) J. Mol. Biol., 277, 363-377.
59. Kawahara, S., Wada, T. and Sekine, M. (1996) J. Am. Chem. Soc., 118, 9461-9468.
60. Eckstein, F. (1985) Annu. Rev. Biochem., 54, 367-402.
61. Adamaik, D.A., Kinas, R., Saenger, W. and Stec, W.J. (1977) Angew. Chem. Int. Ed. Engl., 16, 330.
62. Knöll, R., Bald, R. and Fürste J.P. (1997) RNA, 3, 132-140.
63. Kuimalis, R.G. and McLaughlin, L.W. (1996) Biochemistry, 35, 5308-5317.
64. Kuimalis, R.G. and McLaughlin, L.W. (1997) Bioorg. Med. Chem., 5, 1051-1061.
65. Kumar, P.K.R., Zhou, D.-M., Yoshinari, K. and Taira, K. (1996) In Eckstein, F. and Lilley, D.M J. (eds), Nucleic Acids and Molecular Biology. Vol. 10, Catalytic RNA. Springer, New York, NY, pp. 217-230.