The embedded ribonucleotide assay: A chimeric substrate for studying cleavage of RNA by transesterification

Journal of the American Chemical Society

Volumn 118, Issue 29, 1996, Pages 6822-6825

  Jenkins, Lisa A ^a   Bashkin, James K ^a   Autry, Mark E ^a  

^a WASHINGTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

POLYRIBONUCLEOTIDE; RIBONUCLEOTIDE;

ARTICLE; BINDING SITE; CATALYSIS; DNA SEQUENCE; ESTERIFICATION; METAL BINDING; RNA ANALYSIS; RNA CLEAVAGE; RNA PURIFICATION; RNA SEQUENCE; RNA SYNTHESIS;

EID: 0029906390     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja960191z     Document Type: Article

References (47)

1. Bashkin, J. K.; Frolova, E. I.; Sampath, U. J. Am. Chem. Soc. 1994, 116, 5981-5982.
2. Bashkin, J. K.; Jenkins, L. A. Comments Inorg. Chem. 1994, 16, 77-93.
3. Bashkin, J. K.; Sondhi, S. M.; Modak, A. S.; Sampath, U.; d'Avignon, D. A. New J. Chem. 1994, 18, 305-316.
4. Bashkin, J. K.; Sampath, U. S.; Frolova, E. I. Appl. Biochem. Biotechnol. 1995, 54, 43-56.
5. Bashkin, J. K.; Jenkins, L. A. J. Chem. Soc., Dalton Trans. 1993, 3631.
6. Bashkin, J. K. Bioinorganic Chemistry of Copper, Karlin, K. D., Tyeklar, Z., Eds.; Chapman and Hall: New York, 1993; pp 132-139.
7. Bashkin, J. K.; McBeath, R. J.; Modak, A. S.; Sample, K. R.; Wise, W. B. J. Org. Chem. 1991, 56, 3168.
8. Modak, A. S.; Gard, J. K.; Merriman, M. C.; Winkeler, K. A.; Bashkin, J. K.; Stern, M. K. J. Am. Chem. Soc. 1991, 113, 283.
9. Stern, M. K.; Bashkin, J. K.; Sall, E. D. J. Am. Chem. Soc. 1990, 112, 5357.
10. Bashkin, J. K.; Gard, J. K.; Modak, A. S. J. Org. Chem 1990, 55, 5125.
11. Bashkin, J. K.; Xie, J.; Daniher, A. T.; Jenkins, L. A.; Yeh, G. C. Ribozyme Mimics for Catalytic Antisense Strategies; Meunier, B., Ed.; Kluwer: Netherlands, 1996; pp 355-366.
12. Bashkin, J. K.; Xie, J.; Daniher, A. T.; Sampath. U.; Kao, J. L.-F. J. Org. Chem. 1996, 61, 2314-2321.
13. Bashkin, J. K.; Sampath, U. S.; Frolova, E. I. Appl. Biochem. Biotechnol. 1995, 54, 43-56.
14. Komiyama, M.; Inokawa, T.; Yoshinari, K. J. Chem. Soc., Chem. Commun. 1995, 77-78.
15. Morrow, J. R.; Shelton, V. M. New J. Chem. 1994, 18, 371-375.
16. Magda, D.; Miller, R. A.; Sessler, J. L.; Iverson, B. L. J. Am. Chem. Soc. 1994, 116, 7439-7440.
17. Polushin, N. P.; Chen, B.-C.; Anderson, L. W.; Cohen, J. S. J. Org. Chem. 1993, 58, 4606.
18. Cech, T. R. JAMA 1988, 260, 3030-3034.
19. Hovinen, J.; Guzaev, A.; Azhayeva, E.; Azhayev, A.; Lonnberg, H. J. Org. Chem. 1995, 60, 2205-2209.
20. Linkletter, B.; Chin, J. Angew. Chem., Int. Ed. Engl. 1995, 34, 472-474.
21. Kuusela, S.: Lönnberg, H. J. Phys. Org. Chem. 1993, 5, 347-356.
22. Shelton, V. M.; Morrow, J. R. Inorg. Chem. 1991, 30, 4295-9.
23. Breslow, R. J. Am. Chem. Soc: 1989, 111, 4473.
24. Smith, J.; Anslyn, E. V. Anal. Biochem. 1994, 220, 53-57.
25. Black, C. B.; Cowan, J. A. Inorg. Chem. 1994, 33, 5805-5808.
26. Corcoran, R.; Labelle, M.; Czarnik, A. W.; Breslow, R. Anal. Biochem. 1985, 144, 563-568.
27. Komiyama, M.; Kodama, T.; Takeada, N.; Sumaoka, J.; Shiiba, T.; Matsumoto, Y.; Yashiro, M. J. Biochem. 1994, 115, 809-810.
28. Takasaki, B. K.; Chin, J. J. Am. Chem. Soc. 1994, 116, 1121-1122.
29. Sigman, D. S.; Mazumder, A.; Perrin, D. M. Chem. Rev. 1993, 93, 2295-2316.
30. Duff, R. J.; de Vroom, E.; Geluk, A.; Hecht, S. M. J. Am. Chem. Soc. 1993, 115, 3350.
31. Kuimelis, R. G.; McLaughlin, L. W. J. Am. Chem. Soc. 1995, 117, 11019-11020.
32. Strobel, S. A.; Cech, T. R. Biochemistry 1993, 32, 13593.
33. Dahm, S. C.; Uhlenbeck, O. C. Biochimie 1990, 72, 819.
34. Breaker, R. R.; Joyce, G. F. Chem. Biol. 1994, 1, 223.
35. Schnaith, L. M. T.; Hanson, R. S.; Que L., J. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 569-573.
36. Scaringe, S. A.; Francklyn, C.; Usman, N. Nucl. Acids Res. 1990, 18, 5433-5441.
37. Harris, C. M.; Lockyer, T. N. Aust. J. Chem. 1970, 23, 673-682.
38. obs. The kinetics on the all-RNA substrate are complicated, because the initial cleavage products are substrates for further cleavage reactions, and some initial degradation products are present. Results such as these using all-RNA substrates further demonstrate the utility of the embRNA assay.
39. For the 5′-end labeled substrate, a second product appears in the RNase 1 reaction lane, above the major product. We have not yet identified this minor species; it constitutes 4% of the product in Figure 3.
40. The electrophoretic mobility of the products in the KOH lanes is slightly affected by the higher ionic strength in these lanes.
41. Pan, T.; Uhlenbeck, O. C. Nature 1992, 358, 560-563.
42. Jenkins, L. A.; Bashkin, J. K.; Pennock, J. D. to be submitted.
43. Kierzek, R. Nucl. Acids Res. 1992, 20, 5073-5077.
44. Ikenaga, H.; Inoue, Y. Biochemistry 1974, 13, 577-582.
45. Butzow, J. J.; Eichhorn, G. L. Biochemistry 1971, 10, 2019-2027.
46. Campbell, T. B.; Cech, T. R. RNA 1995, 1, 598-609.
47. Elmroth, S. K. C.; Lippard, S. J. J. Am. Chem. Soc. 1994, 116, 3633-3634.