Trans-acting hepatitis delta virus ribozyme: Catalytic core and global structure are dependent on the 5′ substrate sequence

Biochemistry

Volumn 42, Issue 25, 2003, Pages 7727-7740

  Jeong, Sohee ^a   Sefcikova, Jana ^a   Tinsley, Rebecca A ^a   Rueda, David ^a   Walter, Nils G ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GEL-MOBILITY;

CATALYSTS; CONFORMATIONS; CRYSTAL STRUCTURE; ENERGY TRANSFER; FLUORESCENCE; GENES; LUMINESCENCE; RESONANCE; RNA; SPECTROSCOPIC ANALYSIS;

VIRUSES;

2 AMINOPURINE; NUCLEOTIDE; RIBOZYME; TERBIUM; VIRUS RNA;

ARTICLE; CATALYSIS; CONTROLLED STUDY; DISEASE COURSE; ENERGY; FLUORESCENCE; GEL MOBILITY SHIFT ASSAY; HELPER VIRUS; HEPATITIS B VIRUS; HEPATITIS DELTA VIRUS; LIVER CIRRHOSIS; LUMINESCENCE; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; SPECTROSCOPY; STEADY STATE; SYMPTOM; TIME; TRANS ISOMER; VIRUS CORE; VIRUS GENOME; VIRUS MORPHOLOGY; VIRUS REPLICATION;

FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE EXPRESSION REGULATION, VIRAL; HEPATITIS DELTA VIRUS; RNA, CATALYTIC; SPECTRUM ANALYSIS; SUBSTRATE SPECIFICITY; TRANS-ACTIVATORS;

HEPATITIS B VIRUS; HEPATITIS DELTA VIRUS; LOTUS; RNA VIRUSES;

EID: 0038001437     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi034627g     Document Type: Article

References (52)

1. Lai, M. M. (1995) Annu. Rev. Biochem. 64, 259-286.
2. Hadziyannis, S. J. (1997) J. Gastroenterol. Hepatol. 12, 289-298.
3. Macnaughton, T. B., Shi, S. T., Modahl, L. E., and Lai, M. M. (2002) J. Virol. 76, 3920-3927.
4. Ferre-D'Amare, A. R., Zhou, K., and Doudna, J. A. (1998) Nature 395, 567-574.
5. Wadkins, T. S., Perrotta, A. T., Ferre-D'Amare, A. R., Doudna, J. A., and Been, M. D. (1999) RNA 5, 720-727.
6. Shih, I. H., and Been, M. D. (2002) Annu. Rev. Biochem. 71, 887-917.
7. Ferre-D'Amare, A. R., and Doudna, J. A. (2000) J. Mol. Biol. 295, 541-556.
8. Perrotta, A. T., Shih, I., and Been, M. D. (1999) Science 286, 123-126.
9. Nakano, S., Chadalavada, D. M., and Bevilacqua, P. C. (2000) Science 287, 1493-1497.
10. Nakano, S., and Bevilacqua, P. C. (2001) J. Am. Chem. Soc. 123, 11333-11334.
11. Shih, I., and Been, M. D. (2001) EMBO J. 20, 4884-4891.
12. Oyelere, A. K., Kardon, J. R., and Strobel, S. A. (2002) Biochemistry 41, 3667-3675.
13. Scheit, K. H. (1980) Nucleotide Analogues: Synthesis and Biological Function, John Wiley & Sons, New York.
14. Wang, C., Gao, H., Gaffney, B. L., and Jones, R. A. (1991) J. Am. Chem. Soc. 113, 5486-5488.
15. Legault, P., and Pardi, A. (1997) J. Am. Chem. Soc. 119, 6621-6628.
16. Ravindranathan, S., Butcher, S. E., and Feigon, J. (2000) Biochemistry 39, 16026-16032.
17. Nishikawa, F., and Nishikawa, S. (2000) Nucleic Acids Res. 28, 925-931.
18. Luptak, A., Ferre-D'Amare, A. R., Zhou, K., Zilm, K. W., and Doudna, J. A. (2001) J. Am. Chem. Soc. 123, 8447-8452.
19. Deschenes, P., Lafontaine, D. A., Charland, S., and Perreault, J. P. (2000) Antisense Nucleic Acid Drug Dev. 10, 53-61.
20. Pereira, M. J., Harris, D. A., Rueda, D., and Walter, N. G. (2002) Biochemistry 41, 730-740.
21. Harris, D. A., Rueda, D., and Walter, N. G. (2002) Biochemistry 41, 12051-12061.
22. Tanaka, Y., Tagaya, M., Hori, T., Sakamoto, T., Kurihara, Y., Katahira, M., and Uesugi, S. (2002) Genes Cells 7, 567-579.
23. Harris, D. A., and Walter, N. G. (2003) Curr. Protocols Nucleic Acid Chem. 6.8, Wiley, New York, in press.
24. Walter, N. G., Yang, N., and Burke, J. M. (2000) J. Mol. Biol. 298, 539-555.
25. Hargittai, M. R., and Musier-Forsyth, K. (2000) RNA 6, 1672-1680.
26. Hargittai, M. R., Mangla, A. T., Gorelick, R. J., and Musier-Forsyth, K. (2001) J. Mol. Biol. 312, 985-997.
27. Sigel, R. K., Vaidya, A., and Pyle, A. M. (2000) Nat. Struct. Biol. 7, 1111-1116.
28. Saito, H., and Suga, H. (2002) Nucleic Acids Res. 30, 5151-5159.
29. Feig, A. L., Scott, W. G., and Uhlenbeck, O. C. (1998) Science 279, 81-84.
30. Walter, N, G. (2001) Methods 25, 19-30.
31. Walter, N. G., and Burke, J. M. (2000) Methods Enzymol. 317, 409-440.
32. Lafontaine, D. A., Ananvoranich, S., and Perreault, J. P. (1999) Nucleic Acids Res. 27, 3236-3243.
33. Walter, N. G., Burke, J. M., and Millar, D. P. (1999) Nat. Struct. Biol. 6, 544-549.
34. Ramirez-Carrozzi, V. R., and Kerppola, T. K. (2001) Methods 25, 31-43.
35. Sharp, K. A., and Honig, B. (1990) Annu. Rev. Biophys. Biophys. Chem. 19, 301-332.
36. Misra, V. K., and Draper, D. E. (2000) J. Mol. Biol. 299, 813-825.
37. Nicholls, A., Sharp, K. A., and Honig, B. (1991) Proteins 11, 281-296.
38. Pyle, A. M. (2002) J. Biol. Inorg. Chem. 7, 679-690.
39. Horrocks, W. D., Jr. (1993) Methods Enzymol. 226, 495-538.
40. Frey, M. W., Frey, S. T., Horrocks, W. D., Jr., Kaboord, B. F., and Benkovic, S. J. (1996) Chem. Biol. 3, 393-403.
41. Dickeson, S. K., Bhattacharyya-Pakrasi, M., Mathis, N. L., Schlesinger, P. H., and Santoro, S. A. (1998) Biochemistry 37, 11280-11288.
42. Feig, A. L., Panek, M., Horrocks, W. D., Jr., and Uhlenbeck, O. C. (1999) Chem. Biol. 6, 801-810.
43. Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M., and Scott, W. G. (1998) Chem. Biol. 5, 587-595.
44. Wadkins, T. S., Shih, I., Perrotta, A. T., and Been, M. D. (2001) J. Mol. Biol. 305, 1045-1055.
45. Ciesiolka, J., Marciniec, T., and Krzyzosiak, W. (1989) Eur. J. Biochem. 182, 445-450.
46. Perrotta, A. T., and Been, M. D. (1990) Nucleic Acids Res. 18, 6821-6827.
47. Perrotta, A. T., and Been, M. D. (1992) Biochemistry 31, 16-21.
48. Hardin, C. C., Perry, A. G., and White, K. (2000) Biopolymers 56, 147-194.
49. Orr, J. W., Hagerman, P. J., and Williamson, J. R. (1998) J. Mol. Biol. 275, 453-464.
50. Fersht, A. (1999) Structure and Mechanism in Protein Science, Freeman, New York.
51. Brenowitz, M., Chance, M. R., Dhavan, G., and Takamoto, K. (2002) Curr. Opin. Struct. Biol. 12, 648-653.
52. Tanner, N. K., Schaff, S., Thill, G., Petit-Koskas, E., Crain-Denoyelle, A. M., and Westhof, E. (1994) Curr. Biol. 4, 488-498.