A toggle duplex in hepatitis delta virus self-cleaving RNA that stabilizes an inactive and a salt-dependent pro-active ribozyme conformation

Journal of Molecular Biology

Volumn 279, Issue 2, 1998, Pages 361-373

  Perrotta, Anne T ^a   Been, Michael D ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Hepatitis delta virus; RNA catalysis; RNA folding; RNA structure

Indexed keywords

MAGNESIUM ION; RIBOZYME; SODIUM ION; VIRUS RNA;

ARTICLE; BASE PAIRING; HEPATITIS DELTA VIRUS; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; RNA CONFORMATION; RNA DEGRADATION; RNA SEQUENCE; RNA STRUCTURE; TEMPERATURE DEPENDENCE;

DELTA VIRUS; HEPATITIS DELTA VIRUS; RNA VIRUSES;

EID: 0032486091     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1798     Document Type: Article

References (42)

1. Been M.D. Cis - and trans-acting ribozymes from a human pathogen, hepatitis delta virus. Trends Biochem. Sci. 19:1994;251-256
2. Been M.D., Perrotta A.T. Optimal self-cleavage activity of the hepatitis delta virus RNA is dependent on a homopurine base pair in the ribozyme core. RNA. 1:1995;1061-1070
3. Been M.D., Wickham G.S. The self-cleaving ribozymes of Hepatitis delta virus. Eur. J. Biochem. 247:1997;741-753
4. Been M.D., Perrotta A.T., Rosenstein S.P. Secondary structure of the self-cleaving RNA of hepatitis delta virus: applications to catalytic RNA design. Biochemistry. 31:1992;11843-11852
5. Cate J.H., Hanna R.L., Doudna J.A. A magnesium ion core at the heart of a ribozyme domain. Nature Struct. Biol. 4:1997;553-558
6. Cole P.E., Yang S.K., Crothers D.M. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry. 11:1972;4358-4368
7. Crothers D.M. Physical studies of tRNA in solution. Schimmel P.R., Söll D., Abelson J.A. Transfer RNA: Structure, Properties and Recognition. 1979;163-176 Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
8. Crothers D.M., Cole P.E. Conformation changes of tRNA. Altman S. Transfer RNA. 1978;196-247 The MIT Press, Cambridge, MA
9. Davanloo P., Rosenberg A.H., Dunn J.J., Studier F.W. Cloning and expression of the gene for bacteriophage T7 RNA polymerase. Proc. Natl Acad. Sci. USA. 81:1984;2035-2039
10. Ehresmann C., Baudin F., Mougel M., Romby P., Ebel J.-P., Ehresmann B. Probing the structure of RNAs in solution. Nucl. Acids Res. 15:1987;9109-9128
11. Hampel A., Tritz R. RNA catalytic properties of the minimum (-)sTRSV sequence. Biochemistry. 28:1989;4929-4933
12. Hsieh S.-Y., Taylor J.M. Regulation of polyadenlylation of hepatitis delta virus antigenomic RNA. J. Virol. 65:1991;6438-6446
13. Hsieh S.-Y., Chao M., Coates L., Taylor J. Hepatitis delta virus genome replication a polyadenylated mRNA for delta antigen. J. Virol. 64:1990;3192-3198
14. Kunkel T.A., Roberts J.D., Zakour R.A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 154:1987;367-382
15. Kuo M.Y.-P., Sharmeen L., Dinter-Gottleib G., Taylor J. Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J. Virol. 62:1988;4439-4444
16. Lai M.M.C. The molecular biology of hepatitis delta virus. Annu. Rev. Biochem. 64:1995;259-286
17. Lazinski D.W., Taylor J.M. Regulation of the hepatitis delta virus ribozymes to cleave or not to cleave? RNA. 1:1995;225-233
18. Lazinski D.W., Taylor J.M. Intracellular cleavage and ligation of hepatitis delta virus genomic RNA regulation of ribozyme activity by cis-acting sequences and host factors. J. Virol. 69:1995;1190-1200
19. Lee C.-B., Lai Y.-C., Ping Y.-H., Huang Z.-S., Lin J.-Y., Wu H.-N. The importance of the helix 2 region for the cis-cleaving and trans-cleaving activities of hepatitis delta virus ribozymes. Biochemistry. 35:1996;12303-12312
20. Miller W.A., Silver S.L. Alternative tertiary structure attenuates self-cleavage of the ribozyme in the satellite RNA of barley yellow dwarf virus. Nucl. Acids Res. 19:1991;5313-5320
21. Miller W.A., Hercus T., Waterhouse P.M., Gerlach W.L. A satellite RNA of barley yellow dwarf virus contains a novel hammerhead structure in the self-cleavage domain. Virology. 183:1991;711-720
22. Pan J., Thirumalai D., Woodson S.A. Folding of RNA involves parallel pathways. J. Mol. Biol. 273:1997;7-13
23. Pan T., Sosnick T.T. Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity. Nature Struct. Biol. 4:1997;931-938
24. Perrotta A.T., Been M.D. The self-cleaving domain from the genomic RNA of hepatitis delta virus: sequence requirements and the effects of denaturant. Nucl. Acids Res. 18:1990;6821-6827
25. Perrotta A.T., Been M.D. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature. 350:1991;434-436
26. Perrotta A.T., Been M.D. Cleavage of oligoribonucleotides by a ribozyme derived from the hepatitis δ virus RNA sequence. Biochemistry. 31:1992;16-21
27. Perrotta A.T., Been M.D. Assessment of disparate structural features in three models of the hepatitis delta virus ribozyme. Nucl. Acids Res. 21:1993;3959-3965
28. Perrotta A.T., Been M.D. Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage. Nucl. Acids Res. 24:1996;1314-1321
29. Puttaraju M., Perrotta A., Been M. A circular trans-acting hepatitis delta virus ribozyme. Nucl. Acids Res. 21:1993;4253-4258
30. Rizzetto M. The delta agent. Hepatology. 3:1983;729-737
31. Rosenstein S.P., Been M.D. Self-cleavage of hepatitis delta virus genomic strand RNA is enhanced under partially denaturing conditions. Biochemistry. 29:1990;8011-8016
32. Rosenstein S.R., Been M.D. Hepatitis delta virus ribozymes fold to generate a solvent-inaccessible core with essential nucleotides near the cleavage-site phosphate. Biochemistry. 35:1996;11403-11413
33. Sharmeen L., Kuo M.Y.-P., Dinter-Gottlieb G., Taylor J. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J. Virol. 62:1988;2674-2679
34. Smith J.B., Dinter-Gottlieb G. Antigenomic hepatitis delta virus ribozymes self-cleave in 18 M formamide. Nucl. Acids Res. 19:1991;1285-1289
35. Tanner N.K. The catalytic RNAs from hepatitis delta virus structure, function, and application. Dinter-Gottlieb G. The Unique Hepatitis Delta Virus. 1995;11-29 Springer-Verlag, New York
36. Tanner N.K., Schaff S., Thill G., Petit-Koskas E., Crain-Denoyelle A.-M., Westhof E. A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses. Curr. Biol. 4:1994;488-497
37. Taylor J.M. Fields B.N., Knipe D.M., Howley P.M. Hepatitis Delta Virus and Its Replication. Fields Virology. 1996;Lippincott-Raven, Philadelphia
38. Thill G., Vasseur M., Tanner N.K. Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme. Biochemistry. 32:1993;4254-4262
39. Uhlenbeck O.C. A small catalytic oligoribonucleotide. Nature. 328:1987;596-600
40. Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 153:1987;3-11
41. Wadkins T.S., Been M.D. Core-associated non-duplex sequences distinguishing the genomic and antigenomic self-cleaving RNAs of hepatitis delta virus. Nucl. Acids Res. 25:1997;4085-4092
42. Wu H.-N., Lin Y.-J., Lin F.-P., Makino S., Chang M.-F., Lai M.M.C. Human hepatitis δ virus RNA subfragments contain an autocleavage activity. Proc. Natl Acad. Sci. USA. 86:1989;1831-1835