Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1993 Sep 11;21(18):4253–4258. doi: 10.1093/nar/21.18.4253

A circular trans-acting hepatitis delta virus ribozyme.

M Puttaraju 1, A T Perrotta 1, M D Been 1
PMCID: PMC310058  PMID: 7692400

Abstract

A circular trans-acting ribozyme designed to adopt the motif of the hepatitis delta virus (HDV) trans-acting ribozyme was produced. The circular form was generated in vitro by splicing a modified group I intron precursor RNA in which the relative order of the 5' and 3' splice sites, flanking the single HDV-like ribozyme sequence-containing exon, is reversed. Trans-cleavage activity of the circular HDV-like ribozyme was comparable to linear permutations of HDV ribozymes containing the same core sequence, and was shown not to be due to linear contaminants in the circular ribozyme preparation. In nuclear and cytoplasmic extracts from HeLa cells, the circular ribozyme had enhanced resistance to nuclease degradation relative to a linear form of the ribozyme, suggesting that circularization may be a viable alternative to chemical modification as a means of stabilizing ribozymes against nuclease degradation.

Full text

PDF
4257

Images in this article

4255Image
on p.4255
4255Image
on p.4255
4256Image
on p.4256

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. 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. 1992 Dec 1;31(47):11843–11852. doi: 10.1021/bi00162a024. [DOI] [PubMed] [Google Scholar]
  2. Belinsky M. G., Britton E., Dinter-Gottlieb G. Modification interference analysis of a self-cleaving RNA from hepatitis delta virus. FASEB J. 1993 Jan;7(1):130–136. doi: 10.1096/fasebj.7.1.8422959. [DOI] [PubMed] [Google Scholar]
  3. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1006/abio.1976.9999. [DOI] [PubMed] [Google Scholar]
  4. Branch A. D., Robertson H. D. Efficient trans cleavage and a common structural motif for the ribozymes of the human hepatitis delta agent. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10163–10167. doi: 10.1073/pnas.88.22.10163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cameron F. H., Jennings P. A. Specific gene suppression by engineered ribozymes in monkey cells. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9139–9143. doi: 10.1073/pnas.86.23.9139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cech T. R. Ribozymes and their medical implications. JAMA. 1988 Nov 25;260(20):3030–3034. [PubMed] [Google Scholar]
  7. Chowrira B. M., Burke J. M. Extensive phosphorothioate substitution yields highly active and nuclease-resistant hairpin ribozymes. Nucleic Acids Res. 1992 Jun 11;20(11):2835–2840. doi: 10.1093/nar/20.11.2835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cocquerelle C., Daubersies P., Majérus M. A., Kerckaert J. P., Bailleul B. Splicing with inverted order of exons occurs proximal to large introns. EMBO J. 1992 Mar;11(3):1095–1098. doi: 10.1002/j.1460-2075.1992.tb05148.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Cocquerelle C., Mascrez B., Hétuin D., Bailleul B. Mis-splicing yields circular RNA molecules. FASEB J. 1993 Jan;7(1):155–160. doi: 10.1096/fasebj.7.1.7678559. [DOI] [PubMed] [Google Scholar]
  10. Cotten M., Birnstiel M. L. Ribozyme mediated destruction of RNA in vivo. EMBO J. 1989 Dec 1;8(12):3861–3866. doi: 10.1002/j.1460-2075.1989.tb08564.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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 U S A. 1984 Apr;81(7):2035–2039. doi: 10.1073/pnas.81.7.2035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Eckstein F., Gish G. Phosphorothioates in molecular biology. Trends Biochem Sci. 1989 Mar;14(3):97–100. doi: 10.1016/0968-0004(89)90130-8. [DOI] [PubMed] [Google Scholar]
  13. Forster A. C., Symons R. H. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell. 1987 Apr 24;49(2):211–220. doi: 10.1016/0092-8674(87)90562-9. [DOI] [PubMed] [Google Scholar]
  14. Goodchild J. Enhancement of ribozyme catalytic activity by a contiguous oligodeoxynucleotide (facilitator) and by 2'-O-methylation. Nucleic Acids Res. 1992 Sep 11;20(17):4607–4612. doi: 10.1093/nar/20.17.4607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Harland R., Misher L. Stability of RNA in developing Xenopus embryos and identification of a destabilizing sequence in TFIIIA messenger RNA. Development. 1988 Apr;102(4):837–852. doi: 10.1242/dev.102.4.837. [DOI] [PubMed] [Google Scholar]
  16. Haseloff J., Gerlach W. L. Simple RNA enzymes with new and highly specific endoribonuclease activities. Nature. 1988 Aug 18;334(6183):585–591. doi: 10.1038/334585a0. [DOI] [PubMed] [Google Scholar]
  17. Holmes J., Jr, Clark S., Modrich P. Strand-specific mismatch correction in nuclear extracts of human and Drosophila melanogaster cell lines. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5837–5841. doi: 10.1073/pnas.87.15.5837. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kunkel T. A., Roberts J. D., Zakour R. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 1987;154:367–382. doi: 10.1016/0076-6879(87)54085-x. [DOI] [PubMed] [Google Scholar]
  19. Kuo M. Y., Sharmeen L., Dinter-Gottlieb G., Taylor J. Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J Virol. 1988 Dec;62(12):4439–4444. doi: 10.1128/jvi.62.12.4439-4444.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Matsukura M., Shinozuka K., Zon G., Mitsuya H., Reitz M., Cohen J. S., Broder S. Phosphorothioate analogs of oligodeoxynucleotides: inhibitors of replication and cytopathic effects of human immunodeficiency virus. Proc Natl Acad Sci U S A. 1987 Nov;84(21):7706–7710. doi: 10.1073/pnas.84.21.7706. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Mori K., Boiziau C., Cazenave C., Matsukura M., Subasinghe C., Cohen J. S., Broder S., Toulmé J. J., Stein C. A. Phosphoroselenoate oligodeoxynucleotides: synthesis, physico-chemical characterization, anti-sense inhibitory properties and anti-HIV activity. Nucleic Acids Res. 1989 Oct 25;17(20):8207–8219. doi: 10.1093/nar/17.20.8207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Nigro J. M., Cho K. R., Fearon E. R., Kern S. E., Ruppert J. M., Oliner J. D., Kinzler K. W., Vogelstein B. Scrambled exons. Cell. 1991 Feb 8;64(3):607–613. doi: 10.1016/0092-8674(91)90244-s. [DOI] [PubMed] [Google Scholar]
  23. Paolella G., Sproat B. S., Lamond A. I. Nuclease resistant ribozymes with high catalytic activity. EMBO J. 1992 May;11(5):1913–1919. doi: 10.1002/j.1460-2075.1992.tb05244.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Perrotta A. T., Been M. D. A pseudoknot-like structure required for efficient self-cleavage of hepatitis delta virus RNA. Nature. 1991 Apr 4;350(6317):434–436. doi: 10.1038/350434a0. [DOI] [PubMed] [Google Scholar]
  25. Perrotta A. T., Been M. D. Cleavage of oligoribonucleotides by a ribozyme derived from the hepatitis delta virus RNA sequence. Biochemistry. 1992 Jan 14;31(1):16–21. doi: 10.1021/bi00116a004. [DOI] [PubMed] [Google Scholar]
  26. 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. Nucleic Acids Res. 1990 Dec 11;18(23):6821–6827. doi: 10.1093/nar/18.23.6821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Pieken W. A., Olsen D. B., Benseler F., Aurup H., Eckstein F. Kinetic characterization of ribonuclease-resistant 2'-modified hammerhead ribozymes. Science. 1991 Jul 19;253(5017):314–317. doi: 10.1126/science.1857967. [DOI] [PubMed] [Google Scholar]
  28. Puttaraju M., Been M. D. Group I permuted intron-exon (PIE) sequences self-splice to produce circular exons. Nucleic Acids Res. 1992 Oct 25;20(20):5357–5364. doi: 10.1093/nar/20.20.5357. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Rosenstein S. P., Been M. D. Evidence that genomic and antigenomic RNA self-cleaving elements from hepatitis delta virus have similar secondary structures. Nucleic Acids Res. 1991 Oct 11;19(19):5409–5416. doi: 10.1093/nar/19.19.5409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Sarver N., Cantin E. M., Chang P. S., Zaia J. A., Ladne P. A., Stephens D. A., Rossi J. J. Ribozymes as potential anti-HIV-1 therapeutic agents. Science. 1990 Mar 9;247(4947):1222–1225. doi: 10.1126/science.2107573. [DOI] [PubMed] [Google Scholar]
  32. Saxena S. K., Ackerman E. J. Ribozymes correctly cleave a model substrate and endogenous RNA in vivo. J Biol Chem. 1990 Oct 5;265(28):17106–17109. [PubMed] [Google Scholar]
  33. Sharmeen L., Kuo M. Y., Dinter-Gottlieb G., Taylor J. Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J Virol. 1988 Aug;62(8):2674–2679. doi: 10.1128/jvi.62.8.2674-2679.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sioud M., Drlica K. Prevention of human immunodeficiency virus type 1 integrase expression in Escherichia coli by a ribozyme. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7303–7307. doi: 10.1073/pnas.88.16.7303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Smith J. B., Gottlieb P. A., Dinter-Gottlieb G. A sequence element necessary for self-cleavage of the antigenomic hepatitis delta RNA in 20 M formamide. Biochemistry. 1992 Oct 13;31(40):9629–9635. doi: 10.1021/bi00155a015. [DOI] [PubMed] [Google Scholar]
  36. Suh Y. A., Kumar P. K., Nishikawa F., Kayano E., Nakai S., Odai O., Uesugi S., Taira K., Nishikawa S. Deletion of internal sequence on the HDV-ribozyme: elucidation of functionally important single-stranded loop regions. Nucleic Acids Res. 1992 Feb 25;20(4):747–753. doi: 10.1093/nar/20.4.747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Sullenger B. A., Gallardo H. F., Ungers G. E., Gilboa E. Overexpression of TAR sequences renders cells resistant to human immunodeficiency virus replication. Cell. 1990 Nov 2;63(3):601–608. doi: 10.1016/0092-8674(90)90455-n. [DOI] [PubMed] [Google Scholar]
  38. Sullivan F. X., Cech T. R. Reversibility of cyclization of the Tetrahymena rRNA intervening sequence: implication for the mechanism of splice site choice. Cell. 1985 Sep;42(2):639–648. doi: 10.1016/0092-8674(85)90121-7. [DOI] [PubMed] [Google Scholar]
  39. Taylor N. R., Kaplan B. E., Swiderski P., Li H., Rossi J. J. Chimeric DNA-RNA hammerhead ribozymes have enhanced in vitro catalytic efficiency and increased stability in vivo. Nucleic Acids Res. 1992 Sep 11;20(17):4559–4565. doi: 10.1093/nar/20.17.4559. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Thill G., Blumenfeld M., Lescure F., Vasseur M. Self-cleavage of a 71 nucleotide-long ribozyme derived from hepatitis delta virus genomic RNA. Nucleic Acids Res. 1991 Dec 11;19(23):6519–6525. doi: 10.1093/nar/19.23.6519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Thill G., Vasseur M., Tanner N. K. Structural and sequence elements required for the self-cleaving activity of the hepatitis delta virus ribozyme. Biochemistry. 1993 Apr 27;32(16):4254–4262. doi: 10.1021/bi00067a013. [DOI] [PubMed] [Google Scholar]
  42. Woodson S. A., Cech T. R. Reverse self-splicing of the tetrahymena group I intron: implication for the directionality of splicing and for intron transposition. Cell. 1989 Apr 21;57(2):335–345. doi: 10.1016/0092-8674(89)90971-9. [DOI] [PubMed] [Google Scholar]
  43. Wu H. N., Huang Z. S. Mutagenesis analysis of the self-cleavage domain of hepatitis delta virus antigenomic RNA. Nucleic Acids Res. 1992 Nov 25;20(22):5937–5941. doi: 10.1093/nar/20.22.5937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Wu H. N., Lin Y. J., Lin F. P., Makino S., Chang M. F., Lai M. M. Human hepatitis delta virus RNA subfragments contain an autocleavage activity. Proc Natl Acad Sci U S A. 1989 Mar;86(6):1831–1835. doi: 10.1073/pnas.86.6.1831. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Wu H. N., Wang Y. J., Hung C. F., Lee H. J., Lai M. M. Sequence and structure of the catalytic RNA of hepatitis delta virus genomic RNA. J Mol Biol. 1992 Jan 5;223(1):233–245. doi: 10.1016/0022-2836(92)90728-3. [DOI] [PubMed] [Google Scholar]
  46. Zaug A. J., Kent J. R., Cech T. R. A labile phosphodiester bond at the ligation junction in a circular intervening sequence RNA. Science. 1984 May 11;224(4649):574–578. doi: 10.1126/science.6200938. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES