Advertisement

Ribozymes pp 369-384 | Cite as

Target-Induced SOFA-HDV Ribozyme

  • Michel V. Lévesque
  • Jean-Pierre PerreaultEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 848)

Abstract

Small cis-acting ribozymes have been converted into trans-acting ribozymes possessing the ability to cleave RNA substrates. The Hepatitis Delta Virus (HDV) ribozyme is one of the rare examples of these that is derived from an RNA species that is found in human cells. Consequently, it possesses the natural ability to function in the presence of human proteins in addition to an outstanding stability in human cells, two significant advantages in its use. The development of an additional specific on/off adaptor (SOFA) has led to the production of a new generation of HDV ribozymes with improved specificities that provide a tool with significant potential for future development in the fields of both functional genomics and gene ­therapy. SOFA-HDV ribozyme-based gene inactivation systems have been reported in both prokaryotic and eukaryotic cells. Here, a step-by-step approach for the efficient design of highly specific SOFA-HDV ribozymes with a minimum investment of time and effort is described.

Key words

Ribozyme Gene inactivation Functional genomics Gene therapy 

Notes

Acknowledgments

We thank Jonathan Perreault and Gilles Boire for information about hY RNA. This work was supported by grants from Canadian Institute of Health Research (CIHR; grant numbers MOP-44002 and EOP-38322) to J.P.P. The RNA group is supported by grants both from CIHR and Université de Sherbrooke. M.V.L. was the recipient of a predoctoral fellowship from the Fonds de Recherche en Santé du Québec. J.P.P. holds the Canada Research Chairs in genomics and catalytic RNAs, and is a member of the Centre de Recherche Clinique Étienne Lebel.

References

  1. 1.
    Bagheri, S., and Kashani-Sabet, M. (2004) Ribozymes in the Age of Molecular Therapeutics. Curr. Mol. Med. 4, 489–506.PubMedCrossRefGoogle Scholar
  2. 2.
    Schubert, S., and Kurreck, J. (2004) Ribozyme- and Deoxyribozyme-Strategies for Medical Applications. Curr. Drug Targets. 5, 667–681.PubMedCrossRefGoogle Scholar
  3. 3.
    Asif-Ullah, M., Levesque, M., Robichaud, G., and Perreault, J. P. (2007) Development of Ribozyme-Based Gene-Inactivations; the Example of the Hepatitis Delta Virus Ribozyme. Curr. Gene Ther. 7, 205–216.PubMedCrossRefGoogle Scholar
  4. 4.
    Tedeschi, L., Lande, C., Cecchettini, A., and Citti, L. (2009) Hammerhead Ribozymes in Therapeutic Target Discovery and Validation. Drug Discov. Today. 14, 776–783.PubMedCrossRefGoogle Scholar
  5. 5.
    Teixeira, A., Tahiri-Alaoui, A., West, S., Thomas, B., Ramadass, A., Martianov, I., Dye, M., James, W., Proudfoot, N. J., and Akoulitchev, A. (2004) Autocatalytic RNA Cleavage in the Human Beta-Globin Pre-mRNA Promotes Transcription Termination. Nature. 432, 526–530.PubMedCrossRefGoogle Scholar
  6. 6.
    Salehi-Ashtiani, K., Luptak, A., Litovchick, A., and Szostak, J. W. (2006) A Genomewide Search for Ribozymes Reveals an HDV-Like Sequence in the Human CPEB3 Gene. Science. 313, 1788–1792.PubMedCrossRefGoogle Scholar
  7. 7.
    Levesque, D., Choufani, S., and Perreault, J. P. (2002) Delta Ribozyme Benefits from a Good Stability in Vitro that Becomes Outstanding in Vivo. RNA. 8, 464–477.PubMedCrossRefGoogle Scholar
  8. 8.
    Bergeron, L. J., Ouellet, J., and Perreault, J. P. (2003) Ribozyme-Based Gene-Inactivation Systems Require a Fine Comprehension of their Substrate Specificities; the Case of Delta Ribozyme. Curr. Med. Chem. 10, 2589–2597.PubMedCrossRefGoogle Scholar
  9. 9.
    Peracchi, A. (2004) Prospects for Antiviral Ribozymes and Deoxyribozymes. Rev. Med. Virol. 14, 47–64.PubMedCrossRefGoogle Scholar
  10. 10.
    Bergeron, L. J., and Perreault, J. P. (2005) Target-Dependent on/off Switch Increases Ribozyme Fidelity. Nucleic Acids Res. 33, 1240–1248.PubMedCrossRefGoogle Scholar
  11. 11.
    Bergeron, L. J., Reymond, C., and Perreault, J. P. (2005) Functional Characterization of the SOFA Delta Ribozyme. RNA. 11, 1858–1868.PubMedCrossRefGoogle Scholar
  12. 12.
    Fiola, K., Perreault, J. P., and Cousineau, B. (2006) Gene Targeting in the Gram-Positive Bacterium Lactococcus lactis, using various Delta Ribozymes. Appl. Environ. Microbiol. 72, 869–879.PubMedCrossRefGoogle Scholar
  13. 13.
    Bergeron, L. J., Reymond, C., and Perreault, J. P. (2005) Functional Characterization of the SOFA Delta Ribozyme. RNA. 11, 1858–1868.PubMedCrossRefGoogle Scholar
  14. 14.
    Levesque, M. V., Levesque, D., Briere, F. P., and Perreault, J. P. (2010) Investigating a New Generation of Ribozymes in Order to Target HCV. PLoS One. 5, e9627.PubMedCrossRefGoogle Scholar
  15. 15.
    Robichaud, G. A., Perreault, J. P., and Ouellette, R. J. (2008) Development of an Isoform-Specific Gene Suppression System: The Study of the Human Pax-5B Transcriptional Element. Nucleic Acids Res. 36, 4609–4620.PubMedCrossRefGoogle Scholar
  16. 16.
    von Eije, K. J., ter Brake, O., and Berkhout, B. (2008) Human Immunodeficiency Virus Type 1 Escape is Restricted when Conserved Genome Sequences are Targeted by RNA Interference. J. Virol. 82, 2895–2903.CrossRefGoogle Scholar
  17. 17.
    Haasnoot, J., Westerhout, E. M., and Berkhout, B. (2007) RNA Interference Against Viruses: Strike and Counterstrike. Nat. Biotechnol. 25, 1435–1443.PubMedCrossRefGoogle Scholar
  18. 18.
    Amarzguioui, M., Brede, G., Babaie, E., Grotli, M., Sproat, B., and Prydz, H. (2000) Secondary Structure Prediction and in Vitro Accessibility of mRNA as Tools in the Selection of Target Sites for Ribozymes. Nucleic Acids Res. 28, 4113–4124.PubMedCrossRefGoogle Scholar
  19. 19.
    Ryu, K. J., and Lee, S. W. (2004) Comparative Analysis of Intracellular Trans-Splicing Ribozyme Activity Against Hepatitis C Virus Internal Ribosome Entry Site. J. Microbiol. 42, 361–364.PubMedGoogle Scholar
  20. 20.
    Doran, G., and Sohail, M. (2006) Systematic Analysis of the Role of Target Site Accessibility in the Activity of DNA Enzymes. J. RNAi Gene Silencing. 2, 205–214.PubMedGoogle Scholar
  21. 21.
    Deschenes, P., Lafontaine, D. A., Charland, S., and Perreault, J. P. (2000) Nucleotides -1 to -4 of Hepatitis Delta Ribozyme Substrate Increase the Specificity of Ribozyme Cleavage. Antisense Nucleic Acid Drug Dev. 10, 53–61.PubMedCrossRefGoogle Scholar
  22. 22.
    Lucier, J. F., Bergeron, L. J., Briere, F. P., Ouellette, R., Elela, S. A., and Perreault, J. P. (2006) RiboSubstrates: A Web Application Addressing the Cleavage Specificities of Ribozymes in Designated Genomes. BMC Bioinformatics. 7, 480.PubMedCrossRefGoogle Scholar
  23. 23.
    Ouellet, J., and Perreault, J. P. (2004) Cross-Linking Experiments Reveal the Presence of Novel Structural Features between a Hepatitis Delta Virus Ribozyme and its Substrate. RNA. 10, 1059–1072.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Département de BiochimieUniversité de SherbrookeSherbrookeCanada

Personalised recommendations