Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting

Nucleic Acid Therapeutics

Volumn 21, Issue 4, 2011, Pages 241-252

  Lévesque, Michel V ^a   Rouleau, Samuel G ^a   Perreault, Jean Pierre ^a  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

HAMMERHEAD RIBOZYME; NONSTRUCTURAL PROTEIN 5B; RIBOZYME; SOFA RIBOZYME; UNCLASSIFIED DRUG;

ARTICLE; BIOSENSOR; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SPECIFICITY; FUNCTIONAL GENOMICS; GENE SILENCING; GENE TARGETING; GENE THERAPY; HEPATITIS C VIRUS; HEPATITIS DELTA VIRUS; NONHUMAN; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN DOMAIN; RNA ANALYSIS; RNA INTERFERENCE; RNA SYNTHESIS;

BASE PAIRING; BASE SEQUENCE; CATALYTIC DOMAIN; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; ENZYME ASSAYS; GENE TARGETING; HEPATITIS DELTA VIRUS; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RNA; RNA, CATALYTIC; THERMODYNAMICS; VIRAL NONSTRUCTURAL PROTEINS;

HEPATITIS C VIRUS; HEPATITIS DELTA VIRUS;

EID: 80052235374     PISSN: 21593337     EISSN: None     Source Type: Journal    
DOI: 10.1089/nat.2011.0301     Document Type: Article

References (37)

1. 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.
2. ANANVORANICH, S., and PERREAULT, J.P. (2000). The kinetics and magnesium requirements for the folding of anti-genomic delta ribozymes. Biochem. Biophys. Res. Commun. 270, 600-607. (Pubitemid 30446881)
3. ASHIHARA, E., KAWATA, E., and MAEKAWA, T. (2010). Future prospect of RNA interference for cancer therapies. Curr. Drug Targets 11, 345-360.
4. 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. (Pubitemid 46902202)
5. BEAUDOIN, J.D., and PERREAULT, J.P. (2008). Potassium ions modulate a G-quadruplex-ribozyme's activity. RNA 14, 1018-1025.
6. BERGERON, L.J., and PERREAULT, J.P. (2002). Development and comparison of procedures for the selection of delta ribo-zyme cleavage sites within the hepatitis B virus. Nucleic Acids Res. 30, 4682-4691. (Pubitemid 35331750)
7. BERGERON, L.J., and PERREAULT, J.P. (2005). Target-dependent on/off switch increases ribozyme fidelity. Nucleic Acids Res. 33, 1240-1248. (Pubitemid 41439917)
8. BERGERON, L.J., REYMOND, C., and PERREAULT, J.P. (2005). Functional characterization of the SOFA delta ribozyme. RNA 11, 1858-1868. (Pubitemid 41720035)
9. D'ANJOU, F., BERGERON, L.J., LARBI, N.B., FOURNIER, I., SALZET, M., PERREAULT, J.P., and DAY, R. (2004). Silencing of SPC2 expression using an engineered delta ribozyme in the mouse betaTC-3 endocrine cell line. J. Biol. Chem. 279, 14232-14239. (Pubitemid 38468962)
10. D'ANJOU, F., ROUTIER, S., PERREAULT, J.P., LATIL, A., BONNEL, D., FOURNIER, I., SALZET, M., and DAY, R. (2011). Molecular validation of PACE4 as a target in prostate cancer. Transl. Oncol. 4, 157-172.
11. 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. (Pubitemid 30148190)
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.
13. HAASNOOT, J., WESTERHOUT, E.M., and BERKHOUT, B. (2007). RNA interference against viruses: strike and counter-strike. Nat. Biotechnol. 25, 1435-1443. (Pubitemid 350233142)
14. HENDRY, P., MCCALL, M.J., STEWART, T.S., and LOCKETT, T.J. (2004). Redesigned and chemically-modified hammerhead ribozymes with improved activity and serum stability. BMC Chem. Biol. 4, 1.
15. LAINE, S., SCARBOROUGH, R.J., LEVESQUE, D., DI-DIERLAURENT, L., SOYE, K.J., MOUGEL, M., PERREAULT, J.P., and GATIGNOL, A. (2011). In vitro and in vivo cleavage of HIV-1 RNA by new SOFA-HDV ribozymes and their potential to inhibit viral replication. RNA Biol. 8, 343-353.
16. LAITALA-LEINONEN, T. (2010). Update on the development of microRNA and siRNA molecules as regulators of cell physiology. Recent. Pat. DNA Gene Seq. 4, 113-121.
17. LEVESQUE, D., BRIERE, F.P., and PERREAULT, J.P. (2007). A modern mode of activation for nucleic acid enzymes. PLoS One 2, e673.
18. 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. (Pubitemid 34437717)
19. LEVESQUE, M.V., LEVESQUE, D., BRIERE, F.P., and PER-REAULT, J.P. (2010). Investigating a new generation of ribo-zymes in order to target HCV. PLoS One 5, e9627.
20. LEVESQUE, M.V., and PERREAULT, J.P. (2011). Target Induced SOFA-HDV Ribozyme. Methods Mol. Biol. (in press).
21. MARIN,R.M.,andVANICEK,J.(2011).Efficientuseofaccessibility in microRNA target prediction. Nucleic Acids Res. 39, 19-29.
22. MASQUIDA, B., BECKERT, B., and JOSSINET, F. (2010). Exploring RNA structure by integrative molecular modelling. N. Biotechnol. 27, 170-183.
23. MATVEEVA, O.V., KANG, Y., SPIRIDONOV, A.N., SAETROM, P., NEMTSOV, V.A., OGURTSOV, A.Y., NECHIPURENKO, Y.D., and SHABALINA, S.A. (2010). Optimization of duplex stability and terminal asymmetry for shRNA design. PLoS One 5, e10180.
24. MERCATANTI, A., RAINALDI, G., MARIANI, L., MAR-ANGONI, R., and CITTI, L. (2002). A method for prediction of accessible sites on an mRNA sequence for target selection of hammerhead ribozymes. J. Comput. Biol. 9, 641-653. (Pubitemid 35191756)
25. MUHONEN, P., and HOLTHOFER, H. (2010). Bioinformatic approaches to siRNA selection and optimization. Methods Mol. Biol. 623, 93-107.
26. MULLER-KULLER, T., CAPALBO, G., KLEBBA, C., ENGELS, J.W., and KLEIN, S.A. (2009). Identification and characterization of a highly efficient anti-HIV pol hammerhead ribozyme. Oligonucleotides 19, 265-272.
27. PERACCHI, A. (2004). Prospects for antiviral ribozymes and deoxyribozymes. Rev. Med. Virol. 14, 47-64. (Pubitemid 38133625)
28. REYMOND, C., BEAUDOIN, J.D., and PERREAULT, J.P. (2009). Modulating RNA structure and catalysis: lessons from small cleaving ribozymes. Cell Mol. Life Sci. 66, 3937-3950.
29. REYMOND, C., LEVESQUE, D., BISAILLON, M., and PER-REAULT, J.P. (2010). Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme. Structure 18, 1608-1616.
30. ROBBINS, M., JUDGE, A., AMBEGIA, E., CHOI, C., YA-WORSKI, E., PALMER, L., MCCLINTOCK, K., and MA-CLACHLAN, I. (2008). Misinterpreting the therapeutic effects of small interfering RNA caused by immune stimulation. Hum. Gene Ther. 19, 991-999.
31. 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.
32. SCHUBERT, S., and KURRECK, J. (2004). Ribozyme-and deoxyribozyme- strategies for medical applications. Curr. Drug Targets 5, 667-681.
33. TAMURA, A., and NAGASAKI, Y. (2010). Smart siRNA delivery systems based on polymeric nanoassemblies and nano-particles. Nanomedicine (Lond) 5, 1089-1102.
34. TEDESCHI, L., LANDE, C., CECCHETTINI, A., and CITTI, L. (2009). Hammerhead ribozymes in therapeutic target discovery and validation. Drug Discov. Today 14, 776-783.
35. VOROBJEVA, M., ZENKOVA, M., VENYAMINOVA, A., and VLASSOV, V. (2006). Binary hammerhead ribozymes with improved catalytic activity. Oligonucleotides 16, 239-252. (Pubitemid 44763318)
36. ZHOU, J., and ROSSI, J.J. (2010). Aptamer-targeted cell-specific RNA interference. Silence 1, 4.
37. ZUKER, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415. (Pubitemid 37442169)