Ribozymes: recent advances in the development of RNA tools

10.1016/0092-8674(82)90414-7 Eckstein, F. and Lilley, D.M.J. (1996) Nucleic Acids and Molecular Biology. Catalytic RNA, Vol. 10. Springer, Berlin. 10.1126/science.289.5481.905 10.1126/science.289.5481.947 10.1126/science.289.5481.920 10.1093/nar/14.9.3627 10.1021/bi00438a002 10.1038/350434a0 10.1126/science.3941911 10.1038/328596a0 10.1073/pnas.88.22.10163 Saldanha R. Mohr G. Belfort M. Lambowitz A.M. (1993) Group I and group II introns. FASEB J. 7, 15–24. 10.1016/0092-8674(81)90390-1 10.1146/annurev.bi.59.070190.002551 10.1038/300719a0 10.1016/S0300-9084(82)80349-0 10.1016/0092-8674(83)90348-3 Perea J. Jacq C. (1985) Role of the 5′ hairpin structure in the splicing accuracy of the fourth intron of the yeast cob-box gene. EMBO J. 4, 3281–3288. 10.1016/0092-8674(86)90443-5 10.1016/0092-8674(86)90380-6 Williamson C.L. Tierney W.M. Kerker B.J. Burke J.M. (1987) Site-directed mutagenesis of core sequence elements 9R’, 9L, 9R, and 2 in self-splicing Tetrahymena pre-rRNA. J. Biol. Chem. 262, 14672–14682. 10.1093/nar/17.22.9147 Flor P.J. Flanegan J.B. Cech T.R. (1989) A conserved base pair within helix P4 of the Tetrahymena ribozyme helps to form the tertiary structure required for self-splicing. EMBO J. 8, 3391–3399. 10.1093/nar/17.2.675 10.1016/0092-8674(89)90971-9 10.1038/324429a0 10.1126/science.274.5293.1678 Juneau K. Podell E. Harrington D.J. Cech T.R. (2001) Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions. Structure (Camb.) 9, 221–231. Pyle, A.M. (1996) Catalytic reaction mechanism and structural features of group II intron ribozymes. In: Catalytic RNA (Eckstein, F. and Lilley, D.M.J., Eds.), Vol. 10, pp. 75–107. Springer-Verlag, Berlin. 10.1016/S0168-9525(01)02324-1 Koch J.L. Boulanger S.C. Dib-Hajj S.D. Hebbar S.K. Perlman P.S. (1992) Group II introns deleted for multiple substructures retain self-splicing activity. Mol. Cell Biol. 12, 1950–1958. Jarrell K.A. Dietrich R.C. Perlman P.S. (1988) Group II intron domain 5 facilitates a trans-splicing reaction. Mol. Cell Biol. 8, 2361–2366. 10.1016/0378-1119(89)90026-7 10.1038/36142 10.1038/381332a0 10.1006/jmbi.1999.2922 10.1016/0092-8674(92)90313-2 10.1126/science.289.5478.452 Altman S. Kirsebom L. Talbot S. (1993) Recent studies of ribonuclease P. FASEB J. 7, 7–14. Guerrier-Takada C. Altman S. (1999) Inactivation of gene expression using ribonuclease P and external guide sequences. Methods Enzymol. 313, 442–456. Altman, S. and Kirsebom, L.A. (1999) Ribonuclease P. In: The RNA World (Gesteland, R.F., Atkins, J.F. and Cech, T., Eds.), pp. 511–533. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York. 10.1016/S0166-6851(01)00273-0 10.1073/pnas.70.7.2091 10.1016/0092-8674(83)90117-4 10.1126/science.3122322 10.1006/jmbi.1999.2890 10.1093/nar/28.3.720 Brown, J.W. The ribonuclease P database. Nucleic Acids Res. 27, 1999. 314 10.1093/nar/26.18.4093 10.1073/pnas.93.7.3001 10.1126/science.2443980 10.1126/science.1697102 10.1038/nbt0495-327 10.1017/S1355838200001461 10.1073/pnas.98.2.441 10.1002/1097-4652(200104)187:1<11::AID-JCP1055>3.0.CO;2-K 10.1126/science.8122108 Werner M. Rosa E. George S.T. (1997) Design of short external guide sequences (EGSs) for cleavage of target molecules with RNase P. Nucleic Acids Symp. Ser. 36, 19–21. 10.1146/annurev.bi.61.070192.003233 10.1016/0092-8674(87)90562-9 10.1073/pnas.89.9.3711 10.1073/pnas.94.21.11262 Bruening G. (1989) Compilation of self-cleaving sequences from plant virus satellite RNAs and other sources. Methods Enzymol. 180, 546–558. 10.1093/nar/19.19.5313 10.1093/nar/25.14.2683 10.1006/viro.1997.8962 Di Serio F. Daros J.A. Ragozzino A. Flores R. (1997) A 451-nucleotide circular RNA from cherry with hammerhead ribozymes in its strands of both polarities. J. Virol. 71, 6603–6610. 10.1073/pnas.92.15.6856 10.1016/0092-8674(87)90204-2 Ferbeyre G. Smith J.M. Cedergren R. (1998) Schistosome satellite DNA encodes active hammerhead ribozymes. Mol. Cell Biol. 18, 3880–3888. 10.1093/nar/28.20.4037 10.1126/science.6197756 Keese P. Osorio-Keese M.E. Symons R.H. (1988) Coconut tinangaja viroid: sequence homology with coconut cadang-cadang viroid and other potato spindle tuber viroid related RNAs. Virology 162, 508–510. 10.1006/jmbi.1999.3428 10.1017/S1355838201002461 10.1017/S1355838201002357 10.1006/jmbi.2001.5145 10.1093/nar/14.24.9729 10.1016/0092-8674(87)90657-X 10.1038/334585a0 10.1021/bi00499a018 10.1006/jmbi.1996.0446 10.1093/nar/26.18.4116 10.1038/372068a0 10.1016/S0092-8674(05)80004-2 10.1126/science.7973630 10.1016/0378-1119(89)90029-2 10.1099/0022-1317-71-9-1897 10.1126/science.231.4745.1577 10.1016/S1074-5521(97)90323-9 10.1016/S1074-5521(97)90247-7 10.1093/emboj/17.8.2378 10.1006/jmbi.2000.3560 10.1101/gad.6.1.129 Berzal-Herranz A. Joseph S. Chowrira B.M. Butcher S.E. Burke J.M. (1993) Essential nucleotide sequences and secondary structure elements of the hairpin ribozyme. EMBO J. 12, 2567–2573. 10.1093/nar/22.6.1096 10.1074/jbc.270.50.29648 10.1093/nar/21.8.1991 10.1021/ja00088a004 10.1006/jmbi.1997.1405 10.1038/35071009 Ryder S.P. Oyelere A.K. Padilla J.L. Klostermeier D. Millar D.P. Strobel S.A. (2001) Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping. RNA 7, 1454–1463. 10.1016/S1367-5931(98)80032-X 10.1093/nar/18.2.299 10.1101/gad.7.1.130 10.1038/354320a0 10.1021/bi992024s 10.1074/jbc.274.41.29376 Joseph S. Burke J.M. (1993) Optimization of an anti-HIV hairpin ribozyme by in vitro selection. J. Biol. Chem. 268, 24515–24518. 10.1089/oli.1.1999.9.433 10.1021/bi00023a021 10.1074/jbc.272.21.13629 10.1146/annurev.mi.46.100192.001345 Kuo M.Y. Sharmeen L. Dinter-Gottlieb G. Taylor J. (1988) Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus. J. Virol. 62, 4439–4444. Sharmeen L. Kuo M.Y. Dinter-Gottlieb G. Taylor J. (1988) Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage. J. Virol. 62, 2674–2679. 10.1073/pnas.86.6.1831 10.1093/nar/18.23.6821 Deschenes P. Lafontaine D.A. Charland S. 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. 10.1038/26912 10.1006/jmbi.1999.3398 10.1093/nar/27.3.795 10.1126/science.287.5457.1493 10.1006/jmbi.2000.4368 10.1021/bi00116a004 10.1093/nar/21.18.4253 10.1017/S1355838202020289 10.1074/jbc.M010570200 10.1016/0092-8674(90)90480-3 10.1073/pnas.88.19.8826 10.1101/gad.9.3.294 10.1006/jmbi.1993.1395 10.1006/jmbi.1997.1623 10.1016/S1097-2765(00)80441-4 10.1073/pnas.141039198 Guo H.C. Collins R.A. (1995) Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from Neurospora VS RNA. EMBO J. 14, 368–376. 10.1093/emboj/21.10.2461 Ohkawa J. Yuyama N. Takebe Y. Nisikawa S. Homann M. Sczakiel G. Taira K. (1993) Multiple site-specific cleavage of HIV RNA by transcribed ribozymes from shotgun-type trimming plasmid. Nucleic Acids Symp. Ser. 29, 121–122. Pavco P.A. (2000) Antitumor and antimetastatic activity of ribozymes targeting the messenger RNA of vascular endothelial growth factor receptors. Clin. Cancer Res. 6, 2094–2103. 10.1007/BF02088835 10.1038/nm0395-277 10.1006/bbrc.1999.0537 10.1016/S0168-8278(00)80171-3 10.1038/sj.gt.3300441 Zu Putlitz J. Yu Q. Burke J.M. Wands J.R. (1999) Combinatorial screening and intracellular antiviral activity of hairpin ribozymes directed against hepatitis B virus. J. Virol. 73, 5381–5387. Lieber A. He C.Y. Polyak S.J. Gretch D.R. Barr D. Kay M.A. (1996) Elimination of hepatitis C virus RNA in infected human hepatocytes by adenovirus-mediated expression of ribozymes. J. Virol. 70, 8782–8791. 10.1002/hep.510310331 Welch P.J. Tritz R. Yei S. Leavitt M. Yu M. Barber J. (1996) A potential therapeutic application of hairpin ribozymes: in vitro and in vivo studies of gene therapy for hepatitis C virus infection. Gene Ther. 3, 994–1001. 10.1172/JCI11631 10.1006/bbrc.1998.8387 10.1038/sj.gt.3300780 10.1093/nar/23.15.2909 Wang L. (1998) Preclinical characterization of an anti-tat ribozyme for therapeutic application. Hum. Gene Ther. 9, 1283–1291. 10.1006/viro.1994.1626 10.1093/nar/20.17.4581 10.1126/science.2107573 10.1016/S0042-6822(95)80053-0 10.1006/viro.1999.0112 Weerasinghe M. Liem S.E. Asad S. Read S.E. Joshi S. (1991) Resistance to human immunodeficiency virus type 1 (HIV-1) infection in human CD4+ lymphocyte-derived cell lines conferred by using retroviral vectors expressing an HIV-1 RNA-specific ribozyme. J. Virol. 65, 5531–5534. Koizumi M. (1998) Design and anti-HIV-1 activity of hammerhead and hairpin ribozymes containing a stable loop. Nucleosides Nucleotides 17, 207–218. 10.1038/sj.gt.3301094 10.1073/pnas.89.22.10802 10.1073/pnas.90.13.6340 10.1073/pnas.91.21.9715 Westaway S.K. Cagnon L. Chang Z. Li S. Li H. Larson G.P. Zaia J.A. Rossi J.J. (1998) Virion encapsidation of tRNA(3Lys)-ribozyme chimeric RNAs inhibits HIV infection. Antisense Nucleic Acid Drug Dev. 8, 185–197. 10.1006/mthe.2000.0038 10.1089/108729000421439 10.1006/bbrc.1998.9522 Bauer G. Valdez P. Kearns K. Bahner I. Wen S.F. Zaia J.A. Kohn D.B. (1997) Inhibition of human immunodeficiency virus-1 (HIV-1) replication after transduction of granulocyte colony-stimulating factor-mobilized CD34+ cells from HIV-1-infected donors using retroviral vectors containing anti-HIV-1 genes. Blood 89, 2259–2267. 10.1089/10430349950017239 10.1089/hum.1998.9.16-2407 10.1038/418252a Albuquerque-Silva J. Milican F. Bollen A. Houard S. (1999) Ribozyme-mediated decrease in mumps virus nucleocapsid mRNA level and progeny in infected vero cells. Antisense Nucleic Acid Drug Dev. 9, 279–288. Tang X.B. Hobom G. Luo D. (1994) Ribozyme mediated destruction of influenza A virus in vitro and in vivo. J. Med. Virol. 42, 385–395. 10.1074/jbc.M111360200 10.1073/pnas.95.3.1189 10.1016/0378-1119(92)90727-7 10.1016/0022-2836(92)90244-E Sandberg J.A. (2000) Acute toxicology and pharmacokinetic assessment of a ribozyme (ANGIOZYME) targeting vascular endothelial growth factor receptor mRNA in the cynomolgus monkey. Antisense Nucleic Acid Drug Dev. 10, 153–162. 10.1038/sj.cgt.7700508 10.1038/sj.onc.1205560 10.1002/(SICI)1097-0215(19990730)82:3<346::AID-IJC7>3.0.CO;2-# Kiehntopf M. Brach M.A. Licht T. Petschauer S. Karawajew L. Kirschning C. Herrmann F. (1994) Ribozyme-mediated cleavage of the MDR-1 transcript restores chemosensitivity in previously resistant cancer cells. EMBO J. 13, 4645–4652. 10.1089/10430349950018175 10.1093/nar/22.12.2375 Takahashi M. Funato T. Suzuki Y. Fujii H. Ishii K.K. Kaku M. Sasaki T. (2002) Chemically modified ribozyme targeting TNF-alpha mRNA regulates TNF-alpha and IL-6 synthesis in synovial fibroblasts of patients with rheumatoid arthritis. J. Clin. Immunol. 22, 228–236. 10.1073/pnas.91.6.2051 10.1146/annurev.biochem.67.1.153 10.1021/bi00201a030 10.1017/S1355838298980918 10.1038/sj.gt.3301606 10.1073/pnas.95.13.7327 10.1073/pnas.261560598 10.1074/jbc.M200183200 10.1101/gad.9.4.471 10.1006/jmbi.2000.4022 Cobaleda C. Sánchez-García I. (2000) In vivo inhibition by a site-specific catalytic RNA subunit of RNase P designed against the BCR-ABL oncogenic products: a novel approach for cancer treatment. Blood 95, 731–737. 10.1074/jbc.275.14.10611 Trang P. Hsu A. Zhou T. Lee J. Kilani A.F. Nepomuceno E. Liu F. (2002) Engineered RNase P ribozymes inhibit gene expression and growth of cytomegalovirus by increasing rate of cleavage and substrate binding. J. Mol. Biol. 315, 573–586. 10.1073/pnas.100101797 10.1074/jbc.M203595200 10.1038/371619a0 10.1038/nm0696-643 10.1038/nbt0997-902 10.1006/jmbi.1998.2447 10.1038/ng0498-378 10.1126/science.280.5369.1593 10.1073/pnas.150104097 10.1073/pnas.96.7.3507 10.1101/gad.11.21.2910 10.1016/S0092-8674(00)81586-X Sczakiel, G. (1996) Hammerhead ribozymes with long flanking sequences: a structural and kinetic view. In: Nucleic Acids and Molecular Biology. Catalytic RNA (Eckstein, F.L., D.M.J, Ed.), Vol. 10. Springer, Berlin, pp. 231–242. 10.1093/nar/21.22.5251 10.1093/nar/21.12.2809 10.1002/dvg.1020140403 10.1007/BF00302259 10.1093/nar/22.19.3958 10.1016/0378-1119(91)90432-B 10.1093/nar/22.3.301 10.1093/nar/25.2.333 10.1093/nar/25.4.769 Puerta-Fernández E. Barroso-DelJesus A. Berzal-Herranz A. (2002) Anchoring hairpin ribozymes to long target RNAs by loop-loop RNA interactions. Antisense Nucleic Acid Drug Dev. 12, 1–9. 10.1146/annurev.mi.48.100194.003433 10.1515/BC.2003.040 10.1093/nar/20.17.4607 Goodchild J. (1997) Optimization of hammerhead flanking sequences using oligonucleotide facilitators. Methods Mol. Biol. 74, 265–273. Jankowsky E. Schwenzer B. (1996) Efficient improvement of hammerhead ribozyme mediated cleavage of long substrates by oligonucleotide facilitators. Biochemistry 35, 15313–15321. 10.1093/nar/25.14.2690 10.1093/nar/21.17.4119 Nesbitt S. Goodchild J. (1994) Further studies on the use of oligonucleotide facilitators to increase ribozyme turnover. Antisense Res. Dev. 4, 243–249. Jankowsky E. Schwenzer B. (1998) Oligonucleotide facilitators enable a hammerhead ribozyme to cleave long RNA substrates with multiple-turnover activity. Eur. J. Biochem. 254, 129–134. Hovig E. Maelandsmo G. Mellingsaeter T. Fodstad O. Mielewczyk S.S. Wolfe J. Goodchild J. (2001) Optimization of hammerhead ribozymes for the cleavage of S100A4 (CAPL) mRNA. Antisense Nucleic Acid Drug Dev. 11, 67–75. 10.1093/nar/24.3.423 10.1002/bies.950150503 10.1093/nar/23.13.2434 Bertrand E.L. Rossi J.J. (1994) Facilitation of hammerhead ribozyme catalysis by the nucleocapsid protein of HIV-1 and the heterogeneous nuclear ribonucleoprotein A1. EMBO J. 13, 2904–2912. 10.1126/science.7692597 Herschlag D. Khosla M. Tsuchihashi Z. Karpel R.L. (1994) An RNA chaperone activity of non-specific RNA binding proteins in hammerhead ribozyme catalysis. EMBO J. 13, 2913–2924. 10.1006/jmbi.1994.1612 10.1006/jmbi.1996.0201 10.1073/pnas.091411398 10.1093/embo-reports/kvf098 10.1093/oxfordjournals.jbchem.a003152 Yamada O. Kraus G. Luznik L. Yu M. Wong-Staal F. (1996) A chimeric human immunodeficiency virus type 1 (HIV-1) minimal Rev response element-ribozyme molecule exhibits dual antiviral function and inhibits cell-cell transmission of HIV-1. J. Virol. 70, 1596–1601. Gervaix A. Li X. Kraus G. Wong-Staal F. (1997) Multigene antiviral vectors inhibit diverse human immunodeficiency virus type 1 clades. J. Virol. 71, 3048–3053. 10.1016/S0378-1119(00)00334-6 10.1016/S0079-6603(08)60842-9 10.1016/S0167-7799(99)01383-9 10.1093/nar/28.8.1751 10.1006/jmbi.2001.4981 Komatsu Y. Nobuoka K. Karino-Abe N. Matsuda A. Ohtsuka E. (2002) In vitro selection of hairpin ribozymes activated with short oligonucleotides. Biochemistry 41, 9090–9098. 10.1038/nbt0702-717 10.1038/nbt0295-161 10.1006/jmbi.2001.4811 10.1021/bi0201522 10.1093/nar/30.8.1735 10.1006/jmbi.2000.3825 10.1016/S0167-7799(00)01498-0 10.1093/nar/24.12.2302 10.1038/nbt1098-961 10.1073/pnas.96.5.1886 10.1016/S1097-2765(00)80160-4 10.1021/bm990009x 10.1038/35020190 10.1093/nar/25.15.3074 Tanaka M. Kijima H. Itoh J. Matsuda T. Tanaka T. (2002) Impaired expression of a human septin family gene Bradeion inhibits the growth and tumorigenesis of colorectal cancer in vitro and in vivo. Cancer Gene Ther. 9, 483–488. 10.1042/0264-6021:3540243 10.1016/S0958-1669(00)00173-7 10.1038/365448a0 10.1073/pnas.94.25.13777 Czubayko F. Riegel A.T. Wellstein A. (1994) Ribozyme-targeting elucidates a direct role of pleiotrophin in tumor growth. J. Biol. Chem. 269, 21358–21363. 10.1038/30538 10.1093/nar/28.13.2605 10.1073/pnas.96.7.3584 10.1016/S0958-1669(02)00281-1 10.1016/S0968-0896(01)00027-X 10.1038/86723 Vaish N.K. Dong F. Andrews L. Schweppe R.E. Ahn N.G. Blatt L. Seiwert S.D. (2002) Monitoring post-translational modification of proteins with allosteric ribozymes. Nat. Biotechnol. 20, 810–815. 10.1016/S1074-5521(97)90197-6 10.1093/nar/26.18.4214 10.1016/S0022-2836(02)00046-3 10.1093/nar/29.7.1631 10.1093/nar/26.14.3379 Araki M. Hashima M. Okuno Y. Sugiura Y. (2001) Coupling between substrate binding and allosteric regulation in ribozyme catalysis. Bioorg. Med. Chem. 9, 1155–1163. Soukup G.A. Breaker R.R. (1999) Design of allosteric hammerhead ribozymes activated by ligand-induced structure stabilization. Struct. Fold Des. 7, 783–791. 10.1017/S1355838201002175 10.1038/14947 10.1126/science.279.5347.81 10.1093/nar/28.2.481 10.1126/science.1315076 10.1038/90256 Wang D.Y. Sen D. (2002) Rationally designed allosteric variants of hammerhead ribozymes responsive to the HIV-1 Tat protein. Comb. Chem. High Throughput Screen 5, 301–312. 10.1093/nar/21.2.185 10.1006/geno.2000.6230 10.1073/pnas.97.15.8566 10.1128/MCB.21.24.8357-8364.2001 10.1073/pnas.98.1.130 10.1038/nbt0402-376 10.1016/S0014-5793(02)03193-9 Cech T.R. (1990) Self-splicing and enzymatic activity of an intervening sequence RNA from Tetrahymena . Angew. Chem. Int. Ed. Engl. 29, 759–768. Cech T.R. (1986) RNA as an enzyme. Sci. Am. 255, 64–75. 10.1016/S1367-5931(99)80043-X Hertel, K.J. et al. Numbering system for the hammerhead. Nucleic Acids Res. 20, 1992. 3252 10.1073/pnas.92.10.4686 Krüger, M., Beger, C., Welch, P.J., Barber, J.R., Wong-Staal, F. C-SPACE (cleavage-specific amplification of cDNA ends): a novel method of ribozyme-mediated gene identification. Nucleic Acids Res. 29, 2001. E94