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Alino SF, Crespo J, Bobadilla M, Lejarreta M, Blaya C, Crespo A (1994) Expression of human alpha 1-antitrypsin in mouse after in vivo gene transfer to hepatocytes by small liposomes. Biochem Biophys Res Commun 204:1023–1030
Amontov S, Nishikawa S, Taira K (1996) Dependence on Mg2+ ions of the activities of dimeric hammerhead minizymes. FEBS Lett 386:99–102
Arts GJ, Fornerod M, Mattaj IW (1998a) Identification of a nuclear export receptor for tRNA. Curr Biol 8:305–314
Arts GJ, Kuersten S, Romby P, Ehresmann B, Mattaj IW (1998b) The role of exportin-t in selective nuclear export of mature tRNAs. Embo J 17:7430–7441
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297
Beger C, Pierce LN, Kruger M, Marcusson EG, Robbins JM, Welcsh P, Welch PJ, Welte K, King MC, Barber JR, Wong-Staal F (2001) Identification of Id4 as a regulator of BRCA1 expression by using a ribozyme-library-based inverse genomics approach. Proc Natl Acad Sci USA 98:130–135
Berns K, Hijmans EM, Mullenders J, Brummelkamp TR, Velds A, Heimerikx M, Kerkhoven RM, Madiredjo M, Nijkamp W, Weigelt B, Agami R, Ge W, Cavet G, Linsley PS, Beijersbergen RL, Bernards R (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428:431–437
Bertrand E, Castanotto D, Zhou C, Carbonnelle C, Lee NS, Good P, Chatterjee S, Grange T, Pictet R, Kohn D, Engelke D, Rossi JJ (1997) The expression cassette determines the functional activity of ribozymes in mammalian cells by controlling their intracellular localization. Rna 3:75–88
Braun IC, Rohrbach E, Schmitt C, Izaurralde E (1999) TAP binds to the constitutive transport element (CTE) through a novel RNA-binding motif that is sufficient to promote CTE-dependent RNA export from the nucleus. Embo J 18:1953–1965
Bridge AJ, Pebernard S, Ducraux A, Nicoulaz AL, Iggo R (2003) Induction of an interferon response by RNAi vectors in mammalian cells. Nat Genet 34:263–264
Brisson M, Huang L (1999) Liposomes: conquering the nuclear barrier. Curr Opin Mol Ther 1:140–146
Brummelkamp TR, Bernards R, Agami R (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296:550–553
Caplen NJ, Parrish S, Imani F, Fire A, Morgan RA (2001) Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci USA 98:9742–9747
Caplen NJ, Alton EW, Middleton PG, Dorin JR, Stevenson BJ, Gao X, Durham SR, Jeffery PK, Hodson ME, Coutelle C et al. (1995) Liposome-mediated CFTR gene transfer to the nasal epithelium of patients with cystic fibrosis. Nat Med 1:39–46
Chang Z, Westaway S, Li S, Zaia JA, Rossi JJ, Scherer LJ (2002) Enhanced expression and HIV-1 inhibition of chimeric tRNA(Lys3)-ribozymes under dual U6 snRNA and tRNA promoters. Mol Ther 6:481–489
Chatterton JE, Hu X, Wong-Staal F (2004) Ribozymes in gene identification, target validation, and drug discovery. Target 3:10–17
Cloninger MJ (2002) Biological applications of dendrimers. Curr Opin Chem Biol 6:742–748
Cotten M, Birnstiel ML (1989) Ribozyme mediated destruction of RNA in vivo. Embo J 8:3861–3866
Coumoul X, Li W, Wang RH, Deng C (2004) Inducible suppression of Fgfr2 and Survivin in ES cells using a combination of the RNA interference (RNAi) and the Cre-LoxP system. Nucleic Acids Res 32:e85
Das G, Henning D, Wright D, Reddy R (1988) Upstream regulatory elements are necessary and sufficient for transcription of a U6 RNA gene by RNA polymerase III. Embo J 7:503–512
de la Cruz J, Kressler D, Linder P (1999) Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem Sci 24:192–198
Druker BJ, Tamura S, Buchdunger E, Ohno S, Segal GM, Fanning S, Zimmermann J, Lydon NB (1996) Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells. Nat Med 2:561–566
Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, Tuschl T (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494–498
Famulok M (2004) Green fluorescent RNA. Nature 430:976–977
Ferber D (2001) Gene therapy. Safer and virus-free? Science 294:1638–1642
Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811
Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J (2000) Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408:325–330
Fritsch L, Martinez LA, Sekhri R, Naguibneva I, Gerard M, Vandromme M, Schaeffer L, Harel-Bellan A (2004) Conditional gene knock-down by CRE-dependent short interfering RNAs. EMBO Rep 5:178–182
Fu DJ, Benseler F, McLaughlin LW (1994) Hammerhead ribozymes containing nonnucleoside linkers are active RNA catalysts. J. Am. Chem. Soc. 116:4591–4598
Geiduschek EP, Tocchini-Valentini GP (1988) Transcription by RNA polymerase III. Annu Rev Biochem 57:873–914
Gonczy P, Echeverri C, Oegema K, Coulson A, Jones SJ, Copley RR, Duperon J, Oegema J, Brehm M, Cassin E, Hannak E, Kirkham M, Pichler S, Flohrs K, Goessen A, Leidel S, Alleaume AM, Martin C, Ozlu N, Bork P, Hyman AA (2000) Functional genomic analysis of cell division in C. elegans using RNAi of genes on chromosome III. Nature 408:331–336
Good PD, Krikos AJ, Li SX, Bertrand E, Lee NS, Giver L, Ellington A, Zaia JA, Rossi JJ, Engelke DR (1997) Expression of small, therapeutic RNAs in human cell nuclei. Gene Ther 4:45–54
Grosshans H, Hurt E, Simos G (2000) An aminoacylation-dependent nuclear tRNA export pathway in yeast. Genes Dev 14:830–840
Gruter P, Tabernero C, von Kobbe C, Schmitt C, Saavedra C, Bachi A, Wilm M, Felber BK, Izaurralde E (1998) TAP, the human homolog of Mex67p, mediates CTE-dependent RNA export from the nucleus. Mol Cell 1:649–659
Hartig JS, Grune I, Najafi-Shoushtari SH, Famulok M (2004) Sequence-specific detection of MicroRNAs by signal-amplifying ribozymes. J Am Chem Soc 126:722–723
Hirabayashi K, Nakagawa S, Yamaguchi T, Nogawa M, Kobayashi I, Naito H, Kitagawa H, Ishiyama K, Ohgi T, Yano J (2004) Antitumour activity of siRNA/cationic liposome complex in a mouse model of liver metastasis. Clinical Cancer Research 10:7721–7726
Hodge CA, Colot HV, Stafford P, Cole CN (1999) Rat8p/Dbp5p is a shuttling transport factor that interacts with Rat7p/Nup159p and Gle1p and suppresses the mRNA export defect of xpo1-1 cells. Embo J 18:5778–5788
James H, Mills K, Gibson I (1996) Investigating and improving the specificity of ribozymes directed against the bcr-abl translocation. Leukemia 10:1676
Jankowsky E, Gross CH, Shuman S, Pyle AM (2000) The DExH protein NPH-II is a processive and directional motor for unwinding RNA. Nature 403:447–451
Kanamori T, Nishimaki K, Asoh S, Ishibashi Y, Takata I, Kuwabara T, Taira K, Yamaguchi H, Sugihara S, Yamazaki T, Ihara Y, Nakano K, Matuda S, Ohta S (2003) Truncated product of the bifunctional DLST gene involved in biogenesis of the respiratory chain. Embo J 22:2913–2923
Kang Y, Cullen BR (1999) The human Tap protein is a nuclear mRNA export factor that contains novel RNA-binding and nucleocytoplasmic transport sequences. Genes Dev 13:1126–1139
Kasim V, Miyagishi M, Taira K (2004) Control of siRNA expression using the Cre-loxP recombination system. Nucleic Acids Res 32:e66
Kato Y, Taira K (2003) Expression of siRNA from a single transcript that includes multiple ribozymes in mammalian cells. Oligonucleotides 13:335–343
Kato Y, Kuwabara T, Warashina M, Toda H, Taira K (2001) Relationships between the activities in vitro and in vivo of various kinds of ribozyme and their intracellular localization in mammalian cells. J Biol Chem 276:15378–15385
Katoh T, Susa M, Suzuki T, Umeda N, Watanabe K (2003) Simple and rapid synthesis of siRNA derived from in vitro transcribed shRNA. Nucleic Acids Res Suppl:249–250
Kawasaki H, Taira K (2002a) Identification of genes by hybrid ribozymes that couple cleavage activity with the unwinding activity of an endogenous RNA helicase. EMBO Rep 3:443–450
Kawasaki H, Taira K (2002b) A functional gene discovery in the Fas-mediated pathway to apoptosis by analysis of transiently expressed randomized hybrid-ribozyme libraries. Nucleic Acids Res 30:3609–3614
Kawasaki H, Taira K (2003) Short hairpin type of dsRNAs that are controlled by tRNA(Val) promoter significantly induce RNAi-mediated gene silencing in the cytoplasm of human cells. Nucleic Acids Res 31:700–707
Kawasaki H, Taira K (2004) Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature 431:211–217
Kawasaki H, Onuki R, Suyama E, Taira K (2002) Identification of genes that function in the TNF-alpha-mediated apoptotic pathway using randomized hybrid ribozyme libraries. Nat Biotechnol 20:376–380
Kawasaki H, Ohkawa J, Tanishige N, Yoshinari K, Murata T, Yokoyama KK, Taira K (1996) Selection of the best target site for ribozyme-mediated cleavage within a fusion gene for adenovirus E1A-associated 300kDa protein (p300) and luciferase. Nucleic Acids Res 24:3010–3016
Kawasaki H, Eckner R, Yao TP, Taira K, Chiu R, Livingston DM, Yokoyama KK (1998) Distinct roles of the co-activators p300 and CBP in retinoic-acid-induced F9-cell differentiation. Nature 393:284–289
Kay MA, Meuse L, Gown AM, Linsley P, Hollenbaugh D, Aruffo A, Ochs HD, Wilson CB (1997) Transient immunomodulation with anti-CD40 ligand antibody and CTLA4Ig enhances persistence and secondary adenovirus-mediated gene transfer into mouse liver. Proc Natl Acad Sci U S A 94:4686–4691
Ketting RF, Fischer SE, Bernstein E, Sijen T, Hannon GJ, Plasterk RH (2001) Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev 15:2654–2659
Khvorova A, Reynolds A, Jayasena SD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209–216
Koseki S, Ohkawa J, Yamamoto R, Takebe Y, Taira K (1998) A simple assay system for examination of the inhibitory potential in vivo of decoy RNAs, ribozymes and other drugs by measuring the Tat-mediated transcription of a fusion gene composed of the long terminal repeat of HIV-1 and a gene for luciferase. J Control Release 53:159–173
Koseki S, Tanabe T, Tani K, Asano S, Shioda T, Nagai Y, Shimada T, Ohkawa J, Taira K (1999) Factors governing the activity in vivo of ribozymes transcribed by RNA polymerase III. J Virol 73:1868–1877
Koszul R, Malpertuy A, Frangeul L, Bouchier C, Wincker P, Thierry A, Duthoy S, Ferris S, Hennequin C, Dujon B (2003) The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata. FEBS Lett 534:39–48
Kovesdi I, Brough DE, Bruder JT, Wickham TJ (1997) Adenoviral vectors for gene transfer. Curr Opin Biotechnol 8:583–589
Kutay U, Lipowsky G, Izaurralde E, Bischoff FR, Schwarzmaier P, Hartmann E, Gorlich D (1998) Identification of a tRNA-specific nuclear export receptor. Mol Cell 1:359–369
Kuwabara T, Warashina M, Taira K (2000a) Allosterically controllable ribozymes with biosensor functions. Curr Opin Chem Biol 4:669–677
Kuwabara T, Warashina M, Taira K (2000b) Allosterically controllable maxizymes cleave mRNA with high efficiency and specificity. Trends Biotechnol 18:462–468
Kuwabara T, Amontov SV, Warashina M, Ohkawa J, Taira K (1996) Characterization of several kinds of dimer minizyme: simultaneous cleavage at two sites in HIV-1 tat mRNA by dimer minizymes. Nucleic Acids Res 24:2302–2310
Kuwabara T, Warashina M, Nakayama A, Ohkawa J, Taira K (1999) tRNAVal-heterodimeric maxizymes with high potential as geneinactivating agents: simultaneous cleavage at two sites in HIV-1 Tat mRNA in cultured cells. Proc Natl Acad Sci USA 96:1886–1891
Kuwabara T, Hsieh J, Nakashima K, Taira K, Gage FH (2004) A small modulatory dsRNA specifies the fate of adult neural stem cells. Cell 116:779–793
Kuwabara T, Warashina M, Tanabe T, Tani K, Asano S, Taira K (1997) Comparison of the specificities and catalytic activities of hammerhead ribozymes and DNA enzymes with respect to the cleavage of BCR-ABL chimeric L6 (b2a2) mRNA. Nucleic Acids Res 25:3074–3081
Kuwabara T, Warashina M, Orita M, Koseki S, Ohkawa J, Taira K (1998a) Formation of a catalytically active dimer by tRNA(Val)-driven short ribozymes. Nat Biotechnol 16:961–965
Kuwabara T, Warashina M, Tanabe T, Tani K, Asano S, Taira K (1998b) A novel allosterically trans-activated ribozyme, the maxizyme, with exceptional specificity in vitro and in vivo. Mol Cell 2:617–627
Kuwabara T, Warashina M, Koseki S, Sano M, Ohkawa J, Nakayama K, Taira K (2001a) Significantly higher activity of a cytoplasmic hammerhead ribozyme than a corresponding nuclear counterpart: engineered tRNAs with an extended 3’ end can be exported efficiently and specifically to the cytoplasm in mammalian cells. Nucleic Acids Res 29:2780–2788
Kuwabara T, Warashina M, Sano M, Tang H, Wong-Staal F, Munekata E, Taira K (2001b) Recognition of engineered tRNAs with an extended 3’ end by Exportin-t (Xpo-t) and transport of tRNA-attached ribozymes to the cytoplasm in somatic cells. Biomacromolecules 2:1229–1242
Lee CG, Hurwitz J (1993) Human RNA helicase A is homologous to the maleless protein of Drosophila. J Biol Chem 268:16822–16830
Lee NS, Rossi JJ (2004) Control of HIV-1 replication by RNA interference. Virus Res 102:53–58
Lee NS, Dohjima T, Bauer G, Li H, Li MJ, Ehsani A, Salvaterra P, Rossi J (2002a) Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol 20:500–505
Lee Y, Jeon K, Lee JT, Kim S, Kim VN (2002b) MicroRNA maturation: stepwise processing and subcellular localization. Embo J 21:4663–4670
Li J, Tang H, Mullen TM, Westberg C, Reddy TR, Rose DW, Wong-Staal F (1999) A role for RNA helicase A in post-transcriptional regulation of HIV type 1. Proc Natl Acad Sci USA 96:709–714
Lipowsky G, Bischoff FR, Izaurralde E, Kutay U, Schafer S, Gross HJ, Beier H, Gorlich D (1999) Coordination of tRNA nuclear export with processing of tRNA. Rna 5:539–549
Lund E, Dahlberg JE (1998) Proofreading and aminoacylation of tRNAs before export from the nucleus. Science 282:2082–2085
McCall MJ, Hendry P, Jennings PA (1992) Minimal sequence requirements for ribozyme activity. Proc Natl Acad Sci U S A 89:5710–5714
McManus MT, Sharp PA (2002) Gene silencing in mammals by small interfering RNAs. Nat Rev Genet 3:737–747
Miller AD (2004) Nonviral liposomes. Methods Mol Med 90:107–137
Milner N, Mir KU, Southern EM (1997) Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nat Biotechnol 15:537–541
Mittal V (2004) Improving the efficiency of RNA interference in mammals. Nat Rev Genet 5:355–365
Miyagishi M, Taira K (2002) U6 promoter-driven siRNAs with four uridine 3’ overhangs efficiently suppress targeted gene expression in mammalian cells. Nat Biotechnol 20:497–500
Miyagishi M, Taira K (2003) Strategies for generation of an siRNA expression library directed against the human genome. Oligonucleotides 13:325–333
Miyagishi M, Matsumoto S, Taira K (2004a) Generation of an shRNAi expression library against the whole human transcripts. Virus Res 102:117–124
Miyagishi M, Sumimoto H, Miyoshi H, Kawakami Y, Taira K (2004b) Optimization of an siRNA-expression system with an improved hairpin and its significant suppressive effects in mammalian cells. J Gene Med 6:715–723
Morris KV, Chan SW, Jacobsen SE, Looney DJ (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305:1289–1292
Mountain A (2000) Gene therapy: the first decade. Trends Biotechnol 18:119–128
Muller AJ, Young JC, Pendergast AM, Pondel M, Landau NR, Littman DR, Witte ON (1991) BCR first exon sequences specifically activate the BCR/ABL tyrosine kinase oncogene of Philadelphia chromosome-positive human leukemias. Mol Cell Biol 11:1785–1792
Naldini L (1998) Lentiviruses as gene transfer agents for delivery to non-dividing cells. Curr Opin Biotechnol 9:457–463
Nawrot B, Antoszczyk S, Maszewska M, Kuwabara T, Warashina M, Taira K, Stec WJ (2003) Efficient inhibition of beta-secretase gene expression in HEK293 cells by tRNAVal-driven and CTE-helicase associated hammerhead ribozymes. Eur J Biochem 270:3962–3970
Nelson DL, Suyama E, Kawasaki H, Taira K (2003) Use of random ribozyme libraries for the rapid screening of apoptosis-and metastasis-related genes. Targets 2:191–200
Novina CD, Sharp PA (2004) The RNAi revolution. Nature 430:161–164
Nowell PC, Hungerford DA (1960) A minute chromosome in human chronic granulocytic leukemia. Science 132:1497–1499
Ohkawa J, Taira K (2000) Control of the functional activity of an antisense RNA by a tetracycline-responsive derivative of the human U6 snRNA promoter. Hum Gene Ther 11:577–585
Ohkawa J, Yuyama N, Takebe Y, Nishikawa S, Taira K (1993) Importance of independence in ribozyme reactions: kinetic behavior of trimmed and of simply connected multiple ribozymes with potential activity against human immunodeficiency virus. Proc Natl Acad Sci USA 90:11302–11306
Onuki R, Nagasaki A, Kawasaki H, Baba T, Uyeda TQ, Taira K (2002) Confirmation by FRET in individual living cells of the absence of significant amyloid beta-mediated caspase 8 activation. Proc Natl Acad Sci USA 99:14716–14721
Onuki R, Bando Y, Suyama E, Katayama T, Kawasaki H, Baba T, Tohyama M, Taira K (2004) An RNA-dependent protein kinase is involved in tunicamycin-induced apoptosis and Alzheimer’s disease. Embo J 23:959–968
Oshima K, Kawasaki H, Soda Y, Tani K, Asano S, Taira K (2003) Maxizymes and small hairpin-type RNAs that are driven by a tRNA promoter specifically cleave a chimeric gene associated with leukemia in vitro and in vivo. Cancer Res 63:6809–6814
Pachuk CJ, Yoon K, Moelling K, Coney LR (1994) Selective cleavage of bcr-abl chimeric RNAs by a ribozyme targeted to non-contiguous sequences. Nucleic Acids Res 22:301–307
Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 16:948–958
Paddison PJ, Silva JM, Conklin DS, Schlabach M, Li M, Aruleba S, Balija V, O’Shaughnessy A, Gnoj L, Scobie K, Chang K, Westbrook T, Cleary M, Sachidanandam R, McCombie WR, Elledge SJ, Hannon GJ (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature 428:427–431
Pan WH, Xin P, Bui V, Clawson GA (2003) Rapid identification of efficient target cleavage sites using a hammerhead ribozyme library in an iterative manner. Mol Ther 7:129–139
Patzel V, Sczakiel G (1998) Theoretical design of antisense RNA structures sub-stantially improves annealing kinetics and efficacy in human cells. Nat Biotechnol 16:64–68
Paul CP, Good PD, Winer I, Engelke DR (2002) Effective expression of small interfering RNA in human cells. Nat Biotechnol 20:505–508
Rabinowitz JE, Samulski J (1998) Adeno-associated virus expression systems for gene transfer. Curr Opin Biotechnol 9:470–475
Rossi JJ (1995) Controlled, targeted, intracellular expression of ribozymes: progress and problems. Trends Biotechnol 13:301–306
Rossi JJ, Sarver N (1990) RNA enzymes (ribozymes) as antiviral therapeutic agents. Trends Biotechnol 8:179–183
Sarver N, Cantin EM, Chang PS, Zaia JA, Ladne PA, Stephens DA, Rossi JJ (1990) Ribozymes as potential anti-HIV-1 therapeutic agents. Science 247:1222–1225
Scherr M, Rossi JJ (1998) Rapid determination and quantitation of the accessibility to native RNAs by antisense oligodeoxynucleotides in murine cell extracts. Nucleic Acids Res 26:5079–5085
Scherr M, Reed M, Huang CF, Riggs AD, Rossi JJ (2000) Oligonucleotide scanning of native mRNAs in extracts predicts intracellular ribozyme efficiency: ribozyme-mediated reduction of the murine DNA methyltransferase. Mol Ther 2:26–38
Scherr M, Battmer K, Winkler T, Heidenreich O, Ganser A, Eder M (2003) Specific inhibition of bcr-abl gene expression by small interfering RNA. Blood 101:1566–1569
Scherr M, LeBon J, Castanotto D, Cunliffe HE, Meltzer PS, Ganser A, Riggs AD, Rossi JJ (2001) Detection of antisense and ribozyme accessible sites on native mRNAs: application to NCOA3 mRNA. Mol Ther 4:454–460
Schmitt C, von Kobbe C, Bachi A, Pante N, Rodrigues JP, Boscheron C, Rigaut G, Wilm M, Seraphin B, Carmo-Fonseca M, Izaurralde E (1999) Dbp5, a DEAD-box protein required for mRNA export, is recruited to the cytoplasmic fibrils of nuclear pore complex via a conserved interaction with CAN/Nup159p. Embo J 18:4332–4347
Schwarz DS, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115:199–208
Shimayama T, Nishikawa S, Taira K (1995) Generality of the NUX rule: kinetic analysis of the results of systematic mutations in the trinucleotide at the cleavage site of hammerhead ribozymes. Biochemistry 34:3649–3654
Shiota M, Sano M, Miyagishi M, Taira K (2004) Ribozymes: applications to functional analysis and gene discovery. J Biochem (Tokyo) 136:133–147
Shtivelman E, Lifshitz B, Gale RP, Roe BA, Canaani E (1986) Alternative splicing of RNAs transcribed from the human abl gene and from the bcr-abl fused gene. Cell 47:277–284
Sioud M, ed. (2004) Methods in Molecular Biology: Ribozymes and siRNA Protocols (Totowa, NJ, Humana Press)
Sledz CA, Holko M, de Veer MJ, Silverman RH, Williams BR (2003) Activation of the interferon system by short-interfering RNAs. Nat Cell Biol 5:834–839
Sui G, Soohoo C, Affar el B, Gay F, Shi Y, Forrester WC (2002) A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc Natl Acad Sci USA 99:5515–5520
Suyama E, Kawasaki H, Kasaoka T, Taira K (2003a) Identification of genes responsible for cell migration by a library of randomized ribozymes. Cancer Res 63:119–124
Suyama E, Kawasaki H, Nakajima M, Taira K (2003b) Identification of genes involved in cell invasion by using a library of randomized hybrid ribozymes. Proc Natl Acad Sci USA 100:5616–5621
Suyama E, Wadhwa R, Kaur K, Miyagishi M, Kaul SC, Kawasaki H, Taira K (2004) Identification of metastasis-related genes in a mouse model using a library of randomized ribozymes. J Biol Chem 279:38083–38086
Suzumura K, Takagi Y, Orita M, Taira K (2004) NMR-based reappraisal of the coordination of a metal ion at the pro-Rp oxygen of the A9/G10.1 site in a hammerhead ribozyme. J Am Chem Soc 126:15504–15511
Taira K, Miyagishi M (2001) siRNA expression system and method for producing functional gene knock-down cell using the system. Japanese Patent Application Heisei-13-363385 (PCT/JP02/12447)
Taira K, Miyagishi M (2003) Method and apparatus for predicting RNAi effect of siRNA. Japanese Patent Application PCT/JP2004/014758
Taira K, Miyagishi M, Akashi H (2004) Escape from the interferon response associated with RNA interference using vectors that encode long modified hairpin-RNA. Japanease Patent Application 2003-414591
Taira K, Nakagawa K, Nishikawa S, Furukawa K (1991) Construction of a novel RNA-transcript-trimming plasmid which can be used both in vitro in place of run-off and (G)-free transcriptions and in vivo as multi-sequences transcription vectors. Nucleic Acids Res 19:5125–5130
Taira K, Oda M, Shinshi H, Maeda H, Furukawa K (1990) Construction of a novel artificial-ribozyme-releasing plasmid. Protein Eng 3:733–737
Taira K, Warashina M, Kuwabara T, Kawasaki H (1999) Functional hybrid molecules with sliding ability. Japanese Patent Application
Takagi Y, Taira K (2002) Detection of a proton-transfer process by kinetic solvent isotope effects in NH(4)(+)-mediated reactions catalyzed by a hammerhead ribozyme. J Am Chem Soc 124:3850–3852
Takagi Y, Inoue A, Taira K (2004) Analysis on a cooperative pathway involving multiple cations in hammerhead reactions. J Am Chem Soc 126:12856–12864
Tanabe T, Kuwabara T, Warashina M, Tani K, Taira K, Asano S (2000a) Oncogene inactivation in a mouse model. Nature 406:473–474
Tanabe T, Takata I, Kuwabara T, Warashina M, Kawasaki H, Tani K, Ohta S, Asano S, Taira K (2000b) Maxizymes, novel allosterically controllable ribozymes, can be designed to cleave various substrates. Biomacromolecules 1:108–117
Tanaka Y, Kasai Y, Mochizuki S, Wakisaka A, Morita EH, Kojima C, Toyozawa A, Kondo Y, Taki M, Takagi Y, Inoue A, Yamasaki K, Taira K (2004) Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes. J Am Chem Soc 126:744–752
Tang H, Wong-Staal F (2000) Specific interaction between RNA helicase A and Tap, two cellular proteins that bind to the constitutive transport element of type D retrovirus. J Biol Chem 275:32694–32700
Tang H, Gaietta GM, Fischer WH, Ellisman MH, Wong-Staal F (1997) A cellular cofactor for the constitutive transport element of type D retrovirus. Science 276:1412–1415
Tiscornia G, Tergaonkar V, Galimi F, Verma IM (2004) CRE recombinase-inducible RNA interference mediated by lentiviral vectors. Proc Natl Acad Sci USA 101:7347–7351
Tuschl T (2002) Expanding small RNA interference. Nat Biotechnol 20:446–448
Tuschl T, Eckstein F (1993) Hammerhead ribozymes: importance of stem-loop II for activity. Proc Natl Acad Sci USA 90:6991–6994
Usman N, Blatt LM (2000) Nuclease-resistant synthetic ribozymes: developing a new class of therapeutics. J Clin Invest 106:1197–1202
van de Wetering M, Oving I, Muncan V, Pon Fong MT, Brantjes H, van Leenen D, Holstege FC, Brummelkamp TR, Agami R, Clevers H (2003) Specific inhibition of gene expression using a stably integrated, inducible small-interfering-RNA vector. EMBO Rep 4:609–615
Wadhwa R, Kaul SC, Miyagishi M, Taira K (2004) Vectors for RNA interference. Curr Opin Mol Ther 6:367–372
Wadhwa R, Ando H, Kawasaki H, Taira K, Kaul SC (2003) Targeting mortalin using conventional and RNA-helicase-coupled hammerhead ribozymes. EMBO Rep 4:595–601
Wagner JD, Jankowsky E, Company M, Pyle AM, Abelson JN (1998) The DEAH-box protein PRP22 is an ATPase that mediates ATP-dependent mRNA release from the spliceosome and unwinds RNA duplexes. Embo J 17:2926–2937
Warashina M, Kuwabara T, Nakamatsu Y, Takagi Y, Kato Y, Taira K (2004) Analysis of the conserved P9-G10.1 metal-binding motif in hammerhead ribozymes with an extra nucleotide inserted between A9 and G10.1 residues. J Am Chem Soc 126:12291–12297
Warashina M, Kuwabara T, Taira K (2000a) Working at the cutting edge: the creation of allosteric ribozymes. Structure Fold Des 8:R207–212
Warashina M, Takagi Y, Stec WJ, Taira K (2000b) Differences among mechanisms of ribozyme-catalyzed reactions. Curr Opin Biotechnol 11:354–362
Warashina M, Kuwabara T, Kato Y, Sano M, Taira K (2001) RNA-protein hybrid ribozymes that efficiently cleave any mRNA independently of the structure of the target RNA. Proc Natl Acad Sci USA 98:5572–5577
Welch PJ, Marcusson EG, Li QX, Beger C, Kruger M, Zhou C, Leavitt M, Wong-Staal F, Barber JR (2000) Identification and validation of a gene involved in anchorage-independent cell growth control using a library of randomized hairpin ribozymes. Genomics 66:274–283
Westberg C, Yang JP, Tang H, Reddy TR, Wong-Staal F (2000) A novel shuttle protein binds to RNA helicase A and activates the retroviral constitutive transport element. J Biol Chem 275:21396–21401
Wu N, Ataai MM (2000) Production of viral vectors for gene therapy applications. Curr Opin Biotechnol 11:205–208
Yang Y, Xiang Z, Ertl HC, Wilson JM (1995) Upregulation of class I major histocompatibility complex antigens by interferon gamma is necessary for T-cell-mediated elimination of recombinant adenovirus-infected hepatocytes in vivo. Proc Natl Acad Sci USA 92:7257–7261
Yokota T, Sakamoto N, Enomoto N, Tanabe Y, Miyagishi M, Maekawa S, Yi L, Kurosaki M, Taira K, Watanabe M, Mizusawa H (2003) Inhibition of intracellular hepatitis C virus replication by synthetic and vector-derived small interfering RNAs. EMBO Rep 4:602–608
Yoshinari K, Miyagishi M, Taira K (2004) Effects on RNAi of the tight structure, sequence and position of the targeted region. Nucleic Acids Res 32:691–699
Yu JY, DeRuiter SL, Turner DL (2002) RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc Natl Acad Sci USA 99:6047–6052
Yu M, Ojwang J, Yamada O, Hampel A, Rapapport J, Looney D, Wong-Staal F (1993) A hairpin ribozyme inhibits expression of diverse strains of human immunodeficiency virus type 1. Proc Natl Acad Sci USA 90:6340–6344
Zhou DM, Taira K (1998) The Hydrolysis of RNA: From Theoretical Calculations to the Hammerhead Ribozyme-Mediated Cleavage of RNA. Chem Rev 98:991–1026
Zuker M (1989) Computer prediction of RNA structure. Methods Enzymol 180:262–288
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Miyagishi, M., Taira, K. (2005). Design of Intracellularly Active Ribozymes and siRNAs. In: Taira, K., Kataoka, K., Niidome, T. (eds) Non-viral Gene Therapy. Springer, Tokyo. https://doi.org/10.1007/4-431-27879-6_30
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DOI: https://doi.org/10.1007/4-431-27879-6_30
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