LITERATURE OF siRNA RESEARCH

• Bernstein, E., A.A. Caudy, S.M. Hammond and G.J. Hannon. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409:363-366.
• Bohula, E. et al. (2003) The Efficacy of Small Interfering RNAs Targeted to the Type 1 Insulin-like Growth Factor Receptor (IGF1R) Is Influenced by Secondary Structure in the IGF1R Transcript J. Biol. Chem. 278, 15991-15997.
• Boutla, A., C. Delidakis, I. Livadaras, M. Tsagris and M. Tabler. 2001. Short 5'-phosphorylated double-stranded RNAs induce RNA interference in Drosophila. Curr Biol 11:1776-1780.
• Brown, D., Jarvis, R., Pallotta, V., Byrom, M., and Ford, L. (2002) RNA interference in mammalian cell culture: design, execution, and analysis of the siRNA effect. Ambion TechNotes 9(1): 3-5.
• Brummelkamp, T.R., Bernards, R., and Agami, R. (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296: 550-553.
• Caplen, N.J., S. Parrish, F. Imani, A. Fire and R.A. Morgan. 2001. Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Proc Natl Acad Sci U S A 98:9742-9747.
• Castanotto, D.et al. (2002) Functional siRNA expression from transfected PCR products. RNA 8, 1454-60.
• Chi, J.et al. (2003) Genomewide view of gene silencing by small interfering RNAs. Proc. Natl. Acad. Sci. U.S.A. 100, 6343-6.
• Cogoni, C., N. Romano and G. Macino. 1994. Suppression of gene expression by homologous transgenes. Antonie Van Leeuwenhoek 65:205-209.
• Czauderna, F. et al. (2003) Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells. Nucl. Acids Res. 31, 2705-16.
• Dykxhoorn, D. et al. (2003) Killing the messenger: short RNAs that silence gene expression. Nature Reviews 4, 457-467.
• Editors of Nature Cell Biology (2003) Whither RNAi? Nat Cell Biol. 5:489-490.
• Elbashir SM, Martinez J, Patkaniowska A, Lendeckel W, Tuschl T (2001) Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. EMBO J. 20(23): 6877-­88.
• Elbashir, S. et al. (2002) Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods 26, 99-213.
• Elbashir, S.M., J. Harborth, W. Lendeckel, A. Yalcin, K. Weber and T. Tuschl. 2001. Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411:494-498.
• 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(6669): 806­11.
• Grishok, A., A.E. Pasquinelli, D. Conte, N. Li, S. Parrish, I. Ha, D.L. Baillie, A. Fire, G. Ruvkun and C.C. Mello. 2001. Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing. Cell 106:23-34.
• Hamilton, A.J. and D.C. Baulcombe. 1999. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286:950-952.
• Hammond, S.M., E. Bernstein, D. Beach and G.J. Hannon. 2000. An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. Nature 404:293-296.
• Hohjoh H. (2004) Enhancement of RNAi activity by improved siRNA duplexes. FEBS Lett. 557, 193-8
• Holen, T.et al. (2002) Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucl. Acids Res. 30, 1757-66.
• Hutvagner, G., J. McLachlan, A.E. Pasquinelli, E. Balint, T. Tuschl and P.D. Zamore. 2001. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293:834-838.
• Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, Mao M, Li B, Cavet G, Linsley PS (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol. 21(6): 635­7.
• Jacque, J.-M., Triques, K., and Stevenson, M. (2002) Modulation of HIV-1 replication by RNA interference. Nature 418 : 435-438.
• Kawasaki, H. and 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. 15, 700-707.
• Ketting, R.F., T.H. Haverkamp, H.G. van Luenen and R.H. Plasterk. 1999. Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD. Cell 99:133-141.
• Khvorova A, Reynolds A, Jayasena JD (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115(2): 209-­16.
• Knight, S.W. and B.L. Bass. 2001. A role for the RNase III enzyme DCR-1 in RNA interference and germ line development in Caenorhabditis elegans. Science 293:2269-2271.
• Lee, N.S., Dohjima, T., Bauer, G., Li, H., Li, M.-J., Ehsani, A., Salvaterra, P., and Rossi, J. (2002) Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature Biotechnology 20 : 500-505.
• Martinez J, Patkaniowska A, Urlaub H, Luhrmann R, Tuschl T (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110(5): 563­74.
• Miyagishi, M., and Taira, K. (2002) U6 promoter-driven siRNAs with four uridine 3' overhangs effectively suppress targeted gene expression in mammalian cells. Nature Biotechnology 20 : 497-500.
• Napoli, C., C. Lemieux and R. Jorgensen. 1990. Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. Plant Cell 2:279-289.
• Nykanen A, Haley B, Zamore PD (2001) ATP requirements and small interfering RNA structure in the RNA interference pathway. Cell 107(3): 309­21.
• Paddison, P.J., Caudy, A.A., Berstein, E., Hannon, G.J., and Conklin, D.S. (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Devel. 16: 948-958.
• Parrish, S., J. Fleenor, S. Xu, C. Mello and A. Fire. 2000. Functional anatomy of a dsRNA trigger: differential requirement for the two trigger strands in RNA interference. Mol Cell 6:1077-1087.
• Paul, C.P., Good, P.D., Winer, I., and Engelke, D.R. (2002) Effective expression of small interfering RNA in human cells. Nature Biotechnology 20 : 505-508.
• Persengiev SP, Zhu X, Green MR (2004) Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA 10(1): 12­18
• Reynolds A et al. (2004) Rational siRNA design for RNA interference. Nature Biotechnology 22:326-330
• Romano, N. and G. Macino. 1992. Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 6:3343-3353.
• Scherr, M. et al. (2003) Gene silencing mediated by small interfering RNAs in mammalian cells.
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• Schwarz D, Hutvagner G, Du T, Xu Z, Aronin N, Zamore PD (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell 115(2): 199­-208.
• Semizarov, D. et al. (2003) Specificity of short interfering RNA determined through gene expression signatures. Proc. Natl. Acad. Sci. U.S.A. 100, 6347-52.
• Sijen, T., J. Fleenor, F. Simmer, K.L. Thijssen, S. Parrish, L. Timmons, R.H. Plasterk and A. Fire. 2001. On the role of RNA amplification in dsRNA-triggered gene silencing. Cell 107:465-476.
• Sui, G., Soohoo, C., Affar, E.B., Gay, F., Shi, Y., Forrester, W.C., and Shi, Y. (2002) A DNA vector-based RNAi technology to suppress gene expression in mammalian cells. Proc. Natl. Acad. Sci. US A 99(8): 5515-5520.
• Tabara, H., M. Sarkissian, W.G. Kelly, J. Fleenor, A. Grishok, L. Timmons, A. Fire and C.C. Mello. 1999. The rde-1 gene, RNA interference, and transposon silencing in C. elegans. Cell 99:123-132.
• Tuschl T, Zamore PD, Lehmann R, Bartel DP, Sharp PA (1999) Targeted mRNA degradation by double-stranded RNA in vitro. Genes Dev 13(24): 3191­7.
• Ui-Tei, K. et al. (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference Nucleic Acids Res. 32, 936-948
• Ui-Tei, K., S. Zenno, Y. Miyata and K. Saigo. 2000. Sensitive assay of RNA interference in Drosophila and Chinese hamster cultured cells using firefly luciferase gene as target. FEBS Lett 479:79-82.
• Vickers, T. et al. (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis.J. Biol. Chem. 278, 7108-18.
• Xia T. et al. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37, 14719-35.
• Yu, J.-Y., DeRuiter, S.L., and Turner, D.L. (2002) RNA interference by expression of short-interfering RNAs and hairpin RNAs in mammalian cells. Proc. Natl. Acad. Sci. USA 99(9) : 6047-6052.
• Zamore PD, Tuschl T, Sharp PA, Bartel DP (2000) RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101(1): 25­33.