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Killing the messenger: Short RNAs that silence gene expression. Cell Biol. 4: 457-467.
Wasi, S. (2003). RNA interference: Nature Pub. Group, pp. 1-4.
Zamore, P.D. (2002). Ancient pathways programmed by small RNAs. 1265-1269.
(2001). Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems. Natl.Acad.Sci. 9742-9747.
(2001). RNA interference is mediated by 21- and 22-nucleotide RNAs. 15: 188-200.
Elbashir. (2001). Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. 494-498.
(2001). Functional anatomy of siRNAs for mediating efficient RNAi in Drosophila melanogaster embryo lysate. 6877-6888.
Hamilton, A.J. and Baulcombe, D.C. (1999). A species of small antisense RNA in posttranscriptional gene silencing in plants. 950-952.
Analysis of gene function in somatic mammalian cells using small interfering RNAs. 199-213.
Functional siRNAs and miRNAs exhibit strand bias. 209-216.
Asymmetry in the assembly of the RNAi enzyme complex. 199-208. For knockdown to occur, the antisense strand must be loaded into the RISC.
(2000). An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells. 293-296.
(2001). Argonaute2, a link between genetic and biochemical analyses of RNAi. 1146-1150.
Martinez, J. and Tuschl, T. (2004). RISC is a 5' phophomonoester-producing RNA endonuclease. 975-980.
Schwarz, D. (2004). The RNA-induced silencing complex is a Mg(2+)-dependent endonuclease. 14: 787-791.
Chem. 279: 41815-41821.
Ambros, V. (2001). Development. Dicing up RNAs. 811-813.
Role for a bidentate ribonuclease in the initiation step of RNA interference. 363-366.
Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. 324-328.
(2002). Human Dicer preferentially cleaves dsRNAs at their termini without a requirement for ATP. 5875-5885.
A system for stable expression of short interfering RNAs in mammalian cells. 550-553.
(2003). Inducible shRNA expression for application in a prostate cancer mouse model. Acids Res. E127.
Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. 16: 948-958.
Tuschl, T. (2002). Expanding small RNA interference. 20: 446-448.
(2003). Adenoviral vectors expressing siRNAs for discovery and validation of gene function. 2325-2332.
(2003). Use of lentiviral vectors for delivery of small interfering RNA. 2: 206-210.
A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Natl.Acad.Sci. 1844-1848.
Bartel, D.P. (2004). MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297. This comprehensive review covers miRNAs from transcription to targets.
(2001). Identification of novel genes coding for small expressed RNAs. Science 294: 853-858. This paper identifies the abundant number of microRNA in Drosophila and humans.
MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms. Proc.Natl.Acad.Sci. USA 100: 9779-9784. This paper demonstrates that siRNA and miRNA can be functionally interchangeable.
Off-Target Effects
(2003). Expression profiling reveals off-target gene regulation by RNAi. Nat. Biotechnol. 21: 635-637. Microarray data reveal off-targets effects from siRNA.
(2004). Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA 10: 12-18. A large number of genes are shown to be non-specifically stimulated and repressed by synthetic siRNA.
(2003). Small RNAs with imperfect match to endogenous mRNA repress translation: Implications for off-target activity of siRNA in mammalian cells. J. Biol.Chem. 278: 44312-44319. Discusses implications of off-target activation of the translational repression pathway of miRNA by siRNA.
Non-Specific Effects – Induction of the Interferon Pathway
(2003). Induction of an interferon response by RNAi vectors in mammalian cells. Nat. Genet. 34: 263-264. shRNA expressed from a plasmid vector can induce the interferon pathway.
Moss, E.G. and Taylor, J.M. (2003). Small-interfering RNAs in the radar of the interferon system. Nat. Cell Biol. 5: 771-772. This commentary summarizes the findings of the Sledz et al. paper.
Pebernard, S. and Iggo, R.D. (2004). Determinants of interferon-stimulated gene induction by RNAi vectors. Differentiation 72: 103-111. An extension of the Bridge et al. paper showing that interferon stimulation from U6-based vectors occurs when adenosines are present in the -1/+1 positions.
Note: pENTR™/U6 constructs designed at https://rnaidesigner.lifetechnologies.com do not have this motif.
(2003). Activation of the interferon system by short-interfering RNAs. Nat. Cell Biol. 5: 834-839. Synthetic siRNA are capable of activating the interferon pathway.
Editors (2003). Whither RNAi? Nat. Cell Biol. 5: 489-490. Provides recommendations for the necessary controls to include in RNAi experiments.
(2002). Confirming specificity of RNAi in mammalian cells. Sci. STKE 2002(147): PL13. Discusses the importance of using a “rescue” vector control to confirm specificity of the knockdown phenotype.