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Kim, D. et al. Synthetic dsRNA Dicer substrates enhance RNAi potency and efficacy. Nat Biotechnol. 23, 222-226

Nature Biotechnology (Impact Factor: 39.08). 12/2004; 23(2):222-226. DOI: 10.1038/nbt1051
Source: PubMed

ABSTRACT RNA interference (RNAi) is the process of sequence-specific post-transcriptional gene silencing triggered by double-stranded RNAs1, 2, 3. In attempts to identify RNAi triggers that effectively function at lower concentrations, we found that synthetic RNA duplexes 25–30 nucleotides in length can be up to 100-fold more potent than corresponding conventional 21-mer small interfering RNAs (siRNAs). Some sites that are refractory to silencing by 21-mer siRNAs can be effectively targeted by 27-mer duplexes, with silencing lasting up to 10 d. Notably, the 27-mers do not induce interferon or activate protein kinase R (PKR). The enhanced potency of the longer duplexes is attributed to the fact that they are substrates of the Dicer endonuclease, directly linking the production of siRNAs to incorporation in the RNA-induced silencing complex. These results provide an alternative strategy for eliciting RNAi-mediated target cleavage using low concentrations of synthetic RNA as substrates for cellular Dicer-mediated cleavage.

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Available from: John J Rossi, Jun 22, 2015
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    • "In addition to sticky siRNA, competent Dicer substrate siRNA (dsiRNA) of 25–30 nt can be up to 100-fold more potent than conventional 21-mer duplex siRNA when targeted to the same sequence location (Kim et al., 2005). The increased potency of dsiRNA can be attributed to the fact that Dicer-generated 21–23-mer siRNAs are more efficiently incorporated into RISC through the physical association of Dicer with the TAR RNA-binding protein (TBRP) and Ago2 (Lee et al., 2004; Pham et al., 2004; Tomari et al., 2004). "
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    • "The kind of modifications to employ have to be chosen based on the design of the siRNA used, specific sequence, intended application, and method of delivery. Blunt-ended 27-nt dsRNAs, which are cleaved by Dicer to lead to the release of 21-nt siRNAs, exhibited a higher gene-silencing effect than 21-nt siRNAs (Kim et al. 2005). Dicer-substrate siRNA (DsiRNA), which is an asymmetric duplex RNA composed of a 25-nt sense strand with a blunt-end at the 3´-end and a 27- nt antisense stand with a 2-nt overhang at the 3´-end (25D/27-nt), could be directly cleaved by Dicer in a single 21-nt siRNA product, and exhibited a potent genesilencing effect (Amarzguioui et al. 2006). "
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    • "Today, a variety of siRNA design types are available for gene silencing each offering benefits and disadvantages (Figure 2): The by far most popular siRNA design mimics natural Dicer cleavage products and comprises a 21 nucleotide (nt) guiding strand antisense to a given RNA target and a complementary passenger strand annealed to form a siRNA duplex with a 19-bp dsRNA stem and 2 nt 3 overhangs at both ends (here referred to as canonical 21-mer siRNAs; Elbashir et al., 2001a,b). Longer design types, collectively referred to as Dicer-substrate siRNAs (DsiRNAs) structurally mimic various Dicer substrates to enhance incorporation into RNAi pathways and potentially siRNA potency (Kim et al., 2005; Rose et al., 2005; Siolas et al., 2005; Amarzguioui et al., 2006; Collingwood et al., 2008; Hefner et al., 2008; Tanudji et al., 2009). Also shorter or truncated siRNA designs are gaining popularity such as 16-mer siRNA (Chu and Rana, 2008), shRNAs with RNA stems ≤19 bp (Ge et al., 2009a,b), blunt 19-bp siRNAs (Czauderna et al., 2003; Prakash et al., 2005; Hogrefe et al., 2006; Ghosh et al., 2009), asymmetrical siRNAs (aiRNA; Sun et al., 2008), and asymmetric shorter-duplex siRNA (asiRNA; Chang et al., 2009). "
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