Enhancing RNAi with Synthetic RNA Duplexes

RNA interference (RNAi) is an evolutionarily conserved process by which specific mRNAs are targeted for degradation by complementary small interfering RNAs (siRNAs). It has become the method of choice for mammalian cell genetics and as a potential sequence-specific therapeutic approach (Sharp 1999; Hannon 2002; Hutvagner and Zamore 2002). Long double-stranded (ds) RNAs are degraded by the RNase III class endonuclease Dicer into 21- to 23-nt duplexes that have 2-base 3’-overhangs (Zamore et al. 2000; Bernstein et al. 2001). Dicer’s primary role in RNAi is the endonucleolytic processing of long dsRNAs into short 21- to 23-mer effector molecules (siRNAs) (Bernstein et al. 2001; Ketting et al. 2001). Dicer is also involved in the early steps of RNA induced silencing complex (RISC) complex formation and may be required for entry of the siRNA into RISC (Lee et al. 2004; Pham et al. 2004). In Drosophila, the protein R2D2 associates with Dicer (specifically Dicer-2) and binds siRNAs prior to entry into RISC (Liu et al. 2003). Although no functional homologue for R2D2 has been identified in mammals, a similar link is assumed to exist between the Dicer cleavage step and entry into RISC in mammalian cells. Human Dicer has been cloned and characterized (Zhang et al. 2002). Interestingly, while the recombinant enzyme can be used to process long dsRNA into functional siRNAs, the process is slow and complete “dicing” of a substrate in vitro can take 24h incubation (Zhang et al. 2002). Thus, other factors must be involved in promoting rapid Dicer cleavage in vivo.