Asymmetrically designed siRNAs and shRNAs enhance the strand specificity and efficacy in RNAi

RNAi can mediate allele-specific silencing, and offers an attractive approach for treatment of human diseases caused by dominant, gain-of-function gene mutations. However, allele-specific silencing requires that the RNAi target the mutated region of the mRNA, limiting the choices of the target sequences. This often results in the use of a suboptimal siRNAs or shRNAs. Unfavorable strand asymmetry, which leads to the sense strand rather than the antisense strand to be incorporated into RNA-induced silencing complex (RISC), can cause poor RNAi efficacy. We systematically tested an approach that places mismatches at or near the 5′ of the antisense strand to create favorable strand asymmetry. Here we show that this approach can enhance the RNAi efficacy of not only siRNAs but also shRNAs synthesized from genes, which can be placed in various viral vectors. Thus, this design of asymmetric shRNAs could be potentially used in silencing dominant, gain-of-function gene mutations for gene therapy.