siRNA and isRNA: two edges of one sword

RNA interference mediated by small interfering RNAs (siRNA) has emerged as a powerful tool to target specific knockdown of gene expression in cell culture. siRNA is now the gold standard technique to study gene function, and expectations for the development of new target-specific drugs are high. In addition to the gene-silencing activity of siRNA, a number of recent studies have pointed to immunological effects of siRNAs, including the induction of proinflammatory cytokines and type I interferon. There is good evidence that gene silencing and immunostimulation are two independent functional characteristics of RNA oligonucleotides. Immunorecognition of RNA depends on certain molecular features such as length, double- versus single-strand configuration, sequence motifs, and nucleoside modifications such as triphosphate residues. RNA-sensing immunoreceptors include three members of the Toll-like receptor (TLR) family (TLR3, TLR7, TLR8) and cytosolic RNA-binding proteins like PKR and the helicases RIG-I and Mda5. Detection of RNA molecules occurs during viral infection and triggers antiviral innate defense mechanisms including the induction of type I interferons (IFN-alpha, IFN-beta) and downregulation of gene expression. Type I interferon induction by synthetic siRNAs requires TLR7 and is sequence dependent, similar to the detection of CpG motifs in DNA by TLR9. Identification of the exact molecular mechanisms of immunorecognition of RNA will allow the development of methods to avoid immunostimulation of siRNA and the design of potent immunostimulatory RNA (isRNA) oligonucleotides, depending on the aim. Furthermore, the combination of both gene-silencing and immunostimulation in one RNA molecule may lead to novel drugs that use both functional activities of RNA as two edges of one sword for effective treatment of viral infection and cancer.