Design of small interfering RNAs for antiviral applications

RNA interference (RNAi) is an evolutionarily conserved mechanism for sequence-specific target RNA degradation in animals and plants, which plays an essential role in gene regulation. In addition, it is believed to function as a defense against viruses and transposons. In recent years, RNAi has become a widely used approach for studying gene function by targeted cleavage of a specific RNA. Moreover, the technology has been developed as a new therapeutic option that has already made its way into clinical testing. Treatment of viral infections remains a serious challenge due to the emergence of new viruses and strain variation among known virus species. RNAi holds great promise to provide a flexible approach that can rapidly be adapted to new viral target sequences. A major challenge in the development of an efficient RNAi approach still remains the design of small interfering RNAs (siRNAs) with high silencing potency. While large libraries with validated siRNAs exist for silencing of endogenously expressed genes in human or murine cells, siRNAs still have to be designed individually for new antiviral approaches. The present chapter describes strategies to design highly potent siRNAs by taking into consideration thermodynamic features of the siRNA, as well as the structural restrictions of the target RNA. Furthermore, assays for testing the siRNAs in reporter assays as well as options to improve the properties of siRNAs by the introduction of modified nucleotides will be described. Finally, experimental setups will be outlined to test the siRNAs in assays with infectious viruses.