siRNA Design Principles and Off-Target Effects
Short interfering RNAs (siRNAs) are a major research tool that allows for knock-down of target genes via selective mRNA destruction in almost all eukaryotic organisms. siRNAs typically consist of a synthetic ∼21 nucleotide (nt) RNA-duplex where one strand is designed with perfect complementarity to the target mRNA. Although siRNAs were initially thought to be very target-specific because of their design, it turned out during the last years that all siRNAs have a more or less pronounced intrinsic off-target activity which can make the interpretation of data from siRNA experiments difficult. Here we describe essential rules for siRNA design that should be taken into account in order to obtain potent siRNAs with minimal off-target activity. In addition, we describe how to control for off-target activity in siRNA experiments.
Key wordssiRNA Argonaute proteins siRNA off-target activity siRNA on-target activity siRNA design siRNA modifications
Our research is supported in part by the BMBF (NGFN+, FKZ PIM-01GS0804-5 to G.M.), the Bavarian Genome Research Network (BayGene to G.M.), the Deutsche Forschungsgemeinschaft (DFG), and Roche Kulmbach GmbH. S.P. received a fellowship from the Roche Postdoc Fellowship Program.
- 43.Addepalli H, Meena, Peng CG et al (2010) Modulation of thermal stability can enhance the potency of siRNA. Nucleic Acids Res 38:7320–7331Google Scholar
- 50.Caffrey DR, Zhao J, Song Z et al (2011) siRNA off-target effects can be reduced at concentrations that match their individual potency. PLoS One 6:e21503Google Scholar