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Methods Mol Biol. 2009;487:41-59. doi: 10.1007/978-1-60327-547-7_2.

Deciphering the code of innate immunity recognition of siRNAs.

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Department of Immunology, Institute for Cancer Research, The Norwegian Radium Hospital, University of Oslo, Norway.


Small interfering RNAs (siRNAs) have been widely used for knocking down gene expression in a variety of organisms. Although experiments in cancer cell lines indicate that siRNAs are usually not detected by innate immunity, lipid-mediated delivery of siRNAs into blood cells is often accompanied by the activation of immunity. Recent studies indicated that certain siRNA sequences engage Toll-like receptor TLR7/8 signalling resulting in the activation of a large number of host defense genes including interferons (IFNs), proinflammatory cytokines, Mx proteins, chemokines, chemokine receptors, costimulatory molecules, RNA helicases, galectins, and ubiqitin ligases. In addition to immune activation, most siRNA sequences, if not all, can silence multiple genes in addition to the intended target gene, a phenomenon known as "off-target effects." Hence, one of the major challenges for therapeutic applications of siRNAs is to decipher the mechanisms involved in siRNA recognition by the immune system and to identify strategies that can evade immune activation. In this respect, the replacement of only uridines with their 2'-modified counterparts such as 2'-O-methyl uridines abrogates immune recognition of siRNAs. Interestingly, 2'-O-methyl-modified RNAs not only evade TLR7/8-sensing pathways, but also reduce siRNA off-target effects and antagonize with a variety of immunostimulatory RNAs to activate TLR7/8 signalling. RNA oligonucleotides and duplex siRNAs with 2'-deoxy uridines or thymidines exhibited no significant immunostimulatory effects and binding potency to TLRs. Therefore, I recommend the use of these modifications in order to evade immune sensing of siRNA and off-target effects. This chapter addresses the current state of knowledge regarding the molecular and cellular mechanisms of RNA recognition by the immune system and proposes a range of strategies allowing the design of siRNAs with minimal or maximal immunostimulatory potency for therapeutic applications.

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