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siRNA Design: It's All in the Algorithm

Chris Echeverri, Christoph Sachse, Andrew Walsh, Anne Grabner
Cenix BioScience GmbH
David Brown

Ambion, Inc.


RNA interference (RNAi) has become a powerful tool for understanding gene function. It is a cellular process wherein short double-stranded RNAs called short interfering RNAs (siRNAs) direct the degradation of transcripts containing sequence complementary to at least one of the siRNA strands [1,2]. siRNAs trigger RNA degradation through a protein complex referred to as the RNA Induced Silencing Complex (RISC) [3]. Most evidence indicates that the RISC contains only one of the two siRNA strands [4], suggesting that there is a step prior to, or during, the incorporation of the siRNA into the RISC that eliminates one of the siRNA strands [5]. Either siRNA strand can be taken up by the RISC [5,6], but the RISC can only direct degradation of cellular RNAs that are complementary to the bound siRNA. Recent work suggests that strand selection can be affected by the nucleotide composition of the siRNA [7,8]. It is therefore possible to select siRNA target sites that favor incorporation of the antisense siRNA strand into the RISC to increase the percentage of RISCs containing the correct targeting siRNA strand. This ultimately results in improved efficacy and specificity of the siRNA.


siRNA Design Algorithms
Several siRNA design algorithms have emerged over the last year cl
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