An equally important criterion for a high quality siRNA is its specificity. It is now well established that siRNAs are co-silencing other transcripts beside their target-genes. These so-called off-target effects arise mostly from partial homologies of the siRNA sequence to other mRNAs. esiRNAs possess excellent silencing specificities and produce very few off-target effects. A possible explanation for the increased specificity lays in the complexity of the esiRNA pool. The high numbers of different siRNAs in the mixture share the same on-target but differ in their sequence-dependent off-target signatures. As a consequence, many individual siRNAs add to the overall silencing of the target, while off-target effects are diluted out.

Microarray analysis of the specificity of esiRNAs compared to siRNAs.