Sequence specific off-target effects are one of the primary reasons for false positive results in RNAi experiments. In addition to the potency improvements afforded by the new algorithm and state-of-the-art bioinformatic filtering criteria, Silencer Select siRNAs incorporate novel modifications demonstrated to improve siRNA specificity.

Silencer Select siRNA Modifications Reduce the Number of Off-target, Differentially Expressed Genes.

Three negative control siRNAs with and without the Silencer Select modifications were individually transfected in quadruplicate into HeLa cells at 30 nM. RNA was extracted and analyzed on an Affymetrix Human Genome U133 Plus 2.0 Array in triplicate. The y-axis indicates the average number of differentially expressed genes — those showing ≥2-fold change in expression versus mock transfected samples

Silencer Select siRNA Modifications Reduce Off-target Effects and Yield More Reliable Phenotypic Data.
53 different siRNAs, including older designs previously noted to elicit offtarget phenotypes, were transfected into U2OS cells at 30 nM in both unmodified and Silencer Select modified formats. Mitosis and apoptosis were measured 48 hours later. Data is expressed relative to negative control siRNA transfected cells. Black = similar mitosis/apoptosis levels as control. Green = down-regulation. Red = up-regulation. Note that the expected mitotosis and apoptosis phenotypes for PLK and WEE1 siRNAs are preserved with the modifications. In contrast the off-target apoptotic phenotypes elicited by 10 unmodified siRNAs were completely eliminated with addition of the Silencer Select modifications.

The Chemical Modifications in Silencer Select siRNAs

  • Reduce the number of non-targeted, differentially expressed genes detected by gene expression array by up to 90% as compared to unmodified siRNAs
  • Result in a dramatic reduction of off-target phenotypes as measured by multi-parametric cell-based assays
  • Do not negatively impact silencing efficiency and therefore do not compromise the expected on-target phenotypes
  • Yield cleaner, more consistent cell biology data