The C911 siRNA control generated a lot of excitement in the RNAi world when it emerged ~11 years ago. A former colleague, who was a pioneer in the commercialisation of RNAi, described it then as the biggest breakthrough in the last 10 years of RNAi research.
The idea of the C911 control is to get rid of the on-target effect of the siRNA by using the complement of bases 9-11, while retaining any off-target (seed-based) effects of the siRNA, which are mostly dictated by the bases in positions 2-8.
If the observed phenotype of the siRNA is due to an off-target effect (rather than silencing of the on-target gene), the C911 version will show the same phenotype. i.e., because it is not silencing the target gene, the phenotype must come from an off-target effect.
Despite the initial excitement, the C911 approach did not become that widely used. There are a number of drawbacks to the strategy, perhaps foremost being that new reagents must be ordered and the assay set up to run again. We’ve compared the validation of low-complexity RNAi reagents to the old lady who swallowed a fly.
The best strategy is to avoid getting entangled in off-targets in the first place. And that seems to be the approach preferred by the research community.
The following plot shows Google Scholar citations for siTOOLs (i.e., papers using our reagents) and the C911 method paper.
We see that after an initial adoption period, use of C911s tapered off and it has levelled out in recent years.
None of this suggests that C911s are bad. For single siRNAs or Dharmacon pools, they are indeed an effective control. But the inconvenience of the method has probably hindered its adoption.
The convenience and robustness of the siPOOL are its great advantages. The siPOOL approach ensures maximum on-target silencing and a minimum of off-target effects. We look forward to supporting more great research in the coming years.