Skip to main content

Your siRNA results are probably rubbish

Wednesday, November 06, 2013 — Poster Session I

4:00 p.m. – 6:00 p.m.

FAES Academic Center (Upper-Level Terrace)




  • E.C. Buehler
  • Y. Chen
  • S.E. Martin


Small interfering RNAs have become a ubiquitous experimental tool. Unfortunately, off-target effects are a significant source of false positives in siRNA experiments and an effective control for them has not previously been identified. We introduce C911, a method of mismatched siRNA design for negative controls based on changing bases 9 through 11 of the siRNA to their complement bases. To evaluate these controls, a test set of 20 highly active siRNAs (10 true positives and 10 false positives) was identified from a genome-wide screen. Controls were then synthesized for each of these 20 siRNAs, the first using the C911 method and the second being a simple random permutation of the sequence (scrambled siRNA). When tested in the original assay, the scrambled siRNAs showed significantly reduced activity in comparison to the original siRNAs, regardless of whether they had been identified as true or false positives, indicating that they have little utility as experimental controls. In contrast, the C911 controls were able to completely distinguish between the two groups. The ability of control siRNAs to distinguish between true and false positives, if widely adopted, could reduce erroneous results being reported in the literature and save research dollars spent on expensive follow-up experiments.

back to top