siRNA Design Including Secondary Structure Target Site Prediction
AbstractWhen performing RNAi experiments using siRNAduplexes, the first critical challenge is the design ofefficient siRNA. Recent studies concerning the importanceof mRNA accessibility in relation to the efficiency of siRNAsilencing has led MWG Biotech to create an online designtool allowing researchers to view the mRNA target site.
Preliminary data underlines the correlation between the siRNA knockdown efficiency and the local free energy of the mRNA target site. There is a strong evidence that considering the mRNA secondary structure within the siRNA design algorithm will lead to more efficient siRNAs.