siRNA Design Including Secondary Structure Target Site Prediction
Poster Jan 09, 2006
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.
When there is a need to quickly analyze samples using a number of different PCR assays, it is likely that optimal conditions for each assay will not be the same. First, different assays often will require different annealing temperatures for their primers. In addition, amplicons may be designed to be of different lengths and therefore require varying durations of the extension step.READ MORE