When performing RNAi experiments using siRNA duplexes, the first critical challenge is the design of efficient siRNA. Recent studies concerning the importance of mRNA accessibility in relation to the efficiency of siRNA silencing has led MWG Biotech to create an online design tool 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.

Author: Gerrit Schramm

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