SSD - a free software for designing multimeric mono- bi- andtrivalent shRNAs

摘要

RNA interference (RNAi) is a powerful gene silencing technology, widely used inanalyses of reverse genetics, development of therapeutic strategies andgeneration of biotechnological products. Here we present a free software toolfor the rational design of RNAi effectors, named siRNA and shRNA designer (SSD).SSD incorporates our previously developed software Strand Analysis to constructtemplate DNAs amenable for the large scale production of mono-, bi- andtrivalent multimeric shRNAs, via rolling circletranscription. We tested SSD by creating a trivalent multimeric shRNA againstthe vitellogenin gene of . RT-qPCR analysisrevealed that our molecule promoted a decrease in more than 50% of the targetmRNA, in a dose-dependent manner, when compared to the control group. Thus, SSDsoftware allows the easy design of multimeric shRNAs, for single or multiplesimultaneous knockdowns, which is especially interesting for studies involvinglarge amounts of double-stranded molecules.