SSD - a free software for designing multimeric mono-, bi- and trivalent shRNAs

RNA interference (RNAi) is a powerful gene silencing technology, widely used in analyses of reverse genetics, development of therapeutic strategies and generation of biotechnological products. Here we present a free software tool for the rational design of RNAi effectors, named siRNA and shRNA desig...

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Veröffentlicht in:Genetics and molecular biology 2020-01, Vol.43 (1), p.e20190300-e20190300
Hauptverfasser: Carli, Gabriel José de, Rotela, Abdon Troche, Lubini, Greice, Contiliani, Danyel Fernandes, Candia, Nidia Benítez, Depintor, Thiago S, Abreu, Fabiano Carlos Pinto de, Simões, Zilá Luz Paulino, Ríos, Danilo Fernández, Pereira, Tiago Campos
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Sprache:eng
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Zusammenfassung:RNA interference (RNAi) is a powerful gene silencing technology, widely used in analyses of reverse genetics, development of therapeutic strategies and generation of biotechnological products. Here we present a free software tool for the rational design of RNAi effectors, named siRNA and shRNA designer (SSD). SSD incorporates our previously developed software Strand Analysis to construct template DNAs amenable for the large scale production of mono-, bi- and trivalent multimeric shRNAs, via in vitro rolling circle transcription. We tested SSD by creating a trivalent multimeric shRNA against the vitellogenin gene of Apis mellifera. RT-qPCR analysis revealed that our molecule promoted a decrease in more than 50% of the target mRNA, in a dose-dependent manner, when compared to the control group. Thus, SSD software allows the easy design of multimeric shRNAs, for single or multiple simultaneous knockdowns, which is especially interesting for studies involving large amounts of double-stranded molecules.
ISSN:1415-4757
1678-4685
1678-4685
DOI:10.1590/1678-4685-GMB-2019-0300