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

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

Abstract 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.

Saved in:
Bibliographic Details
Main Authors: 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
Format: Digital revista
Language:English
Published: Sociedade Brasileira de Genética 2020
Online Access:http://old.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572020000100802
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Abstract 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.

Similar Items