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

Gabriel José De Carli,Thiago S Depintor,Danilo Fernández Ríos,Tiago Campos Pereira,Zilá Luz Paulino Simões,Abdon Troche Rotela,Fabiano Carlos Pinto De Abreu,Greice Lubini,Nidia Benítez Candia,Danyel Fernandes Contiliani

doi:10.1590/1678-4685-gmb-2019-0300

Gabriel José De Carli, Thiago S Depintor + Show 8 more

Open Access

https://doi.org/10.1590/1678-4685-gmb-2019-0300

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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.

Highlights

RNA interference (RNAi) is a gene silencing technology (Fire et al, 1998) with broad applications, from reverse genetics and functional genomics (Suzuki et al, 2018), to treating diseases (Matthiesen et al, 2019), combating cancer (Ganesh et al, 2018), generating animal models (Guerreo-Rubio et al, 2019) and biotechnological products (Metwali et al, 2015)
In the last decade, such multimeric shRNAs generated by rolling circle transcription have been used by other groups and have been shown to be an interesting option for RNAi (Wang et al, 2015; Shopsowitz et al, 2016; Wu et al, 2016; Kim et al, 2018)
Once the small interfering RNAs (siRNAs) duplex is determined, siRNA and multimeric shRNA designer” (SSD) can generate a DNA sequence whose transcription will result in the multimeric shRNAs (mshRNAs)

Summary

Introduction

RNA interference (RNAi) is a gene silencing technology (Fire et al, 1998) with broad applications, from reverse genetics and functional genomics (Suzuki et al, 2018), to treating diseases (Matthiesen et al, 2019), combating cancer (Ganesh et al, 2018), generating animal models (Guerreo-Rubio et al, 2019) and biotechnological products (Metwali et al, 2015). We present a software tool for a fast and rational design of siRNAs and mshRNAs named “siRNA and multimeric shRNA designer” (SSD) (Figure 1). SSD incorporates the siRNA design tool from our previously developed software Strand Analysis (Pereira et al, 2007), since the design of mshRNAs requires siRNA sequences as input.

Results

Conclusion