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SSD - a free software for designing multimeric mono-, bi- and trivalent shRNAs
Gabriel José de Carli1,2, Abdon Troche Rotela3,4, Greice Lubini2
1Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil.
Genetics and Molecular Biology
|March 7, 2020
Summary
A new free software tool, siRNA and shRNA designer (SSD), enables efficient design of multimeric RNA interference (RNAi) molecules for gene silencing. This tool facilitates single or multiple gene knockdown studies, proving effective in reducing target mRNA levels.
Area of Science:
- Molecular Biology
- Bioinformatics
- Genetics
Background:
- RNA interference (RNAi) is a crucial gene silencing mechanism.
- Applications include reverse genetics, therapeutics, and biotechnology.
- Efficient design of RNAi effectors is essential for research and development.
Purpose of the Study:
- To introduce siRNA and shRNA designer (SSD), a free software tool.
- To enable rational design of multimeric short hairpin RNAs (shRNAs).
- To facilitate large-scale production of RNAi molecules for gene knockdown.
Main Methods:
- SSD integrates Strand Analysis software for template DNA construction.
- Utilizes in vitro rolling circle transcription for multimeric shRNA production.
- Designed and tested a trivalent multimeric shRNA targeting the vitellogenin gene in Apis mellifera.
Main Results:
- The designed trivalent multimeric shRNA significantly reduced target mRNA by over 50%.
- Gene silencing effect was dose-dependent compared to control groups.
- SSD demonstrated effectiveness in designing functional multimeric shRNAs.
Conclusions:
- SSD software simplifies the design of multimeric shRNAs for single or multiple gene knockdowns.
- This tool is valuable for studies requiring large quantities of double-stranded RNA molecules.
- SSD enhances the utility of RNAi technology in various biological research areas.
