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.
A medida que los análisis de grandes volúmenes de datos y el uso de técnicas multi-ómicas se están generalizando, la competencia en el pensamiento computacional es una destreza esencial como parte del conjunto de herramientas de un científico que trabaja con datos biológicos. Todos los estudios de "ómicas" requieren biología computacional: la implementación de análisis requiere habilidades de programación, mientras que el diseño experimental y la interpretación requieren una sólida comprensión del enfoque analítico. Aunque los núcleos académicos, los servicios comerciales y las colaboraciones pueden ayudar en la implementación de los análisis, los conocimientos computacionales necesarios para diseñar e interpretar los estudios ómicos no pueden ser reemplazados o complementados. Sin embargo, muchos profesionales de biociencias están exclusivamente entrenados en técnicas experimentales.
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