PFRED: A computational platform for siRNA and antisense oligonucleotides design

Abstract

PFRED a software application for the design, analysis, and visualization of antisense oligonucleotides and siRNA is described. The software provides an intuitive user-interface for scientists to design a library of siRNA or antisense oligonucleotides that target a specific gene of interest. Moreover, the tool facilitates the incorporation of various design criteria that have been shown to be important for stability and potency. PFRED has been made available as an open-source project so the code can be easily modified to address the future needs of the oligonucleotide research community. A compiled version is available for downloading at https://github.com/pfred/pfred-gui/releases as a java Jar file. The source code and the links for downloading the precompiled version can be found at https://github.com/pfred .

The Challenges and Strategies of Antisense Oligonucleotide Drug Delivery

“…siRNA is double stranded, a feature that while making it more potent than ASOs also makes its design and manufacture more complex and costly, and more prone to inducing toxicities due to activation of innate immune response via Toll-like receptors and off-target effects [ 8 , 9 , 10 ]. Finally, the ease and accuracy with which ASO sequences can be customized allows virtually any mutated gene to be targeted, creating great progress in precision and personalized medicine [ 11 ]. Milasen, for example, is a 22-base ASO that was designed to treat a single six-year-old patient with Batten disease, a rare and fatal neurodegenerative disease.…”