Hi! I have used an online program to produce siRNAs for a custom target. I seem to be getting some sort of off-target silencing with some of my siRNAs. I was wondering if anyone knows of a free program available online that will allow me to input both my target plasmid vector and my siRNA sequence to pinpoint possible places where I might have a slight mismatch that may be producing unwanted silencing. Does anyone know of such an "in-silico" program? Finding ones to design the siRNA is not a problem, this is more specific though.
RNAhybrid (https://bibiserv.cebitec.uni-bielefeld.de/rnahybrid?id=rnahybrid_view_submission) is a widely used software tool for predicting the hybridization potential of an siRNA with its target mRNA and potential off-target mRNAs. It allows you to input both the siRNA sequence and the target sequence and provides information on the predicted binding sites and binding energies.
RNA22 (https://cm.jefferson.edu/rna22/) is a program specifically designed for identifying potential microRNA binding sites, but it can also be useful for identifying siRNA off-target sites.
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