Computational prediction and biochemical characterization of novel RNA aptamers to Rift Valley fever virus nucleocapsid protein
A family of RNA aptamers selected for their ability to bind to a viral protein, but whose secondary structures were uncharacterized, was folded and numerically scored in silico. The predicted structural characteristics of randomly generated RNA sequences were pairwise compared to those of the bona fide aptamers. The novel in silico aptamers that clustered structurally using multidimensional scaling with the bona fide aptamers were synthesized in the laboratory for further investigation. The in silico aptamers displayed good binding characteristics to Rift Valley fever virus nucleocapsid protein in vitro. Several of the in silico aptamers exhibited antiviral activity when transfected into cells prior to infection with RVFV.
aptamers rift valley fever virus nucleocapsid protein rna structure prediction viral inhibition