Studies of a viral suppressor of RNA silencing p19-CFP fusion protein: a FRET-based probe for sensing double-stranded fluorophore tagged small RNAs.

Eukaryotes have evolved complex cellular responses to double-stranded RNA. One response that is highly conserved across many species is the RNA silencing pathway. Tombusviruses have evolved a mechanism to evade the RNA silencing pathway that involves a small protein, p19, that acts as a suppressor of RNA silencing. This protein binds specifically to small-interfering RNAs (siRNAs) with nanomolar affinity in a sequence-independent manner and with size selectivity. Here we demonstrate a new approach for rapidly determining the quantities of siRNA using fluorescence resonance energy transfer (FRET) between the Carnation Italian ringspot virus (CIRV) p19-CFP fusion protein and Cy3-labeled siRNA. The CIRV p19 fusion protein binds double-stranded siRNAs with nanomolar affinity as determined by FRET. [corrected]