Dissection of specific binding of HIV-1 Gag to the 'packaging signal' in viral RNA

Selective packaging of HIV-1 genomic RNA (gRNA) requires the presence of a cis acting RNA element called the 'packaging signal' (psi). However, the mechanism by which W promotes selective packaging of the gRNA is not well understood. We used fluorescence correlation spectroscopy and quenching data to monitor the binding of recombinant HIV-1 Gag protein to Cy5-tagged 190-base RNAs. At physiological ionic strength, Gag binds with very similar, nanomolar affinities to both psi-containing and control RNAs. We challenged these interactions by adding excess competing tRNA; introducing mutations in Gag; or raising the ionic strength. These modifications all revealed high specificity for psi. This specificity is evidently obscured in physiological salt by non-specific, predominantly electrostatic interactions. This nonspecific activity was attenuated by mutations in the MA, CA, and NC domains, including CA mutations disrupting Gag-Gag interaction. We propose that gRNA is selectively packaged because binding to J nucleates virion assembly with particular efficiency.