Secondary Structure Analysis of a Minimal Avian Leukosis-Sarcoma Virus Packaging Signal

We previously identified a 160-nucleotide packaging signal, MΨ, from the 5′ end of the Rous sarcoma virus genome. In this study, we determine the secondary structure of MΨ by using phylogenetic analysis with computer modeling and heterologous packaging assays of point mutants. The results of the in vivo studies are in good agreement with the computer model. Additionally, the packaging studies indicate several structures which are important for efficient packaging, including a single-stranded bulge containing the initiation codon for the short open reading frame, uORF3, as well as adjacent stem structures. Finally, we show that the L3 stem-loop at the 3′ end of MΨ is dispensable for packaging, thus identifying an 82-nucleotide minimal packaging signal, μΨ, composed of the O3 stem-loop.