HIV-1 frameshift efficiency is primarily determined by the stability of base pairs positioned at the mRNA entrance channel of the ribosome

Mouzakis, Kathryn D.; Lang, Andrew L.; Vander Meulen, Kirk A.; Easterday, Preston D.; Butcher, Samuel E.

The stem-loop is flanked by a 5 0 -U and 3 0 -G ( Figure 1A) , that could potentially form a U-G wobble at the base of the stem. Inclusion of this wobble pair in the local stability term produces consistently weaker correlations between frameshift efficiency and local stability (Supplementary Figure S3) . To further address whether or not this U-G wobble pair can form during frameshifting, we modeled the frameshift site stem-loop and spacer onto the eukaryotic ribosome ( Figure 5 ). The spacer was connected to the terminal nt in the A-site, to recapitulate the position of the ribosome when it is engaged on the slippery sequence in the 0 reading frame. The model indicates that the minimal spacer distance between the slippery site and the stem-loop is 7 nt; however, formation of a U-G wobble at the base of the stem is blocked by steric clash with the ribosomal S3 protein ( Figure 5B and D). Therefore, experimental data and structural modeling support an HIV-1 frameshift site spacer length of 8 nt.