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.

When plotting the data from all 18 RNA constructs studied (including the MS13-17 RNAs) as a function of overall RNA stability, no correlation is observed ( Figure 4E ). However, we observe a strong correlation between frameshifting and the thermodynamic stability of the first 3-4 bp 8 nt downstream of the slippery site ( Figure 4F and G) . Conversely, the correlations grow considerably weaker as more base pairs are considered in the analysis (Supplementary Figure S2) . Likewise, no correlation is observed between local stability of base pairs at the top of the stem-loop and frameshift efficiency (Supplementary Figure S2L) . The observed correlations are exponential functions with baselines of 2-4% frameshifting, which correspond to the lowest observed frameshift efficiencies in the presence of a stem-loop secondary structure downstream of the slippery site.