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.

Average hyperchromicity data for each RNA were fit using Equation (2) and overall thermodynamic stabilities were calculated using Equation (4) (Prism 4.3, GraphPad). For RNAs with melting temperatures approaching or >95 C, a linear extrapolation of ÁG Global versus urea concentration was applied to determine the ÁG Global at 0 M urea (Supplementary Figure S1) (58) . For all other RNAs, determination of ÁG Global at standard buffer conditions was sufficient to produce minimal error in ÁG Global . All the data used to calculate the reported ÁG Global values were established using a minimum of three independently prepared samples at each buffer condition. A small and non-cooperative transition was observed in the 40-50 C range for RNAs with less stable terminal base pairs (WT, MS2, MS6, MS7, MS10 and MS12). This transition was not present for RNAs with very stable terminal base pairs (e.g. MS1 and MS5) and can be attributed to helical fraying. For all RNAs, only the major cooperative unfolding transitions were used in data fitting. Starting values were determined by examining the first derivative plots for each set of averages. Local stabilities, ÁG Local , for base pairs were calculated using nearest-neighbor parameters at 1 M NaCl, 37 C (59-61) (Supplementary Table S2 ).