Inhibition of IRES translation activity by varying the pseudoknot–AUG distance. (A) Sequences of mutations made to either lengthen or shorten the pseudoknot–AUG distance. Inserted nucleotides are shown in lowercase letters, and the start codon and SII are in bold. (B) Translation activity plotted against the pseudoknot–AUG distance with deletions plotted to the left of the WT AUG position and insertions to the right. Translation activities from the WT IRES background are plotted on the left vertical axis and those from a compromised pseudoknot (SII top 5′× mutant) on the right vertical axis, with 100% activity on the left axis scaled to 40% starting activity on the right. Plotted points represent the mean activities of four translation reactions from two independent transcriptions and the error bars extend 1 SD above and below the mean.
