Stem II base pairs form in the HCV IRES pseudoknot and contribute to IRES translation efficiency. (A) A line diagram of the predicted HCV IRES secondary structure with the major domains and the AUG start codon labeled. Dom I is shown in gray and is not included in the IRES-luciferase reporter constructs. The inset shows the sequence and predicted secondary structure of the pseudoknot with the stem and loop nomenclature indicated. SI is shown in light blue and SII is shown in light green. (B) Mutations of the entire (Ent) SII sequence, as previously reported in Kieft et al. (2001) and (C) mutations of SII made two base pairs at a time. Mutated nucleotides are shown in lowercase and the mutants are boxed in colors corresponding to their translation activity levels as defined in B. Disruptive mutations are named according to whether the 5′ or 3′ side of SII (in the primary sequence) was mutated to its complement.
