Figure 6.

Postulated RNA secondary structure of the first ∼900 nt of the HCV genome, based on a SHAPE/FAST analysis. RNA structures in the core gene are labelled A–J. The HCV IRES (domains II–IV) are accurately determined, along with previously postulated RNA structures within the core gene labelled A, B, G and I. Six novel RNA helical/stem–loop structures were also determined, labelled C, D, E, F, H and J. Structure G (SL248) contains codon 91, where another internal initiation of translation has been proposed to occur. The region between domain IV and V (Structure A), is unstructured and proposed to encode an alternative reading frame protein.