FIG. 1.
Schematic representation of the secondary structure of the HCV IRES (based on references 11 and 41), showing sites in nt 40-372.NS′ mRNA that are protected from cleavage by RNases T1 and V1 or at which cleavage is enhanced following binding of a 40S ribosomal subunit. These sites and the position of toeprints caused by bound 40S subunits are indicated by symbols shown at the upper right. Smaller symbols indicate weaker protection from cleavage. Domain IV (nt 331 to 354) is shown as an unstructured linear sequence for greater clarity. The initiation codon (AUG342-344) is underlined. The nomenclature used to describe subdomains of the IRES is from reference 12; the helices that constitute the pseudoknot are labeled 1 and 2.