FIG. 5.

RNase V₁ footprinting of the binary ribosomal complex formed on HCV nt 40-372 RNA lacking subdomain IIIc (nt 229 to 238). Polyacrylamide-urea gel fractionation of cDNA products obtained after primer extension shows the sensitivity of the HCV RNA upstream of nt 255 to cleavage (lanes 1 and 2) either alone (lane 2) or bound by a 40S subunit (lane 1). cDNA products obtained after primer extension of untreated HCV RNA are shown in lane 3. A dideoxynucleotide sequence generated with the same primer and run in parallel is shown to the left; HCV nucleotides are indicated by black squares at 50-nt intervals from nt 100 to 250. IRES subdomains II, IIIa, and IIIb are indicated on the left, and the positions of protected residues are indicated to the right. The position of the nt 229-238 deletion is indicated by an asterisk.