Translation of hepatitis C virus (HCV) RNA is initiated
via the internal ribosome entry site (IRES), located
within the 5′ untranslated region. Although the secondary
structure of this element has been predicted, little information
on the tertiary structure is available. Here we report
the first structural characterization of the HCV IRES using
electron microscopy. In vitro transcribed RNA appeared
as particles with characteristic morphology and gold labeling
using a specific oligonucleotide confirmed them to be HCV
IRES. Dimerization of the IRES by hybridization with tandem
repeat oligonucleotides allowed the identification of domain
III and an assignment of domains II and IV to distinct
regions within the molecule. Using immunogold labeling,
the pyrimidine tract binding protein (PTB) was shown to
bind to domain III. Structure–function relationships
based on the flexible hinge between domains II and III
are suggested. Finally, the architecture of the HCV IRES
was seen to be markedly different from that of a picornavirus,
foot-and-mouth disease virus (FMDV).