Structural organization of a viral IRES depends on the integrity of the GNRA motif

Secondary structure of FMDV IRES. RNA structure was predicted using the Mfold program of GCG package, version 10. Domains are numbered 1 to 5, and span positions 1–85, 84–297, 306–415, and 416–462, respectively; a dot is used to mark positions each 10 nucleotides. The conserved GNRA, RAAA and C-rich motifs in domain 3 are highlighted. An arrow at position 287 points to the 3′ end of the antisense oligonucleotide used in primer extension assays.