Figure 3. Secondary RNA structure of the FMDV IRES region.

The modular organization of the IRES element in domains (1–2, 3, 4, and 5) is indicated. The first 20 nt of the IRES belong to the right arm of cre (Fig. 1A); nucleotide numbering has been maintained for consistency with previous works. The position of conserved RNA motifs refer to in the text are indicated. In-frame initiator codons AUG1 and AUG2 are separated by 84 nt (dashed line). Blue-boxed nucleotides depict the annealing nucleotide position of the 3′end of each antisense oligonucleotide. The approximate annealing position of the customized 2′O-Me AONs in the linear IRES sequence is depicted in the bottom. AON sequences are described in Table 1.