Fig. 3.

(a and b) Target structures S₁ at temperature 30 °C (a) and S₂ at temperature 42 °C (b) for domain 5 thermo-IRES element with added AUG codon (blue). IUPAC sequence constraints are determined from an alignment of 183 IRES sequences as shown in Figure 1 of Fernandez et al. (2011). Domain 5 stem-loop (positions 3-24 in red) and unpaired polypyrimidine tract (PPT positions 25–32 in green) are known to be essential for IRES activity (Kuhn et al., 1990). Target structure S₁ was designed to sequester the PPT at low temperature, thus creating a thermo-IRES which should be functional only at high temperature. (c) Ratio of normalized IRES activity at 42 °C over that at 30 °C for wild-type FMDV IRES, a negative control, and two thermosensors designed using RNAiFold2T