Figure 4.

Four candidate models derived from combinations of two four-way Junctions I and II of Figure 3. (A) Secondary structure of domain 3 in FMDV IRES. (B) Combinations of the two four-way junctions considered. To accommodate the long-range interactions between helices H₄ and H₅, helix H₃ must be either parallel or perpendicular to the helices H₄ and H₅ in space. Two arrangements, c and h, of junctions I and II do not satisfy the long-range interactions and are thus eliminated. (C) Four complete junction topology models where Junctions I (dotted red box) and II (dotted green box) are stitched via helix H₃ considering the GNRA tetraloop long-range interaction between H₄ and H₅.