The structurally distinct strands of three-way junctions with formally unpaired linking segments, and possible structures for the IRES junction. (A) The component strands of a three-way junction with two coaxially stacked helices are distinct. The con strand turns about the shared axis of the stacked helices, while the en and ex strands have their 5′ and 3′ termini in the nonstacked helix. (B) Three possible forms of a junction with unpaired RNA linking the unstacked helix to the coaxially stacked pair of helices. If the linker (or longer linker where there are two) lies on the en or ex strand, we term the structures Len or Lex, respectively, while if there are two linking segments of equal length we call it Leq. (C) In principle the three-way junction of the IRES might adopt alternative secondary structures, so there are a number of structures possible. The 3HS4 secondary structure has a single segment linking the D and E arms, and could therefore adopt either Len (C-on-E stacking) or Lex (D-on-C stacking) structures in principle, or both in equilibrium. The 2HS1HS3 or 2HS2HS2 structures would be expected to fold by C-on-E stacking, forming Len and Leq structures, respectively.
