Coaxial stacking is a tertiary interaction where separate stacks in an RNA align along a common axis.
Flush vs. Mismatch-Mediated StackingEdit
In flush stacking, the coaxially-stacked helices are not separated by any unpaired bases. This is depicted in panel C to the right.
In mismatch-mediated stacking, the coaxially-stacked helices are separated by one or more unpaired bases. This is depicted in panels B and D in the figure at right.
Treatment in EteRNAEdit
The energy model used by EteRNA accounts for coaxial stacking in multiloops and external loops with closely-spaced stacks. GA and CA mismatches can be used to boost multiloops with mismatch-mediated coaxial stacking.