Coaxial Stacking

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Coaxial stacking in a 4-branched multiloop.
Coaxial stacking is a tertiary interaction where separate stacks in an RNA align along a common axis.

 

Flush vs. Mismatch-Mediated Stacking

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 EteRNA

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.

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