Coaxial Stacking
From Eterna Wiki
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.
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Treatment in EteRNA
