Alternative, or suboptimal structures are structures that a given sequence could fold into aside from the minimum free energy structure. As an RNA folds, it may pass through several suboptimal structures before it adopts a stable structure. These alternative structures may also exist in equilibrium with one another, and the MFE structure.


The following examples show two suboptimal structures and the minimum free energy structure for the sequence:



Suboptimal structure #1

Notice that the second suboptimal structure has a rather low value of free energy. Many stable GC pairs would have to be broken in order to bring this from the second suboptimal structure to the minimum free energy structure.

Suboptimal structure #2

This is of the several downsides of "christmas tree" designs in lab.

MFE structure