Suboptimal Structure

From EteRNA WiKi
(Redirected from Alternative Structure)
Jump to: navigation, search

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.

Example

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

GGAAACCGCCCGCGCGGGCGCGGGCGAAAACGCCCGCGAAACCGCCGCGAAAACGCGGCGGCCCGCGCGGGCGGAAAAGAAACAACAACAACAAC

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


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

Personal tools
Main page
Introduction to the Game