Internal Loop Ex

An AA mismatch creating 1-1 internal loop.

A mismatch occurs when two non-complementary bases lie across from one another in a stack. In the image at right, an AA mismatch is depicted.

Though mismatched bases cannot form a canonical base pair, they may be capable of hydrogen bonding with one another and/or stacking with neighboring bases. In this way, mismatches can still contribute to the stability of a secondary structure.