Can anyone give a scientific explanation for why internal loops larger than 2-2 get U-U mismatch energy bonuses in the energy model we use, while almost every other mismatch does not yield a bonus?
It is thought due to the extra hydrogen bonding U-U mismatches (and C-C mismatches) get. Eterna may only properly account for U-U.
Do a google search on U-U mismatch RNA stability or add internal loop to the search.