3-branched multiloops are unique in that the loss of any one branch transforms the multiloop into an internal loop. These multiloops may contain one branch with positive free energy, so long as free energy change of forming the internal loop is positive.
The energy calculation for multiloops and internal loops differs in two significant ways. The energy of multiloops is size-independent, but the energy of internal loops increases with increasing size. Additionally, multiloops can be boosted by CA mismatches that have no effect on internal loops. Together, these factors allow 3-branched multiloops to contain features would not be predicted to form if they occured in an external loop or larger multiloop.
Solving 3-Branched Multiloop PuzzlesEdit
Puzzles with 3-branched multiloops may have one positive-energy branch. Try to identify this branch, and focus on destabilizing the internal loop that would form if every base pair in this branch were broken. Avoid boosting the stable branches of the 3-branched multiloop with G - this will also boost the internal loop formed by opening the positive-energy branch.