A multiloop, sometimes called a junction or multi-branched loop, is a region where three or more stacks come together. These stacks may or may not be separated by unpaired bases.
One convenient way of describing the size of a multiloop is to specify the number of unpaired bases between stacks. Begin with the stack that contains the ends (5' and 3' termini) of the RNA, and move in the direction of increasing numbers. The example to the right is a 1-2-0-3 multiloop.
The energy of multiloops is determined by size, symmetry, closing base pair, and terminal mismatch. Energy for multiloops with stacks are separated by 1 or fewer unpaired bases is calculated differently than for other multiloops.
Multiloops can be boosted by the formation of GA and CA terminal mismatches.
To boost a multiloop, the closing base pair must be properly oriented. In the image to the right, the CA terminal mismatch is only stabilizing with the closing base pair in a specific orientation. The same is true of GA terminal mismatches.
In contrast to hairpins and internal loops, the UU terminal mismatch is always destabilizing in multiloops.