Figure 4.

The nearest neighbor model decomposes RNA secondary structures into loop substructures. Hairpin loops are closed by a single base pair. Loop substructures that are closed by two base pairs with no unpaired bases are called stackings, those with unpaired bases on one strand are called bulge loops and those with unpaired bases on both strands are called internal loops. Multi-branch loops are loop substructures that are closed by three or more base pairs. Loop substructures closed by no base pairs are called external loops.