Internal Loop
An internal loop is a region of unpaired bases with two adjacent stacks. In an internal loop, unpaired bases are found on both sides of the stack. This differs from a bulge, where only one side contains unpaired bases.
Nomenclature
Internal loops are named according to the number of unpaired bases on either side of the stack. An x-y loop has x unpaired bases on the lower-numbered (5') side of the stack, and y unpaired bases on the higher-numbered (3') side of the stack. If x and y are equal, the internal loop is called a symmetric internal loop.
Boosting
Main Article: Boosting
All internal loops can be boosted by the formation of a GA or UU terminal mismatch. Boosting can allow 1-1, 2-2, and 3-3 loops to make a negative contribution to free energy.
Special Internal Loops
The 1-1, 1-2, 2-1, and 2-2 loops each have special energy parameters.
