Decomposition of Secondary Structures of RNA

A secondary structure can be decomposed in a unique way into a number of distinct substructures. Consider the cycle as determined by the number of accessible base pairs that are interior to a base pair .

If , the terms between and are said to form a hairpin loop.

If and , the pair and together form a stacked base pair. If and , the -cycle closed by and form a bulge or an interior loop. If either one of and form a pair within , the structure is said to be a bulge. Otherwise the -cycle is called an interior loop. (See Figure)

A -cycle where is called a multiloop or multiple loop.

A sequence term that is not contained in any -cycle is called an external base.

It is trivial that every non-external term is either part of a hairpin, base pair stack, interior loop, bulge or multiple loop.