A hairpin loop is a region of unpaired bases with only one adjoining stack.
Hairpin loops are described in terms of the number of unpaired bases in the loop. A prefix (tri-, tetra-, penta-, hexa-, hepta-, octa-, etc...) and the word "loop" can be combined to describe any given hairpin. Alternatively, one can describe the loop as an x-nucleotide hairpin, where x is the number of unpaired bases in the loop. The structure at right is an octaloop, or an 8-nucleotide hairpin loop.
Hairpin Loop Energy
The energy calculation for hairpin loops depends on the size. Currently, the energy of triloops depends only on the identity of the closing base pair. Tetraloops have special energy parameters that can be found here. The energy of hairpins larger than 4 nucleotides is determined by loop size, closing base pair, and terminal mismatch.