Other structure elements
- A collection of single stranded bases not accessible from any base
pair is called an exterior (or external) loop (see figure 22.29F). These regions do not
contribute to the total free energy.
- Dangling nucleotide (
). A dangling nucleotide is
a single stranded nucleotide that forms a stacking interaction with
an adjacent base pair. A dangling nucleotide can be a 
or
-dangling nucleotide depending on the orientation (see figure 22.29G). The energy
contribution is determined by the single stranded nucleotide, its
orientation and on the adjacent base pair.
- Non-GC terminating stem (
). If a base pair other than a G-C pair is found at the end of a stem, an energy penalty is assigned (see figure 22.29H).
- Coaxial interaction (
). Coaxial stacking is a favorable interaction of two stems where the base pairs at the ends can form a stacking interaction.
This can occur between stems in a multi loop and between the stems of two different
sequential structures. Coaxial stacking can occur between stems with no intervening nucleotides (adjacent
stems) and between stems with one intervening nucleotide from each
strand (see figure 22.29I). The energy contribution is determined by the adjacent base
pairs and the intervening nucleotides.