Turner 1999

Dangling Ends


            Dangling ends are nucleotides that stack on the ends of helices. In secondary structures, they occur in multibranch and exterior loops. They occur as either 5' dangling ends (an unpaired nucleotide 5' to the helix end) or 3' dangling ends (an unpaired nucleotide 3' to the helix end). In RNA, 3' dangling ends are generally more stabilizing than 5' dangling ends. Note that if a helix end is extended on both the 5' and 3' strands, then a terminal mismatch exists (not the sum of 5' and 3' dangling ends).

The tables of parameters are available as plain text or html

A list of references is here.

A tutorial is available.