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).
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