34  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).

34.1 Examples

ΔG°₃₇ = ΔG°₃₇(Watson-Crick-Franklin Helix) + ΔG°₃₇(\(3'\) dangling C adajacent to GC) + ΔG°₃₇(\(5'\) dangling M adjacent CG)

ΔG°₃₇ = -6.0 kcal/mol - 0.4 kcal/mol + 0.0 kcal/mol

ΔG°₃₇ = -6.4 kcal/mol

Note that this example contains both a \(5'\) and a \(3'\) dangling end (at opposite ends of the duplex).

34.2 Parameter Tables

The tables of parameters are available as plain text for free energy change.