Folding Free Energy Change
Multibranch loops stabilities are predicted using the following equation:
ΔG°37 multibranch = ΔG°37 initiation + ΔG°37 stacking
where the stacking is the optimal configuration of dangling ends, terminal mismatches, or coaxial stacks, noting that each nucleotide or helix end can participate in only one of these favorable interactions.
When there are six or fewer unpaired nucleotides in the loop, initiation is predicted using:
ΔG°37 initiation = a + b×[number of unpaired nucleotides] + c×[number of branching helices]
where a, b, and are parameters.
For multibranch loops with greater than six unpaired nucleotides, a logarithmic dependence on the number of upaired nucleotides is used:
ΔG°37 initiation = a + 6b + (1.1 kcal/mol)×ln([number of unpaired nucleotides]/6) + c×[number of branching helices]
Tables of parameters are available in html format.
A set of references is available here.