Turner 2004Folding 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 a nucleotide or helix end can participate in only one of these favorable interactions.
Initiation is predicted using:
ΔG°37 initiation = a + b×[average asymmetry] + c×[number of branching helices] + ΔG°37 strain(three-way branching loops with fewer than two unpaired nucleotides)
where the average asymmetry is calculated as:
average asymmetry = min[2.0,mean difference in unpaired nucleotides on each side of each helix]
Folding Enthalpy Change
Similar to free energy change, multibranch loops enthalpy changes are predicted using the following equation:
ΔH°multibranch = ΔH°initiation + ΔH°stacking
where the stacking is the configuration of dangling ends, terminal mismatches, or coaxial stacks with lowest folding free energy change.
Initiation is predicted using an equation analagous to that folding free energy initiation:
ΔH°initiation = a + b×[average asymmetry] + c×[number of branching helices] + ΔH°strain(three-way branching loops with fewer than two unpaired nucleotides)
where the average asymmetry is calculated as:
average asymmetry = min[2.0,mean difference in unpaired nucleotides on each side of each helix]
Parameter Tables
Tables of parameters are available in html format.
References
A set of references is available here.
Example