Free Energy Change at 37 °C
Folding free energy changes for Watson-Crick helices are predicted using the equation:
ΔG°37 Watson-Crick = ΔG°37 intermolecular initiation + ΔG°37 AU end penalty (per AU end) + ΔG°37 symmetry (self-complementary duplexes) + Σ[ΔG°37 stacking]
where intermolecular initiation is applied for bimolecular structure formation, the AU end penalty is applied once per each AU pair at the end of a helix, the symmetry correction is applied to self-complementary duplexes, and the stacking term is a sum of sequence-dependent parameters over all base pair stacks. For helices of P uninterrupted basepairs, there are P-1 stacks of pairs.
Enthalpy changes for Watson-Crick helices are predicted using the equation:
ΔH°Watson-Crick = ΔH°intermolecular initiation + ΔH°AU end penalty (per AU end) + Σ[ΔH°stacking]
where terms are the same as those above for free energy changes. Note that the symmetry correction for self-complementary duplexes is absent because that stability cost is an entropic cost.
The table of parameters is available as plain text for free energy change, plain text for enthalpy change, or html. The plain text tables include GU pairs; see the GU section for special cases for 5'GGUC/3'CUGG and 5' GG/3'UU motifs.
A list of references is here.