#
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 Change

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.

# Tables

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.

# References

A list of references is here.