Turner 1999

Watson-Crick Helices


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.          


The table of parameters is available as plain text (including GU pairs; see the GU section for special cases for 5'GGUC/3'CUGG and 5' GG/3'UU motifs) or html


A list of references is here.