22 GT Pairs
GT pairs are treated as nearest neighbor stacks, similar to Watson-Crick-Franklin helices, and unlike RNA, GT pairs at the ends of helices are not penalized. Parameters for stacks containing GT pairs were calculated separately from those containing AT and GC base pairs only.
22.1 Examples
ΔG°37 = ΔG°37 intermolecular initiation + ΔG°37(GC followed by GT) + ΔG°37(GT followed by TG) + ΔG°37(TG followed by CG) + ΔG°37(CG followed by GT) + ΔG°37(GT followed by TG) + ΔG°37(TG followed by GC) + ΔG°37(GC followed by TG)
ΔG°37 = 1.0 kcal/mol + 0.1 kcal/mol + 1.2 kcal/mol + 0.1 kcal/mol - 0.5 kcal/mol + 1.2 kcal/mol - 0.5 kcal/mol - 0.6 kcal/mol
ΔG°37 = 2.0 kcal/mol
ΔH° = ΔH°intermolecular initiation + ΔH°(GC followed by GT) + ΔH°(GT followed by TG) + ΔH°(TG followed by CG) + ΔH°(CG followed by GT) + ΔH°(GT followed by TG) + ΔH°(TG followed by GC) + ΔH°(GC followed by TG)
ΔH° = -7.2 kcal/mol + 4.3 kcal/mol + 5.0 kcal/mol + 4.3 kcal/mol - 4.3 kcal/mol + 5.0 kcal/mol - 4.3 kcal/mol - 2.4 kcal/mol
ΔH° = 0.4 kcal/mol
22.2 Parameter Tables
The table of parameters is available as plain text for free energy change (including Watson-Crick-Franklin pairs) and enthalpy change (including Watson-Crick-Franklin pairs).