Turner 2004
∆G°37 = ∆G°37(Watson-Crick Pairs) + ∆G°37 intermolecular initiation + ∆G°37(Bulge Loop)
∆G°37 =
∆G°37(GC
followed by CG) + ∆G°37(CG
followed by CG) + ∆G°37 intermolecular initiation + ∆G°37 bulge initiation(1) + ∆G°37(special C bulge) + ∆G°37(CG followed by GC) – RT ln(3)
∆G°37 =
–3.42 kcal/mol – 3.26 kcal/mol + 4.09 kcal/mol + 3.81 kcal/mol
–
0.9 kcal/mol – 2.36 kcal/mol – 0.616×1.099 kcal/mol
∆G°37 =
–2.7 kcal/mol
∆H° = ∆H°(Watson-Crick Pairs) + ∆H°intermolecular initiation + ∆H°(Bulge Loop)
∆H° = ∆H°(GC
followed by CG) + ∆H°(CG
followed by CG) + ∆H°intermolecular initiation + ∆H°bulge initiation(1) + ∆H°(CG followed by GC)
∆H° = –14.88 kcal/mol – 13.39 kcal/mol + 3.61 kcal/mol + 10.6 kcal/mol – 10.64 kcal/mol
∆H° =
–24.7 kcal/mol
Note that this loop has three available states because any of the three Cs in the top strand can be the bulge.