Turner 2004 Hairpin Example 4

example structure

∆G°₃₇ = ∆G°₃₇(Watson-Crick Pairs) + ∆G°₃₇(Hairpin Loop)

∆G°₃₇ = ∆G°₃₇(Watson-Crick Pairs) + ∆G°₃₇(terminal mismatch) + ∆G°_{37 Hairpin initiation}(6) + ΔG°_{37
penalty}(all C loops)

∆G°₃₇ = ∆G°₃₇(CG followed by AU) + ∆G°₃₇(AU followed by CG) + ∆G°₃₇(CG followed by AU) + ∆G°_{37 AU end penalty}+ ∆G°₃₇(AU followed by CC) + ∆G°_{37 Hairpin initiation}(6) + 6×A + B

∆G°₃₇ = –2.11 kcal/mol – 2.24 kcal/mol – 2.11 kcal/mol + 0.45 kcal/mol – 0.7 kcal/mol + 5.4 kcal/mol + 6×0.3 kcal/mol + 1.6 kcal/mol

∆G°₃₇ = +2.1 kcal/mol

∆H° = ∆H°(Watson-Crick Pairs) + ∆H°(Hairpin Loop)

∆H° = ∆H°(Watson-Crick Pairs) +∆H°(terminal mismatch) + ∆H°_{Hairpin initiation}(6) + ΔH°_penalty(all C loops)

∆H° = ∆H°(CG followed by AU) + ∆H°(AU followed by CG) + ∆H°(CG followed by AU) + ∆H°_{AU end penalty}+ ∆H°(AU followed by CC) + ∆H°_{Hairpin initiation}(6) + 6×A + B

∆H° = –10.44 kcal/mol – 11.40 kcal/mol – 10.44 kcal/mol + 3.72 kcal/mol + 6.0 kcal/mol – 2.9 kcal/mol + 6×3.4 kcal/mol + 7.6 kcal/mol

∆H° = +2.5 kcal/mol

Turner 2004
Hairpin Example 4

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