Turner 2004 Internal Loop Example 2

example structure

∆G°₃₇ = ∆G°₃₇(Watson-Crick Pairs) + ∆G°_{37 intermolecular initiation} + ∆G°₃₇(Internal Loop)

∆G°₃₇ = ∆G°₃₇(CG followed by AU) + ∆G°₃₇(CG followed by GC) + ∆G°_{37 intermolecular initiation}+ ∆G°_{37 initiation}(6) + ΔG°_{37 asymmetry}×| n₁ - n₂| + ΔG°_{37 mismatch}(mismatch 1) + ΔG°_{37 mismatch}(mismatch 2) + ΔG°_{37 AU/GU closure}

∆G°₃₇ = –2.11 kcal/mol – 2.36 kcal/mol +4.09 kcal/mol + 2.0 kcal/mol + 0.6×|1 - 5| kcal/mol + 0 kcal/mol + 0 kcal/mol + 0.7 kcal/mol

∆G°₃₇ = +4.7 kcal/mol

∆H° = ∆H°(Watson-Crick Pairs) + ∆H°_{intermolecular initiation} + ∆H°(Internal Loop)

∆H°= ∆H°(CG followed by AU) + ∆H°(CG followed by GC) + ∆H°_{intermolecular initiation}+ ∆H°_initiation(6) + ΔH°_asymmetry×| n₁ - n₂| + ΔH°_mismatch(mismatch 1) + ΔH°_mismatch(mismatch 2) + ΔH°_{AU/GU closure}

∆H° = –10.44 kcal/mol – 10.64 kcal/mol + 3.61 kcal/mol – 1.3 kcal/mol + 3.2×|1 - 5| kcal/mol + 0 kcal/mol + 0 kcal/mol + 5.0 kcal/mol

∆H° = –1.0 kcal/mol

Note that the free energy and enthalpy changes for first mismatches in 1×(n-1) internal loops are 0 kcal/mol.

Turner 2004
Internal Loop Example 2

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