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Turner 2004

Hairpin Loops

Example 5

 

 

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(GG first mismatch) + ∆G°37 Hairpin initiation(5) + ΔG°37 (special GU closure)

 

∆G°37 = ∆G°37(CG followed by GC) + ∆G°37(GC followed by GC) + ∆G°37(GC followed by GU) + ∆G°37 GU end penalty+ ∆G°37(GU followed by GG) + ∆G°37(GG first mismatch) + ∆G°37 Hairpin initiation(5) + ΔG°37 (special GU closure)

 

∆G°37 = –2.36 kcal/mol – 3.26 kcal/mol – 1.53 kcal/mol + 0.45 kcal/mol – 0.8 kcal/mol – 0.8 kcal/mol + 5.7 kcal/mol – 2.2 kcal/mol

 

∆G°37 = –4.8 kcal/mol

 

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

 

∆H° = ∆H°(Watson-Crick Pairs) +∆H°(terminal mismatch) + ∆H°Hairpin initiation(5) + ΔH°(special GU closure)

 

∆H° = ∆H°(CG followed by GC) + ∆H°(GC followed by GC) + ∆H°(GC followed by GU) + ∆H°GU end penalty+ ∆H°(GU followed by GG) + ∆H°Hairpin initiation(5) + ΔH°(special GU closure)

 

∆H° = –10.64 kcal/mol – 13.39 kcal/mol – 8.33 kcal/mol + 3.72 kcal/mol – 3.5 kcal/mol + 3.6 kcal/mol – 14.8 kcal/mol

 

∆H° = –43.3 kcal/mol