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Turner 2004

Hairpin Loops

Example 1

 

 

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)

 

∆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 AA) + ∆G°37 Hairpin initiation(6)

 

∆G°37 = –2.11 kcal/mol – 2.24 kcal/mol – 2.11 kcal/mol + 0.45 kcal/mol – 0.8 kcal/mol + 5.4 kcal/mol

 

∆G°37 = –1.4 kcal/mol

 

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

 

∆H° = ∆H°(Watson-Crick Pairs) +∆H°(terminal mismatch) + ∆H°Hairpin initiation(6)

 

∆H° = ∆H°(CG followed by AU) + ∆H°(AU followed by CG) + ∆H°(CG followed by AU) + ∆H°AU end penalty+ ∆H°(AU followed by AA) + ∆H°Hairpin initiation(6)

 

∆H° = –10.44 kcal/mol – 11.40 kcal/mol – 10.44 kcal/mol + 3.72 kcal/mol – 3.9 kcal/mol – 2.9 kcal/mol

 

∆H° = –35.4 kcal/mol

 

Note that for unimolecular secondary structures, the helical intermolecular initiation does not appear.