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Turner 2004

Internal Loops

Example 1

 

 

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(2×2 Internal Loop)

 

∆G°37 = –2.11 kcal/mol – 2.36 kcal/mol +4.09 kcal/mol – 1.1 kcal/mol

 

∆G°37 = –1.5 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°(2×2 Internal Loop)

 

∆H° = –10.44 kcal/mol – 10.64 kcal/mol + 3.61 kcal/mol – 19.7 kcal/mol

 

∆H° = –37.2 kcal/mol

 

 

Note that the internal loop lookup tables account for terminal AU pairs that are adjacent to internal loops.