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Turner 2004

Bulge Loops

Example 1

 

 

example structure        

∆G°37 = ∆G°37(Watson-Crick Pairs) + ∆G°37 intermolecular initiation + ∆G°37(Bulge Loop)


∆G
°37 = ∆G°37(GC followed by CG) + ∆G°37(CG followed by CG) + ∆G°37 intermolecular initiation + ∆G°37 bulge initiation(1) + ∆G°37(special C bulge) + ∆G°37(CG followed by GC) – RT ln(3)

 

∆G°37 = 3.42 kcal/mol 3.26 kcal/mol + 4.09 kcal/mol + 3.81 kcal/mol – 0.9 kcal/mol – 2.36 kcal/mol – 0.616×1.099 kcal/mol

 

∆G°37 = –2.7 kcal/mol

 

∆H° = ∆H°(Watson-Crick Pairs) + ∆H°intermolecular initiation + ∆H°(Bulge Loop)


∆H
° = ∆H°(GC followed by CG) + ∆H°(CG followed by CG) + ∆H°intermolecular initiation + ∆H°bulge initiation(1) + ∆H°(CG followed by GC)

 

∆H° = 14.88 kcal/mol 13.39 kcal/mol + 3.61 kcal/mol + 10.6 kcal/mol – 10.64 kcal/mol

 

∆H° = –24.7 kcal/mol

 

 

Note that this loop has three available states because any of the three Cs in the top strand can be the bulge.