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Turner 1999

Internal Loops

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 + 0.48×|1 - 5| kcal/mol + 0 kcal/mol + 0 kcal/mol + 0.65 kcal/mol

 

∆G°37 = +4.2 kcal/mol

 

 

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