Sequence dependence for the energetics of terminal mismatches in ribooligonucleotides

Stability increments of terminal mismatches on the core helixes AUGCAU and UGCGCA are reported. Enthalpy, entropy, and free energy changes of helix formation were measured spectrophotometrically for 15 oligoribonucleotides containing the core sequences and various mismatches. Free energy increments for mismatches in this series range from -0.5 to -1.1 kcal/mol. These increments for mismatches on AU base pairs are smaller than those measured previously on GC base pairs [Freier, S.M., Kierzek, R., Caruthers, M.H., Neilson, T., & Turner, D.H. (1986) Biochemistry 25, 3209-3213]. The terminal GU mismatches in the sequences GAUGCAUUp and UAUGCAUGp add approximately the same stability increment as the corresponding terminal AU mismatch. The stability increments for pyrimidine-pyrimidine and pyrimidine-purine mismatches can be approximated within 0.3 kcal/mol by adding the stability increments for the corresponding 3' and 5' unpaired nucleotides (dangling ends). Stability increments for purine-purine mismatches are approximated well by the stability increment for the corresponding 3' dangling end made more favorable by 0.2 kcal/mol. These approximations are used to provide a table of stability increments for all 48 possible sequences of mismatches.