NEAREST-NEIGHBOR THERMODYNAMICS OF INTERNAL A-CENTER-DOT-C MISMATCHESIN DNA - SEQUENCE DEPENDENCE AND PH EFFECTS

Thermodynamics of 27 oligonucleotides with internal A.C mismatches at two different pHs were determined from UV absorbance versus temperatur e melting profiles. The data were combined with four literature values and used to derive nearest-neighbor parameters for all 16 trimer sequ ences with internal A.C mismatches at pH 7.0 and 5.0. The results indi cate that the contribution of single A.C mismatches to duplex stabilit y is strongly dependent on the solution pH and the nearest-neighbor co ntext. On average, the protonation of an internal A.C mismatch stabili zes the duplex by 1.39 kcal/mol for Delta G(37)degrees and 7.0 degrees C for the T-M The nearest-neighbor parameters predict Delta G(37)degr ees Delta H degrees, Delta S degrees and T-M of oligonucleotides prese nted in this study with average deviations of 6.3%, 11.0%, 12.2%, and 1.8 degrees C, respectively, at pH 7.0 and 4.7%, 5.9%, 6.1%, and 1.3 d egrees C, respectively, at pH 5.0. At pH 7.0, the contribution of sing le A.C mismatches to helix stability ranges from 2.25 kcal/mol for TCA /AAT to 1.22 kcal/mol for GCG/CAC. At pH 5.0, however, the contributio n of A(+).C mismatches ranges from 1.09 kcal/mol for TCT/AAA to -0.43 kcal/mol for GCC/CAG. Implications of the results for replication fide lity and mismatch repair are discussed.