Thermodynamics of internal C•T mismatches in DNA

Thermodynamics of 23 oligonucleotides with internal single C-T mismatches were obtained by measuring UV absorbance as a function of temperature. Results from these 23 duplexes were combined with three measurements from the literature to derive nearest-neighbor thermodynamic parameters for seven linearly independent trimer sequences with internal C-T mismatches. The data show that the nearest-neighbor model is adequate for predicting thermodynamics of oligonucleotides with internal C-T with average deviations for Delta G degrees(37), Delta H degrees, Delta S degrees and T-m of 6.4%, 9.9%, 10.6%, and 1.9 degrees C respectively. C-T mismatches destabilize the duplex in all sequence contexts. The thermodynamic contribution of C-T mismatches to duplex stability varies weakly depending on the orientation of the mismatch and its context and ranges from +1.02 kcal/mol for G (C) under bar G/C (T) under bar C and C (C) under bar G/G (T) under bar C to +1.95 kcal/mol for T-(C under bar) C/A (T) under bar G.