Thermodynamics of internal C·T mismatches in DNA

Abstract

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 ΔG°37, ΔH°, ΔS°and T(m) of 6.4%, 9.9%, 10.6%, and 1.9°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 GCG/CTC and CCG/GTC to +1.95 kcal/mol for TCC/ATG.