(209d) An Integrated Thermodynamical Approach to Predict the Melting Temperature and Stability of an Oligonucleotide Duplex in Solution and on Surface

The most commonly used method to predict the melting temperature of an oligonucleotide duplex is the nearest neighbor method, which relies on the sequential arrangement of different dinucleotides based on the stabilization effect of the base-stacking interactions between them. The contribution of the structure stiffness on the stability of the duplex as well as the temperature effect on the thermodynamical parameters, enthalpy, entropy, and free energy changes, are not included in the model. An alternative semi-empirical approach to predict the melting temperature and stability of an oligonucleotide molecule is proposed to account for inter- and intra- strand interactions (hydrophobic, base stacking, hydrogen bonding, van der Waals, electrostatic and a tri-nucleotide-level helix stiffness) and the ionic environment outside the molecule, and the temperature dependence of the entropy, enthalpy and free energy changes. The melting temperature and stability predictions of the model are in agreement with experimental values in solution. The model is extended to incorporate the effect of the surface on the thermal denaturation of a target and a surface-bound probe on a microarray platform with a high surface probe density. Several blocking mechanisms on the surface affecting the transition are integrated into the model. The effect of the presence of the surface on the prediction of the melting temperature and the representative thermodynamical quantities are discussed.