A thermodynamic investigation into the binding affinities between aptamer-DNA and aptamer- protein based on the displacement reaction for thrombin was presented. Some thermodynamic parameters such as the equilibrium constant, enthalpy and entropy of the dissociation reaction and the displacement reaction were evaluated. The results showed that the change of entropy played an important role in the conversion of the duplex DNA into aptamer-protein binding. This has been the first attempt to compare the stability of the duplex aptamer-DNA and the aptamer-protein complex, and it will provide an insight into how the conformation changes. The obtained thermal parameter will direct us to find out the basic principle for designing the aptamer based biosensor and to deeply understand the thermal properties of the aptamer toward protein, and it will be great importance of developing new methods for disease diagnosis.

Key words: aptamer, protein, thermodynamics