Comparative termodynamic analysis of thrombin interaction with anti-thrombin aptamers and their heterodimeric construct

Aptamers interacting selectively with the anion-binding exosites 1 and 2 of thrombin were merged into dimeric oligonucleotide constructs with use of a poly-(dT)-linker of 35 nucleotides (nt) long. Complexes of thrombin with the aptamers and their hetero- and homodimeric constructs were measured using the optical biosensor Biacore-3000. KD values measured for the hetero- and homodimeric constructs were correspondingly 25-30- and 2-3-fold lower than those for the primary aptamers. Analysis of temperature dependencies of KD values within the temperature interval of 10°C-40°C has shown that the values of enthalpy change ΔH upon formation of complexes of thrombin with the aptamers and the hetrodimeric construct are close. The value of the entropy change ΔS upon complex formation of thrombin with the aptamer heterodimeric construct was 1.5-2-fold higher than ΔS values for the complexes with the aptamers. The complex formation and dissociation rates increased with the elevation of temperature from 10°С to 37°С. However, the dissociation rate for the complex of thrombin with the heterodimeric construct was evidently lower that that for the complexes with the aptamers.