New structural information expands the understanding of the thrombin modulation with oligonucleotide aptamers

During the last decades, thrombin binding aptamer (TBA) was one of the most extensively studied oligonucleotide G-quadruplex aptamers [1] and, despite the advent of new anti-thrombin aptamers [2], the search for mutations that are able to improve TBA properties is still ongoing [3]. In this context, an extensive analysis of twenty-two TBA variants with N3-modified residues Thy3 and Thy12, two key residues of the two TT loops that guide the binding with thrombin, was performed in the course of a collaborative research with Engelhardt Institute of Molecular Biology (Russian Academy of Sciences, Russia). Among them, some mutants with enhanced affinity and improved anticoagulant activity were identified (data to be published). Here, we present the crystal structures of the complexes between thrombin and three of these TBA variants, containing a modification in the Thy3 nucleobase. The data revealed that the modified pyrimidine base invariably allocates in proximity to thrombin residues Tyr76 and Ile82 due to the directing role of the unmodified TT loop. Moreover, the modifications were found to induce an increase in the contact areas between thrombin and the modified TBAs by a slight conformation adaptation of the aptamer to the thrombin binding site. Details will be presented in the poster.