Structural and functional characterization of thrombin binding aptamer minor loop

The thrombin binding aptamer (29hTBA), identified with a SELEX approach, shows a significant affinity for the coagulation factor thrombin by recognizing the protein Exosite II (heparin binding site). The structure of 29hTBA consists of a G-quadruplex core flanked by two partially paired terminal strands. Literature data underline that the structure and stability of intramolecular G-quadruplexes can be profoundly influenced by the length and composition of the loops. Here, we investigated the role of the minor loop (10-11) composition by introducing a single A-T mutation at position 11. A comparative structural investigation of the wild type and the mutant aptamers evidenced that this loop is not largely impairing the folding of the G-quadruplex core. Additionally, thrombin binding analysis suggested that this loop is not directly involved in protein binding at exosite II.