High-Performance Thrombin Aptamers with a Peptide-Extended Recognition Interface

Improving the affinity and inhibitory characteristics of aptamers is important in the context of their applications in therapy and diagnostics. The use of peptide-aptamer conjugates with an extended aptamer-protein interface is an efficient strategy toward this goal. Here, we report GLE peptide conjugates of the bimodular duplex-quadruplex thrombin aptamers Re31 and NU172. Biophysical studies of the aptamer conjugates revealed that the presence of the tripeptide subunit does not have a significant effect on the thermodynamic stability or structure of the aptamers. In contrast, the affinity and anticoagulant activity of the conjugates were significantly improved. The NU172-GLE conjugate appeared to be the most effective inhibitor of thrombin-induced fibrinogen polymerization. Further clotting studies in human plasma showed that due to the presence of prothrombin, an alternative target for aptamers, the antithrombin activity of aptamers in plasma samples may be significantly underestimated.