Improving Structural Stability and Anticoagulant Activity of a Thrombin Binding Aptamer by Aromatic Modifications

The thrombin binding aptamer (TBA) is a 15-mer DNA oligonucleotide (5'-GGT TGG TGT GGT TGG-3'), that can form a stable intramolecular antiparallel chair-like G-quadruplex structure. This aptamer shows anticoagulant properties by interacting with one of the two anion binding sites of thrombin, namely the fibrinogen-recognition exosite. Here, we demonstrate that terminal modification of TBA with aromatic fragments such as coumarin, pyrene and perylene diimide (PDI), improves the G-quadruplex stability. The large aromatic surface of these dyes can pi-pi stack to the G-quadruplex or to each other, thereby stabilizing the aptamer. With respect to the original TBA, monoPDl-functionalized TBA exhibited the most remarkable improvement in melting temperature (Delta T-m approximate to + 18 degrees C) and displayed enhanced anticoagulant activity.

Automated summary

In this study, terminal modification of the thrombin binding aptamer with aromatic fragments was shown to enhance the stability of the G-quadruplex structure and improve its anticoagulant activity.