Studying DNA G-Quadruplex Aptamer by 19F NMR

In this study, we demonstrated that F-19 NMR can be used to study the thrombin-binding aptamer (TBA) DNA G-quadruplex, widely used as a model structure for studying G-quadruplex aptamers. We systematically examined the structural feature of the TBA G-quadruplex aptamer with fluorine-19 (F-19) labels at all of the thymidine positions. We successfully observed the structural change between the G-quadruplex and the unstructured single strand by F-19 NMR spectroscopy. The thermodynamic parameters of these DNA G-quadruplex aptamers were also determined from the F-19 NMR signals. We further showed that the F-19 NMR method can be used to observe the complex formed by TBA G-quadruplex and thrombin. Our results suggest that F-19 NMR spectroscopy is a useful approach to study the aptamer G-quadruplex structure.