The team of Professor Tan Weihong, Professor Han Da, and Professor Guo Pei from the Hangzhou Institute of Pharmaceutical Sciences, Chinese Academy of Sciences, has published research results in the Proceedings of the National Academy of Sciences (PNAS). They successfully resolved the tertiary structure of a DNA aptamer binding to adenosine triphosphate (ATP) and, on this basis, developed an optimized variant with sub-micromolar affinity. This work provides a new direction for the application of DNA molecular tools in biosensing and therapeutic fields.
As molecular recognition tools, the application of DNA aptamers is limited by insufficient understanding of their tertiary structures and binding mechanisms. The research team took the ATP-targeting DNA aptamer 1301b as the object and resolved the tertiary structure of its shortened variant 1301b_v1 binding to ATP in a 1:1 ratio using nuclear magnetic resonance technology. The structure shows that ATP is embedded in a pocket formed by two internal loops and achieves stable binding through hydrogen bonding and base stacking interactions.
The study also found that magnesium ions play a key role in neutralizing the negative charge of phosphate groups and promoting the formation of the aptamer's semi-folded conformation, indicating that the DNA aptamer recognizes ATP through an adaptive mechanism. Based on structural insights, the team introduced 2'-O-methyl modifications in the central linker region, which significantly improved binding affinity and reduced dependence on magnesium ions. The optimized aptamer has a dissociation constant (K_D) for ATP of approximately 0.7 micromolar, which is among the highest levels reported for similar aptamers, while maintaining good specificity.
This study not only reveals the potential of DNA to form complex tertiary structures, but also provides a structural basis for designing high-performance DNA tools for diagnosis and targeted therapy. Tan Weihong said: "This work demonstrates the feasibility of optimizing DNA aptamers through rational design and lays the foundation for developing next-generation biosensing and therapeutic strategies."
