Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer

A 36-mer guanine (G)-rich DNA aptamer (OBA36) is able to distinguish one atomic difference between ochratoxin analogues A(OTA) and B (OTB), showing prominent recognition specificity andaffinity among hundreds of aptamers for small molecules. Why OBA36has >100-fold higher binding affinity to OTA than OTB remains a long-standing question due to the lack of high-resolution structure. Here wereport the solution NMR structure of the aptamer-OTA complex. It wasfound that OTA binding induces the aptamer to fold into a well-definedunique duplex-quadruplex structural scaffold stabilized by Mg2+and Na+ions. OTA does not directly interact with the G-quadruplex, butspecifically binds at the junction between the double helix and G-quadruplex through pi-pi stacking, halogen bonding (X-bond), andhydrophobic interaction. OTB has the same binding site as OTA butlacks the X-bond. The strong X-bond formed between the chlorine atom of OTA and the aromatic ring of C5 is the key todiscriminating the strong binding toward OTA. The present research contributes to a deeper insight of aptamer molecularrecognition, reveals structural basis of the high-affinity binding of aptamers, and provides a foundation for further aptamer engineering and applications

Automated summary

This research reports the solution structure of a DNA aptamer complexed with ochratoxin A (OTA), revealing the structural basis for its high-affinity binding. The study finds that OTA specifically binds at the junction between the double helix and G-quadruplex through pi-pi stacking, halogen bonding, and hydrophobic interaction. The presence of a strong halogen bond between OTA and the aptamer is the key to discriminating the strong binding toward OTA.