7W9N
THE STRUCTURE OF OBA33-OTA COMPLEX
Summary for 7W9N
| Entry DOI | 10.2210/pdb7w9n/pdb |
| Descriptor | OTA DNA APTAMER (33-MER), (2~{S})-2-[[(3~{R})-5-chloranyl-3-methyl-8-oxidanyl-1-oxidanylidene-3,4-dihydroisochromen-7-yl]carbonylamino]-3-phenyl-propanoic acid (2 entities in total) |
| Functional Keywords | duplex, g-quadruplex, dna |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 10776.45 |
| Authors | |
| Primary citation | Xu, G.,Zhao, J.,Yu, H.,Wang, C.,Huang, Y.,Zhao, Q.,Zhou, X.,Li, C.,Liu, M. Structural Insights into the Mechanism of High-Affinity Binding of Ochratoxin A by a DNA Aptamer. J.Am.Chem.Soc., 144:7731-7740, 2022 Cited by PubMed Abstract: 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 and affinity among hundreds of aptamers for small molecules. Why OBA36 has >100-fold higher binding affinity to OTA than OTB remains a long-standing question due to the lack of high-resolution structure. Here we report the solution NMR structure of the aptamer-OTA complex. It was found that OTA binding induces the aptamer to fold into a well-defined unique duplex-quadruplex structural scaffold stabilized by Mg and Na ions. OTA does not directly interact with the G-quadruplex, but specifically binds at the junction between the double helix and G-quadruplex through π-π stacking, halogen bonding (X-bond), and hydrophobic interaction. OTB has the same binding site as OTA but lacks the X-bond. The strong X-bond formed between the chlorine atom of OTA and the aromatic ring of C5 is the key to discriminating the strong binding toward OTA. The present research contributes to a deeper insight of aptamer molecular recognition, reveals structural basis of the high-affinity binding of aptamers, and provides a foundation for further aptamer engineering and applications. PubMed: 35442665DOI: 10.1021/jacs.2c00478 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
Download full validation report
