7W9N

THE STRUCTURE OF OBA33-OTA COMPLEX

7W9N の概要

• エントリーDOI: 10.2210/pdb7w9n/pdb
• 分子名称: 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)
• 機能のキーワード: duplex, g-quadruplex, dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 10776.45

構造登録者

Xu, G.H.,Li, C.G. (登録日: 2021-12-10, 公開日: 2022-01-19, 最終更新日: 2024-05-15)

主引用文献

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

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: 35442665
DOI: 10.1021/jacs.2c00478

実験手法

SOLUTION NMR