8IF5

AFB1-AF26 APTAMER COMPLEX

8IF5 の概要

• エントリーDOI: 10.2210/pdb8if5/pdb
• 分子名称: AFB1 DNA aptamer (26-MER), AFLATOXIN B1 (2 entities in total)
• 機能のキーワード: dna aptamer, aflatoxin b1 (afb1), stem-loop, 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: 8255.36

構造登録者

Xu, G.H.,Wang, C.,Li, C.G. (登録日: 2023-02-17, 公開日: 2023-07-19, 最終更新日: 2024-05-15)

主引用文献

Xu, G.,Wang, C.,Yu, H.,Li, Y.,Zhao, Q.,Zhou, X.,Li, C.,Liu, M.
Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer.
Nucleic Acids Res., 51:7666-7674, 2023

PubMed Abstract: The 26-mer DNA aptamer (AF26) that specifically binds aflatoxin B1 (AFB1) with nM-level high affinity is rare among hundreds of aptamers for small molecules. Despite its predicted stem-loop structure, the molecular basis of its high-affinity recognition of AFB1 remains unknown. Here, we present the first high-resolution nuclear magnetic resonance structure of AFB1-AF26 aptamer complex in solution. AFB1 binds to the 16-residue loop region of the aptamer, inducing it to fold into a compact structure through the assembly of two bulges and one hairpin structure. AFB1 is tightly enclosed within a cavity formed by the bulges and hairpin, held in a place between the G·C base pair, G·G·C triple and multiple T bases, mainly through strong π-π stacking, hydrophobic and donor atom-π interactions, respectively. We further revealed the mechanism of the aptamer in recognizing AFB1 and its analogue AFG1 with only one-atom difference and introduced a single base mutation at the binding site of the aptamer to increase the discrimination between AFB1 and AFG1 based on the structural insights. This research provides an important structural basis for understanding high-affinity recognition of the aptamer, and for further aptamer engineering, modification and applications.

PubMed: 37351632
DOI: 10.1093/nar/gkad541

実験手法

SOLUTION NMR