8IF5

AFB1-AF26 APTAMER COMPLEX

Summary for 8IF5

• Entry DOI: 10.2210/pdb8if5/pdb
• Descriptor: AFB1 DNA aptamer (26-MER), AFLATOXIN B1 (2 entities in total)
• Functional Keywords: dna aptamer, aflatoxin b1 (afb1), stem-loop, dna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 8255.36

Authors

Xu, G.H.,Wang, C.,Li, C.G. (deposition date: 2023-02-17, release date: 2023-07-19, Last modification date: 2024-05-15)

Primary citation

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

Experimental method

SOLUTION NMR