Structure-guided post-SELEX optimization of an ochratoxin A aptamer

SELEX is the cornerstone for aptamer research with broad applications in biosensors and medicine. To improve the affinity of selected aptamers, we propose a structure-guided post-SELEX approach, an optimization method based on the precise secondary structure of the aptamer-ligand complex. We demonst...

Full description

Saved in:
Bibliographic Details
Published in:Nucleic acids research 2019-06, Vol.47 (11), p.5963-5972
Main Authors: Xu, Guohua, Zhao, Jiajing, Liu, Na, Yang, Minghui, Zhao, Qiang, Li, Conggang, Liu, Maili
Format: Article
Language:English
Subjects:
Aptamers, Nucleotide - chemistry
Aspergillus ochraceus - metabolism
Biosensing Techniques - methods
Chlorine - chemistry
DNA, Single-Stranded - chemistry
Halogens - chemistry
Hydrogen Bonding
Ligands
Limit of Detection
Magnetic Resonance Spectroscopy
Molecular Conformation
Ochratoxins - chemistry
Penicillium - metabolism
Protein Conformation
Protein Structure, Secondary
SELEX Aptamer Technique
Structural Biology
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:SELEX is the cornerstone for aptamer research with broad applications in biosensors and medicine. To improve the affinity of selected aptamers, we propose a structure-guided post-SELEX approach, an optimization method based on the precise secondary structure of the aptamer-ligand complex. We demonstrate this approach using the Ochratoxin A (OTA) aptamer. Guided by the structure, we designed a new aptamer whose affinity is improved by more than 50-fold. We also determined the high-resolution NMR structure of the new aptamer-OTA complex and elucidated the discriminatory recognition mechanism of one atomic difference between two analogs, OTA and OTB. The aptamer forms an unusual hairpin structure containing an intramolecular triple helix, which is not seen in the previously determined aptamer complex. The π-π stacking, the hydrophobic interaction, hydrogen bonds and halogen bonds between OTA and the aptamer contribute to the recognition of OTA, and the halogen bonds play an important role in discriminating between OTA and OTB. Our results demonstrate that the structure-guided post-SELEX approach improves aptamers affinity. An improved OTA biosensor system might be developed using this new strategy.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkz336