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In Vitro Selection of Aptamers to Differentiate Infectious from Non-Infectious Viruses

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

Guohua Xu¹, Jiajing Zhao^1,2, Na Liu^1,2

¹Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.

Nucleic Acids Research

|May 8, 2019

Summary

A new structure-guided method significantly enhances aptamer affinity for Ochratoxin A (OTA) by over 50-fold. This approach optimizes aptamer selection for improved biosensor development.

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Area of Science:

Biochemistry
Molecular Biology
Biotechnology

Background:

Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is crucial for aptamer discovery.
Improving aptamer affinity is essential for applications in biosensors and medicine.
Existing aptamer optimization methods lack structure-guided precision.

Purpose of the Study:

To introduce and validate a structure-guided post-SELEX approach for enhancing aptamer affinity.
To investigate the molecular interactions governing aptamer-Ochratoxin A (OTA) recognition.
To develop a high-affinity aptamer for potential use in OTA biosensors.

Main Methods:

Structure-guided design of aptamers post-SELEX.
Nuclear Magnetic Resonance (NMR) spectroscopy to determine aptamer-ligand complex structure.
Analysis of molecular interactions, including hydrogen and halogen bonds.

Main Results:

A novel aptamer with over 50-fold increased affinity for OTA was designed.
The high-resolution NMR structure revealed an unusual hairpin conformation with an intramolecular triple helix.
Specific interactions (π-π stacking, hydrophobic, hydrogen, and halogen bonds) were identified, with halogen bonds crucial for discriminating OTA from OTB.

Conclusions:

The structure-guided post-SELEX approach effectively enhances aptamer affinity.
Detailed structural insights explain the high-affinity and specific recognition of OTA.
This strategy holds promise for developing advanced OTA biosensor systems.