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Coronavirus

Coronavirus

Coronaviruses, including the severe acute respiratory syndrome coronavirus (SARS-CoV), are enveloped viruses characterized by their single-stranded, positive-sense RNA genome and helical nucleocapsid structure. The hallmark of these viruses is their club-shaped spike (S) glycoproteins that protrude from the viral envelope, facilitating attachment to host cells. Typically, coronaviruses infect the upper respiratory tract, often causing mild or asymptomatic disease. However, certain strains like...

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Updated: Jul 8, 2026

Engineering Antiviral Agents via Surface Plasmon Resonance

Engineering Antiviral Agents via Surface Plasmon Resonance

Published on: June 14, 2022

Engineering functionally-optimized aptamers against SARS-Cov-2 for blocking spike-ACE2 interaction and aptasensor

Xiangdong Lai¹, Weiwei Zhao², Lihua Jiang³

¹State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China.

Materials Today. Bio

|July 11, 2025

Summary

This study introduces a novel strategy using exonuclease III (Exo III) digestion and in silico simulation to engineer high-affinity aptamers. This method optimizes aptamers for detecting SARS-CoV-2 spike protein (S1) and improves aptasensor performance.

Keywords:

Aptamer optimization Aptasensors Exonuclease III digestion In silico simulation Inactivated virus detection SARS-CoV-2 spike

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Area of Science:

Biotechnology
Molecular Biology
Nanotechnology

Background:

Limited understanding of aptamer structure-function relationships and conformational dynamics hinders aptamer engineering.
Developing high-affinity aptamers with defined structures is crucial for advanced applications.

Purpose of the Study:

To present a novel optimization strategy for aptamer engineering using Exo III digestion and in silico simulation.
To clarify the 3D structure and conformational dynamics of aptamer-target complexes.
To develop a high-affinity aptamer for SARS-CoV-2 spike protein (S1) and construct a functional aptasensor.

Main Methods:

Combined exonuclease III (Exo III) digestion with in silico simulation for aptamer optimization.
Mutated and truncated a parent aptamer (Apt2) against SARS-CoV-2 S1 to create derivatives.
Fabricated an aptasensor using a nickel-doped zeolitic imidazolate framework-8 (NZIF-8) loaded with Rhodanine (Rho) and the optimized aptamer (Seq3).

Main Results:

Developed an optimized aptamer (Seq3) with higher affinity for S1 and improved blocking of S1-angiotensin-converting enzyme 2 (ACE2) interaction.
Demonstrated the efficacy of the post-SELEX strategy for functional aptamer acquisition.
The fabricated aptasensor (NZIF-8-Rho-Apt) showed excellent performance in detecting inactivated SARS-CoV-2 in spiked samples.

Conclusions:

The combined Exo III digestion and in silico simulation strategy is effective for engineering high-affinity and functional aptamers.
This approach aids in elucidating aptamer-target complex structures and conformational dynamics.
The developed aptasensor offers a promising tool for detecting inactivated viruses.