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Related Concept Videos

Coronavirus01:29

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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High-throughput Confocal Imaging of Quantum Dot-Conjugated SARS-CoV-2 Spike Trimers to Track Binding and Endocytosis in HEK293T Cells
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In-Silico Selection of Aptamer Targeting SARS-CoV-2 Spike Protein.

Yu-Chao Lin1,2, Wen-Yih Chen3, En-Te Hwu4

  • 1Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, China Medical University Hospital, Taichung 404333, Taiwan.

International Journal of Molecular Sciences
|May 28, 2022
PubMed
Summary

Researchers developed a new aptamer, RBD-1CM1, for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This aptamer shows improved binding affinity and stability, offering a promising tool for rapid SARS-CoV-2 diagnostics.

Keywords:
COVID-19DNA aptamerSARS-CoV-2aptamer–protein interactioninfectious diseasemolecular dynamics simulationspike protein

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Area of Science:

  • Biotechnology
  • Molecular Biology
  • Virology

Background:

  • Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection is crucial for timely diagnosis and control.
  • Conventional diagnostic methods often rely on DNA amplification or antibody detection.
  • Aptamers offer a promising alternative for specific molecular recognition.

Purpose of the Study:

  • To develop and identify novel aptamers with enhanced binding affinity and stability for SARS-CoV-2 detection.
  • To screen mutated aptamer sequences targeting the SARS-CoV-2 spike protein receptor-binding domain (RBD).
  • To evaluate the potential of aptamers as diagnostic tools for SARS-CoV-2.

Main Methods:

  • Generation and screening of mutated aptamer sequences derived from a known SARS-CoV-2 RBD aptamer.
  • Utilizing structural similarity, molecular docking, and molecular dynamics (MD) simulations for aptamer selection.
  • Experimental validation using quartz crystal microbalance (QCM) to assess binding affinity and signal response.

Main Results:

  • Identified two mutated aptamers, RBD-1CM1 and RBD-1CM2, with superior docking results compared to the parent aptamer.
  • MD simulations confirmed RBD-1CM1 forms the most stable complex with the SARS-CoV-2 S protein RBD.
  • QCM analysis demonstrated that RBD-1CM1 exhibits improved binding affinity and larger signal changes.

Conclusions:

  • The RBD-1CM1 aptamer is a highly promising candidate for SARS-CoV-2 detection.
  • This aptamer demonstrates enhanced stability and binding affinity for the SARS-CoV-2 spike protein RBD.
  • RBD-1CM1 offers a potential alternative biological element for developing advanced SARS-CoV-2 diagnostic tests.