A highly specific aptamer for the SARS-CoV-2 spike protein from the authentic strain

Area of Science:

• Molecular Biology
• Biochemistry
• Biotechnology

Background:

• DNA aptamers offer an alternative to antibodies for molecular recognition.
• SARS-CoV-2 spike protein's receptor-binding domain (RBD) is a key target for diagnostics and therapeutics.

Purpose of the Study:

• To identify and characterize a novel DNA aptamer with high specificity for the SARS-CoV-2 Wuhan-Hu-1 RBD.
• To elucidate the binding mechanism and strain-specific recognition of the identified aptamer.

Main Methods:

• Systematic Evolution of Ligands by Exponential Enrichment (SELEX) for aptamer selection.
• Nanopore sequencing for aptamer identification.
• Chemical synthesis and biophysical characterization of the aptamer (e.g., K_d determination).

Main Results:

• Identified the MEZ DNA aptamer with high affinity (K_d = 6.5 nM) for the Wuhan-Hu-1 SARS-CoV-2 RBD.
• Demonstrated strain-specific binding; MEZ does not bind to RBD from Beta, Delta, or Omicron variants.
• Revealed that the MEZ aptamer binds to the same site as ACE2 and identified key functional regions (3'-end for specificity, 5'-end for structure).

Conclusions:

• The MEZ aptamer is a potent and specific binder of the ancestral SARS-CoV-2 RBD.
• Its strain-specificity and small size make it a promising candidate for diagnostic and therapeutic applications.
• Understanding the binding mechanism provides insights for aptamer design.