Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics

• Main Authors: Suttinee Poolsup (Author), Emil Zaripov (Author), Nico Hüttmann (Author), Zoran Minic (Author), Polina V. Artyushenko (Author), Irina A. Shchugoreva (Author), Felix N. Tomilin (Author), Anna S. Kichkailo (Author), Maxim V. Berezovski (Author)
• Format: Book
• Published: Elsevier, 2023-03-01T00:00:00Z.
• Subjects: article
• Online Access: Connect to this object online.

Summary

The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6-3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.

Item Description

2162-2531
10.1016/j.omtn.2023.02.010