In Silico Analysis of Toehold-Aptamer Sequences Targeting the SARS-CoV-2 Nucleocapsid Protein Gene for Biosensor Development

Abstract

The COVID-19 pandemic has emphasized the need for rapid and affordable on-site virus detection. While enzyme-linked aptamer-based biosensors have proven effective, their utility for SARS-CoV-2 detection remains unexplored. We performed in silico analysis of three toehold-aptamer sequences targeting the SARS-CoV-2 nucleocapsid protein gene, with secondary and tertiary structures modeled using mFold and RNAComposer web servers. Molecular docking simulations were challenging due to computational and molecular constraints. Nevertheless, our findings indicate that experimental procedures to assess aptamer–target interactions in vitro under optimal assay conditions are feasible. Successful development of a biosensor using these aptamers could offer a quick and inexpensive method for SARS-CoV-2 detection, addressing the COVID-19 pandemic.

Keywords

• SARS-CoV-2 virus
• biosensors
• aptamers
• nanozymes
• point-of-care-diagnosis
• COVID-19 disease