In Silico RNA Aptamer targeting the Receptor Binding Domain of the SARS-CoV-2 Omicron Variant Spike Protein

The rise of SARS-CoV-2 variants, especially Omicron, underscores the necessity for specific diagnostic tools. Aptamers are promising due to their high specificity and strong target affinity. This study aims to develop an RNA aptamer targeting the Omicron receptor binding domain (RBD. Initially, an oligonucleotide pool was constructed using RANDNA software and evaluated based on secondary structure properties. The 3D structures of the filtered sequences were modelled and docked with the Omicron RBD to identify the best aptamer candidates. The top three aptamer candidates which exhibited the highest number of binding site interactions, have been chosen for further analysis using molecular dynamics simulations. APT 6 exhibited negative docking score (-19.2 kcal/mol) and formed the greatest number of interactions with the mutated amino acids (G446S, Q493R, G496S, Q498R, N501Y and N505H) within the binding site. The RMSD and RMSF analyses of complex indicate good stability and flexibility, while Rg measurements reflected a compact and stable structure. The findings suggest that this APT 6 is tailored for detecting the Omicron variant, indicating its potential utility as a diagnostic tool.