In vitro Selection of an Aptamer Targeting SARS-CoV-2 Spike Protein with Nanopore Sequence Identification Reveals Discrimination Between the Authentic Strain and Omicron

DNA aptamers are oligonucleotides specifically bound to target molecules that can serve as antibodies of nucleic acid nature. For diagnosing the infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), methods using antibodies specific to antigens on the virus are broadly used. We generated by classical SELEX a number of aptamers, interacting with the receptor-binding domain of SARS-CoV2 spike protein (SARS-CoV2 Spike RBD) from Wuhan-Hu-1 strain. The sequence identification was performed using a novel methodology based on the nanopore sequencing. For sequence identification of selected aptamers, we created the novel protocol for aptamer identification based on nanopore sequencing. We identified the best aptamer candidate named MEZ. It was chemically synthesized and tested for binding with SARS CoV2 Spike RBD domain of the S-protein from different strains. Kd of the complex is 6.5 nM being comparable with known aptamers. Virus neutralization tests demonstrate similar results for already known and MEZ aptamers. We identified differences for aptamers binding to SARS-CoV-2 Spike RBD from Wuhan-Hu-1 and Omicron strains. MD simulations reveal that the number of hydrogen bonds between the protein and aptamer is higher for the more stable complex. Moreover, dynamic network analysis show that the motions of the aptamer and protein are correlated to a higher extent in a more stable complex. Based on the experimental data and computational results we can conclude that the authentic RBD-aptamer complex has two specific points for interaction and the 3'-end of aptamer is responsible for strain identification. Therefore, the selected aptamer based on experimental data can be an alternative biological element for the development of SARS-CoV-2 diagnostic testing with strain specificity and cost efficiency due to the short length of aptamer being 31 nucleotides.