A Topology-Matching Spike Protein-Capping Tetrahedral DNA Nanocrown for SARS-CoV-2 Neutralization

The constantly mutating severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) poses great risk of efficacy loss to the present neutralizing therapeutics. Thus, it is urgently needed to develop versatile strategies that enable rapid design and engineering of potent neutralizing therapeutics for newly emerging variants. Herein, we present an unprecedented DNA nanocrown that can topologically match and multivalently bind the S-trimer of SARS-CoV-2 and thereby inhibit its infection to host cells. A neutralizing aptamer binding the N-terminal domain (NTD) supersite of the S protein was first screened and identified. It was further elaborately engineered onto the best fitting tetrahedral DNA nanostructure to form a spike protein-capping nanocrown, which can effectively block not only wild-type (WT) SARS-CoV-2 pseudovirus, but also several important mutants including D614G, N501Y, and Delta 69-70. Significantly, it can evidently diminish the RNA copies of authentic WT SARS-CoV-2 in host cells by 4.6 orders of magnitude. Therefore, utilizing the aptamer selection method and the dedicated engineering route, our topology-matching DNA framework provides a versatile platform for SARS-CoV-2 inhibition and has the potential to be facilely expanded to newly emerging variants and other fatal coronaviruses. [GRAPHICS] .