Engineered DNA Aptamer-Spike RBD-ACE2 Tri-Complex: Mechanism of Pan-Variant Steric Inhibition

This 3D model illustrates the structural basis of broad-spectrum viral neutralization mediated by an engineered DNA aptamer with high selectivity for the SARS-CoV-2 Spike glycoprotein Receptor Binding Domain (RBD). Unlike conventional monoclonal antibody therapeutics, which remain vulnerable to single-point mutational escape, this synthetic oligonucleotide is rationally designed to engage structurally conserved, conformationally constrained epitopes at the ACE2-interacting interface, residues subject to strong purifying selection pressure across circulating variants.

The visualization renders a ternary molecular complex comprising the human ACE2 ectodomain, the viral Spike RBD in its receptor-accessible "up" conformation, and the bound DNA aptamer. Derived from all-atom molecular dynamics (MD) simulations, the model captures a steric occlusion event in which the aptamer outcompetes ACE2 for overlapping contact residues, inhibiting productive receptor engagement through direct competitive exclusion.

The surface mesh quantifies a minimum intermolecular distance between the RBD and ACE2 interface exceeding the threshold required for stable receptor-ligand complex formation. This geometry reflects the aptamer's capacity to sustain high-avidity neutralization across phylogenetically distinct lineages including Omicron subvariants BA.2, BA.4/5, and XBB. This establishes it as a mutation-resilient antiviral scaffold with broad translational relevance.