SARS-CoV‑2 RNA's Dual Identity: G‑Quadruplex versus Hairpin.

Regardless of advances in biophysical assays for studying G-quadruplexes formation, their high-resolution structural characterization remains limited. In this computational study, the 2D and 3D geometry, energetics, and dynamics of the SARS-CoV-2 potential quadruplex at position 28903 were studied. Two- and three-dimensional structures for four G4-Quadruplexes and three hairpins were predicted using bioinformatics tools. The dynamics, relative stability, impact, and presence of a pseudouridine site were examined in detail. It was hypothesized that the dynamic stability of G4-quadruplexes critically depends on the number of Hoogsteen connections, which stabilize the G4-quadruplex structure. It was also shown that the presence of pseudouridine colocalized with potential quadruplex at position 28903 could enhance the dynamic stability of hairpins and destabilize the structure of G4-quadruplex up to direct unwinding.