A1 - Dynamic interplay between G-quadruplex RNA structures and pseudoknot formation

G-quadruplexes (G4) are unusual nucleic acid structures, formed by several stacks of G-tetrads. G4 formation is very dynamic, and their formation and unfolding are modulated by proteins in cells. It has been demonstrated that G4s form in living cells where they act as regulatory elements that dynamically support and modulate cellular processes (e.g., transcription). The recently emerged coronavirus SARS-CoV-2 has brought the alarming lack of antiviral treatment options against these pathogens to our attention. In preliminary analyses, we identified the presence of a G4 RNA structure in a programmed frameshift region of the viral genome. Because it involves several nucleotides engaged in a known pseudoknot at this region, it has been suggested that these two nucleic acid structures are incompatible. We hypothesize that G4 acts as a dynamic riboswitch element that contributes to viral replication by modulating the potential of forming a pseudoknot. How the G4 structure is regulated and how the dynamic interplay with the pseudoknot is mediated is unclear. Intriguingly, it was identified that the viral non-structural protein 3 (nsp3) can bind to viral RNA and is essential for viral replication. Interestingly, in vitro, it binds to G4 RNA. We will combine in vitro and in cellulo structural and functional analysis to unravel the dynamic formation and unfolding of viral G4 RNA and how this modulates pseudoknot formation. Further, we will address how nsp3 protein binding to G4 impacts these dynamic processes.