Crystallographic and cryoEM analyses reveal SARS-CoV-2 SL5 is a mobile T-shaped four-way junction with deep pockets

Fluorescence resonance energy transfer (FRET) analysis of stem–loop 5 (SL5) in solution. (A) Overview of labeling scheme. Cy3 was placed at C203, while Cy5 was at either C241 or the 3′ end. Distances predicted from the crystal structure are noted. (B) E_FRET values measured for each RNA with Cy5 at C241 or the 3′ end in the presence and absence of Mg²⁺. (C) Corresponding distances (R) using an R₀ of 60 Å for the Cy3–Cy5 FRET pair. Error bars indicate standard deviations (n = 6 independent measurements). The changes observed upon Mg²⁺ addition are not statistically significant.