Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot
Fig 7
Convergence to the most stable structures that contain the 3_3 motif.
144 nt window Shapify predictions with initial stems 1 and 2 as constraint result in the MFE and most stable structures that contain the 3_3 motif. Initial stems are labeled on the left (e.g., S1 for initial stem 1). Darker grey path indicates the structure predicted with a specific initial stem was the same for two SHAPE datasets. Light grey path indicates the structure predicted with an initial stem was specific to one SHAPE dataset. Structures on the right are labeled by free energy proximity to the MFE structure. For example, MFE-1 is the lowest free energy structure after the MFE structure. Differences from the MFE structure are marked in bold, with parentheses representing changes in paired bases, and asterisks representing predicted unpaired bases that were paired in the MFE structure. The 3_3 motif pseudoknotted base pairs are shown in light blue.