Tying the knot: Unraveling the intricacies of the coronavirus frameshift pseudoknot
Fig 2
Dominant SARS-CoV-2 pseudoknot motif predictions via Shapify.
SARS-CoV-2 frameshift element sequence shown as a horizontal line from 5′ (left) to 3′ (right). Arcs represent predicted base pairs. Top arc diagram includes 3_6 motif components (see Table 2 for dot-bracket format) of the fifth most stable structure predicted via Shapify (see Sections 2.4–2.6) for the 144 nt sequence (free energy −29.45 kcal/mol). Initial stem 5 base pairs in red (free energy −4.22 kcal/mol). Downstream pseudoknot target sequence highlighted in red. Bottom arc diagram includes 3_3 motif component of the MFE structure predicted via Shapify for the 144 nt sequence (free energy −30.93 kcal/mol). Initial stem 2 base pairs in light blue (free energy −6.1 kcal/mol). Initial stem 1 base pairs in dark blue (free energy −11.48 kcal/mol).