Extended Data Fig. 2: Secondary structure of the SARS-CoV-2 Frameshift Stimulation Element (FSE). | Nature Structural & Molecular Biology

Extended Data Fig. 2: Secondary structure of the SARS-CoV-2 Frameshift Stimulation Element (FSE).

From: Cryo-EM and antisense targeting of the 28-kDa frameshift stimulation element from the SARS-CoV-2 RNA genome

Extended Data Fig. 2

a. M2-seq Z-score plot for the 88 nt FSE, with numbering convention as used in the main text. b. Bootstrap confidence values for each base-pair, obtained from ShapeKnots guided by M2-seq Z-scores and the 1D DMS chemical mapping signal from M2-seq. Key structural features are indicated. c. Secondary structure of the FSE, as determined by using ShapeKnots guided by M2-seq Z-scores and the 1D DMS chemical mapping signal from M2-seq. Bootstrapping (100 iterations) support for each continuous helix is shown as an underlined percentage. Nucleotides are colored by 1D DMS chemical mapping signal, and nucleotides unreactive to DMS are depicted in grey. Inset depicts literature secondary structure. d. Secondary structure of the FSE as determined by 1D chemical SHAPE mapping with SHAPE reactivity data overlaid. Structure shown here is computed from ShapeKnots allowing for pseudoknots. Bootstrapping (100 iterations) support for each continuous helix is shown as an underlined percentage. e. Secondary structure as determined by 1D SHAPE mapping with DMS reactivity data overlaid. Helices that are also predicted with ShapeKnots guided by DMS mapping have bootstrapping support indicated.

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