Structure of the 5′ Untranslated Region of Enteroviral Genomic RNA

Figures

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  FIG 1. SHAPE reactivity traces by position. Reactivity traces for independent SHAPE experiments are overlaid on the graphs. Raw data for all SHAPE reactivity values for all experiments and all positions, together with means and standard deviations for each position, are listed in Table S3. (A) Reactivity traces for positions 150 to 300. (B) Reactivity traces for positions 301 to 450.

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  FIG 2. Secondary-structure model for the CV-B3 5′ UTR. SHAPE reactivity at each position is indicated by red shading. No shading shows no/low reactivity, with a normalized reactivity value below 0.3. Light-red shading shows moderate reactivity, with a normalized reactivity value between 0.3 and 0.7. Dark-red shading shows high reactivity, with a normalized reactivity value above 0.7. Domains are labeled I to VI. Stem-loops in domains with junction loops are labeled with letters. Two long-range interactions are labeled as LR-1 and LR-2.

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  FIG 3. Circle diagram comparing secondary-structure models generated by SHAPE reactivity and base-specific reactivity. Nucleotide positions are displayed outside the circle. Base pairs are connected by lines inside the circle. Differences in the models generated are shown in red and black. PPV, positive predictive value.

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  FIG 4. WebLogos showing sequence conservation of positions in proposed long-range interactions LR-1 (A) and LR-2 (B) and in the domain V stem (C). Proposed base-pairing interactions are shown by connecting lines.

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  FIG 5. SHAPE reactivity traces by position for positions 503 to 608. Reactivity traces for independent SHAPE experiments are overlaid on the graph. The traces show consistent reactivity for regions upstream and downstream of the proposed intrinsically disordered RNA region (positions 561 to 581).