Figure 4: SHAPE reactivity of domain A^ISO mapped onto the secondary structure.

Base pairs predicted from the secondary structure of the intact SSU are indicated by black lines. Base pairs in the linkers are indicated by red lines. Helix and nucleotide numbers are indicated. (a) Absolute SHAPE reactivity of domain A^ISO in the presence of Na⁺ only (250 mM). The red circles indicate high reactivity while the blue circles indicate low reactivity. The color scale is shown in the outbox. (b) Difference in SHAPE reactivity upon addition of Mg²⁺ (2 mM) (c) Difference in SHAPE reactivity upon mutation of C18 to A18. (d) Difference in SHAPE reactivity upon excision of helix 28. For panels b-c, red indicates a increase in reactivity, while blue indicates a decrease. Green indicates no change. The coloring scheme is shown in the outbox. Shape data for mutant and truncated domain A^ISO were acquired in the presence of both Na⁺ and Mg²⁺. Data were not obtained for the uncolored nucleotides. The primer binding tail is omitted for clarity. The full sequence of the construct is shown in the Supplementary Information (Supplementary Fig. 7).