Figure 6.

Secondary structure analysis of ribozyme 51 using SHAPE chemical probing. Error bars represent standard deviations from triplicate experiments. (A) Dependence of SHAPE reactivity on the presence of K⁺ and Mg²⁺. Colored symbols indicate the presence of K⁺ (blue), Mg²⁺ (red), and K⁺ and Mg²⁺ (green) during the probing reaction. (B) Secondary structure prediction, constrained by SHAPE probing data. The positions where the SHAPE accessibility was changed outside of error by the addition of cations were colored for K⁺ (blue), Mg²⁺ (red), and both K⁺ and Mg²⁺ (green). (C) Dependence of SHAPE reactivity on the presence of both Yb³⁺ and cTmp in the presence of K⁺ and Mg²⁺ (blue), compared to K⁺ and Mg²⁺ alone (green). (D) Secondary structure as in (A), showing the influence of the Yb³⁺/cTmp complex. Nucleotides colored in solid color had increased SHAPE reactivity, whereas letters colored in outlines had decreased SHAPE reactivity due to the Yb³⁺ / cTmp complex. Nucleotides in light grey were used for annealing the reverse transcription primer of the SHAPE assay.