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. 2012 Mar 1;109(12):4639–4644. doi: 10.1073/pnas.1116269109

Fig. 5.

Fig. 5.

SHAPE analysis of the 66-nt element and mutants. Upper: SHAPE reactivities, determined from the sequencing gels in Fig. S6. Residues with intensities between 0 and 20%, 20% and 50%, and 50% and 100% are labeled gray, yellow, and red, respectively. Bars show the amounts of modification at each position relative to the most highly modified nucleotide. Numbers denote nucleotide position. Lower: SHAPE modification intensities mapped onto the predicted secondary structures; structures were generated using RNAfold (35). Residues with intensities between 0 and 20%, 20% and 50%, and 50% and 100% are shown in gray, yellow, and red, respectively. Both ΔG and ΔGs (predicted with SHAPE data) were generated using RNAstructure (28). Numbers denote nucleotide position.