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. Author manuscript; available in PMC: 2011 Jul 28.
Published in final edited form as: J Am Chem Soc. 2010 Jul 28;132(29):9940–9943. doi: 10.1021/ja103781u

Figure 4.

Figure 4

Absolute SHAPE reactivities determined by RNase R degradation superimposed on secondary structure models for the 80 nt TPP riboswitch in the (A) absence and (B) presence of TPP ligand. Nucleotides are colored by SHAPE reactivity using the scale shown in Figure 3. All nucleotides in the RNA are shown; the small number of positions for which no data were obtained are gray. (C) Increases (red) or decreases (blue) in SHAPE reactivity upon TPP ligand binding superimposed on the three-dimensional riboswitch structure.