Supplementary Figure 5: Nucleotide trace reactivity profiles for key regions of the WT fluoride riboswitch over the course of transcription.
From: Cotranscriptional folding of a riboswitch at nucleotide resolution
(a) Single nucleotide trajectories displaying changes in the reactivities of nucleotides G12, G13, A14, G15, and U16 of the wt fluoride riboswitch when transcribed with either 0 mM (gray) or 10 mM NaF (black). Data for part (a), and all subsequent parts, is taken from the cotranscriptional SHAPE-Seq matrices in Fig. 3b. (b) Single nucleotide trajectories displaying changes in the reactivities of nucleotides A24, A25, and C27 of the wt fluoride riboswitch when transcribed with either 0 mM (gray) or 10 mM NaF (black). Positions U23 and A26 in this region show low reactivities that persist throughout transcription. (c) Single nucleotide trajectories displaying changes in the reactivities of nucleotides A52, G53, U54, and A55 of the wt fluoride riboswitch when transcribed with either 0 mM (gray) or 10 mM NaF (black). These nucleotides are found on the upper 5’ side of the terminator. (d) Single nucleotide trajectories displaying changes in the reactivities of nucleotides A67, G68, G69, A70, G71, and U72 of the wt fluoride riboswitch when transcribed with either 0 mM (gray) or 10 mM NaF (black). These nucleotides comprise the ribosome binding site (RBS) found in the 3’ side of the terminator stem. Results shown are extracted from Fig. 3b.
