FIGURE 3.

Experimentally informed models of the cotranscriptional and equilibrium-refolded RNA folding pathways for E. coli thiB riboswitch in the presence and absence of TPP. R2D2 models of secondary structure intermediate in the folding pathway. One hundred secondary structure models were generated from the experimental data for each intermediate RNA length. Models are depicted as RNA bow plots (0 mM TPP top, 1 mM TPP bottom), where arcs between nucleotides represent base pairs in a particular structure, arc thickness is proportional to the number of times that base pair is present in the one hundred structure set, and arcs are color coded according to portions of the riboswitch models. Secondary structure depictions are the consensus structure over the 100 iterations. Models and consensus structures from cotranscriptional SHAPE-Seq data sets at TLs (A) 87 nt, (B) 100 nt, (C) 131 nt, (D) 142 nt, and from equilibrium-refolded SHAPE-Seq data sets at TL (E) 89 nt, (F) 105 nt, (G) 133 nt, (H) 142 nt. Representative lengths for cotranscriptional and refolded conditions were chosen to be similar but do not exactly match due to differences in read coverage (see Materials and Methods).