Fig. 4: Effect of RNAP and Mn²⁺ on the conformational dynamics of the riboswitch.

Representative FRET trajectories for PEC-104 in the presence of only Mg²⁺ (a) and in the presence of both Mg²⁺ and Mn²⁺ (c) along with the corresponding Transition Occupancy Density Plots (TODP) and the transition rate constants calculated in the absence (b) and in the presence (d) of Mn²⁺, See also Supplementary Figs. 5 and 6. e–h Representative FRET trajectories for LNA-104 in the presence of only Mg²⁺ (e) and in the presence of both Mg²⁺ and Mn²⁺ (g) along with the corresponding Transition Occupancy Density Plots (TODP) and the transition rate constants calculated in the absence (f) and in the presence (h) of Mn²⁺, See also Supplementary Figs. 8 and 9. TODPs represent dynamic traces as “off-diagonal” and the static traces as “on-diagonal” contour, where the color scale shows the prevalence of each population. The riboswitch conformational state corresponding to each FRET value is indicated. U = Undocked, D* = Pre-Docked, D = Docked. Source data are provided with this paper at https://doi.org/10.7302/22513.