Fig. 6: Effect of NusA on the global conformation of the riboswitch.
From: A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration
a smFRET experimental setup. Paused Elongation Complex (PEC) immobilization utilizes biotinylated E. coli RNAP. Location of donor (Cy3 – green) and acceptor (Cy5 – red) fluorophores are indicated. Representative donor-acceptor (top) and smFRET (bottom) traces for NusA-Bound PEC-104 in the absence (b) and presence (c) of 0.5 mM Mn2+. Probability FRET histogram for each trace is indicated on the right. SmFRET histograms of NusA-bound PEC-104 in the presence of only Mg2+ (d) along with the corresponding Transition Occupancy Density Plots (TODP) and the determined transition rate constants (e). SmFRET histograms of NusA-bound PEC-104 in the presence of both Mg2+ and Mn2+ (f) along with the corresponding Transition Occupancy Density Plots (TODP) and the determined transition rate constants (g). The SD of each FRET value is reported. The total number of traces (N) included in each histogram is indicated on top right corner. See also Supplementary Figs. 16 and 17. 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.
