Fig. 4: The effect of slower unwinding speed and artificial pausing on riboswitch folding.
a VF histograms for WT ZTP riboswitch unwound by PcrA-X in the presence of 0.1 mM ZMP are shown with Gaussian fits to heteroduplex (blue), terminator (green), and aptamer (magenta) populations. b The percentage of aptamer-containing conformation obtained by VF with Rep-X (black) and PcrA-X (red) are shown in the presence of 0.01 to 1 mM ZMP. The percentage of aptamer-containing conformation obtained by VF for pause mimics at positions 40 and 55 (magenta and cyan, respectively) are shown. All values are mean ± s.d. shown as large open circles with n = 2–4 independent experiments shown as small circles and offset for clarity. c Cartoon depicting the pause mimic complex at position 54, in which a cDNA is hybridized only to nt 55–94 of the WT ZTP riboswitch. Addition of ATP initiates unwinding starting from nt 55 in this complex. d EFRET histograms of the cDNA:WT heteroduplexes mimicking a pause at position 55 before (top) and after (bottom) addition of ATP in the presence of 0.1 mM ZMP, as measured by VF with Rep-X. e EFRET histograms of the pause-mimicking heteroduplexes at position 40 before (top) and after (bottom) addition of ATP in the presence of 0.1 mM ZMP, as measured by VF with Rep-X.
