Fig. 6: Delaying EP nucleation sensitizes diverse riboswitches.
From: RNA folding kinetics control riboswitch sensitivity in vivo
a Schematic of the Bsu pbuE* leader truncation variant of the pbuE transcriptional ON riboswitch62. A weak direct toehold facilitates nucleation of the EP, in which an invader (gold) strand displaces P1 (black and red) to form the terminator hairpin. Arrow indicates the position of polyA bulge extension (d) EC50 measurements of pbuE polyA bulge variants. b Schematic of the Bce crcB fluoride transcriptional ON riboswitch. A direct toehold facilitates nucleation of the EP, in which an invader (gold) strand displaces the pseudoknot (black and red) to form the terminator hairpin. Boxes show terminator extension inserts appended to the end of the terminator hairpin. c Schematic of the Bsu yxjA transcriptional OFF riboswitch. A weak toehold comprising P4 and an internal loop facilitates nucleation of the EP, in which an invader (gold) strand displaces P1 (black and red) to form the central helix. The terminator loop (teal) can close to allow a second invader (blue) to displace the central helix (red and gold) and form the terminator hairpin. The second strand displacement process gives this switch OFF logic. Boxes show terminator loop extension variants, and two types of P4 spacer mutations: P4 truncations with different lengths added back, and P4 extensions. e EC50 measurements of crcB terminator extension variants. f EC50 values of yxjA terminator loop extension mutants. g EC50 measurements of yxjA P4 spacer mutations. Data in panels (d), (e), (f), and (g) are determined as described in Methods, from dose response curves including n = 9 biological replicates at each of 8 concentrations. Error bars in (d), (e), (f), and (g) indicate standard error of the fit parameter. Source data are provided as a Source Data file.
