Fig. 2: PolyA loop stacking mediates tradeoff between sensitivity and dynamic range.

a Secondary structure schematic of A→C mutational scans in which riboswitch variants with different length polyA loops were mutated at each position within the loop from A to C to disrupt local A-A stacking. Positional coordinates refer to the distance from the 3’ end of the loop. b EC₅₀ measurements for mutational scans of different length terminator loops into which single A→C mutations have been made at every position. c Fold change of the mutational scans in (b). d EC₅₀ measurements of riboswitch variants with polyA loops of varying lengths into which either no mutations have been made (polyA), the third to last residue relative to the 3’ end of the loop has been mutated to C (−3C), the initial invading residue G108 has been mutated to C (G108C), or both mutations have been made (−3C G108C). e Fold change of the mutational scans in (d). f Vfold3D models of the nucleated Cbe pfl terminator loop featuring either a length 7 or length 3 polyA loop. The longer loop allows continuous stacking of A residues within the 3’ end of the loop and the G108 invader residue, while the shorter loop does not allow enough slack for stacking to occur in this conformation. Additional loop length models in Fig. S7. Data in (b), (c), (d) and (e) are determined as described in Methods, from dose response curves including n = 9 biological replicates at each of 8 concentrations. Error bars in (b), (c), (d) and (e) indicate standard error of the fit parameter. Source data are provided as a Source Data file.