Figure 6.

Ligand modulated structural stability of the pseudoknot determines S1-mediated unfolding. Representative smFRET traces, corresponding histograms and TODP plots for the ligand-bound pseudoknots in the absence (A, C, E) and presence (B, D, F) of 250 nM S1. Ligand concentrations were 200 nM preQ₁ (A, B), 5 μM Gua (C, D) and 500 μM of DAP (E, F). The folded pseudoknot conformation is significantly stabilized in the presence of saturating concentrations of ligand. However, S1 can unfold the pseudoknot in the presence of weak ligands (Gua or DAP).