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. 2019 Dec 13;48(4):2107–2125. doi: 10.1093/nar/gkz1166

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 8. — Model of S1-mediated unfolding of the Tte-pseudoknot. S1 preferentially binds to the pre-folded conformation (E_FRET = 0.82) of the Tte riboswitch pseudoknot and stabilizes a partially unfolded conformation (E_FRET = 0.77). The S1 bound pseudoknot can also transiently form a more completely unfolded conformation (E_FRET = 0.45) that folds quickly to either the pre-folded conformation or folded conformation (E_FRET = 0.96). The ability of S1 to unfold the pseudoknot strongly depends on the stability of the pseudoknot, which can be altered by using ligands of varying affinity to the pseudoknot. S1 cannot interact with the strong ligand-bound, stably-folded pseudoknot, but can significantly interact with and unfold the weak ligand-bound, weakly-folded pseudoknot.