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Fig. 2 | BMC Bioinformatics

Fig. 2

From: Tractable RNA–ligand interaction kinetics

Fig. 2

Kinetics plots showing the probabilities of prominent monomer and dimer states (y-axis) over time in seconds (x-axis) at a RNA folding rate of 106 s −1 and a dimerization rate of 600M−1 s −1. Additionally, we visualize the the most prominent macrostates by their local minimum structures, which enables tracking of their coarse-grained refolding. a–c Complete riboswitch RS3 at concentrations 104 M (a), 105 M (b), and 105 M (c). d–f Partially transcribed riboswitch RS3 (without 3’-half of terminator stem) at concentrations 10−7 M (d), 10−6 M (e), and 10−3 M (f). Note that since subfigures a–c are based on exactly the same landscapes, they share the same macrostates (e. g., mon1 in a and mon1 in b are equal). As well, this holds among subfigures d–f. However, across the two groups of subfigures, macrostates are not comparable (e. g., mon1 of a ≠ mon1 of d), since the landscapes differ

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