Folding Kinetics of Riboswitches A tractable concentration-dependent approach

The interaction of RNAs and their ligands strongly depends on folding kinetics and thus requires explanations that go beyond thermodynamic effects. Whereas the computational prediction of minimum energy secondary structures, and even RNA–RNA and RNA–ligand interactions, are well established, the analysis of their kinetics is still in its infancy. Due to enormous conformation spaces, the exact analysis of the combined processes of ligand binding and structure formation requires either the explicit modeling of an intractably large conformation space or—often debatable—simplifications. Moreover, concentration effects play a crucial role. This increases the complexity of modeling the interaction kinetics fundamentally over single molecule kinetics. This work presents a novel tractable method for computing RNA–ligand interaction kinetics under the widely-applicable assumption of ligand excess, which allows the pseudo-first order approximation of the process. It rigorously outlines the approach and discusses model parametrization from empirical measurements. Furthermore, the kinetics of the designed theophylline riboswitch RS3 are studied at different ligand concentrations and with respect to co-transcriptional effects. Additionally, the concept of canonical landscapes is put on a solid theoretical foundation, defining a symmetrical move set yielding a connected landscape as well as direct paths in these. Furthermore, a heuristic approach for partially exploring energy landscapes around a given structure of interest is described. All results are implemented as usable software tools.