Molecular Dynamics Simulations with Grand-Canonical Reweighting Suggest Cooperativity Effects in RNA Structure Probing Experiments

Chemical probing experiments such as SHAPE are routinelyused toprobe RNA molecules. In this work, we use atomistic molecular dynamicssimulations to test the hypothesis that binding of RNA with SHAPEreagents is affected by cooperative effects leading to an observedreactivity that is dependent on the reagent concentration. We developa general technique that enables the calculation of the affinity forarbitrary molecules as a function of their concentration in the grand-canonicalensemble. Our simulations of an RNA structural motif suggest that,at the concentration typically used in SHAPE experiments, cooperativebinding would lead to a measurable concentration-dependent reactivity.We also provide a qualitative validation of this statement by analyzinga new set of experiments collected at different reagent concentrations.

Automated summary

In this study, we used atomistic molecular dynamics simulations to investigate the binding of RNA with SHAPE reagents. We proposed and tested the hypothesis that cooperative effects can lead to concentration-dependent reactivity. Our simulations and analysis of experimental data support the idea that cooperative binding can indeed affect the reactivity of SHAPE experiments.