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Chemical probing experiments such as SHAPE are routinely used to probe RNAmolecules. In this work, we use atomistic molecular dynamics simulations totest the hypothesis that binding of RNA with SHAPE reagents is affected bycooperative effects leading to an observed reactivity that is dependent on thereagent concentration. We develop a general technique that enables thecalculation of the affinity for arbitrary molecules as a function of theirconcentration in the grand-canonical ensemble. Our simulations of an RNAstructural motif suggest that, at the concentration typically used in SHAPEexperiments, cooperative binding would lead to a measurableconcentration-dependent reactivity. We also provide a qualitative validation ofthis statement by analyzing a new set of experiments collected at differentreagent concentrations.

Molecular dynamics simulations with grand-canonical reweighting suggest cooperativity effects in RNA structure probing experiments