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Prediction of RNA structure is an important problem in understanding biological processes in living organism. Computational models have been created to study the processes with the aim of unravelling the RNA structure. In this work, a novel formalism for formal analysis of RNA structure prediction is described. A graph rewriting system is formalized to represent structural dynamics of RNA structure under uncertainty. Probabilistic model checking is performed on queries seeking structural properties in RNA. Experiments were conducted to evaluate the computational feasibility of the model.more » « less