Fluctuations and resulting competing pathways in RNA folding: The activation of splicing

We implement a parallel processing Monte Carlo simulation to explore RNA configuration space that takes into account fluctuations in base-pairing patterns. The choice of folding pathways is biased by the refolding events that occur as the chain is being assembled. We prove that fluctuations in the initial stages of folding might lead to either active or inactive emerging structures. As an illustration, competing pathways that are the result of fluctuation propagation are computed for the splicing YC4 intron (a segment of the mitochondrial RNA from fungi), and the emerging structures are proved to be biologically relevant.