RNA-ligand complexes and the attenuation of neutral confinement in the evolution of RNA secondary structures

RNA molecules with identical nucleotide sequences can adopt different structures. Mutations can alter their properties; for example, some mutations increase the stability of a functionally relevant structure at the expense of other structures’ stability. Interestingly, the structural diversity a sequence produces is correlated with the number of structures it can access upon mutation. Thus, enhancing a structure’s stability can lead to neutral confinement, an evolutionary dead-end in which mutational access to novel structures is increasingly difficult. If the structure is critical to biological function, how do RNA molecules escape neutral confinement? We have developed a model in which an RNA molecule’s function depends on binding to a ligand, and we applied it to study sequences that fold according to RNA biophysics, also simulating their evolution. Our analyses and simulations have identified effects that decrease the selective advantage of augmenting a structure’s stability. By disfavouring the evolution of highly stable structures and favouring the accumulation of genetic variation, these effects hinder neutral confinement. The most important effect stems from the sequestration of high-affinity structures in RNA-ligand complexes and their replenishment through thermal fluctuations. In this perspective, a common scenario may help to explain how RNA evolution avoids coming to a halt.