RNA Shapes: Folding Dynamics and Evolution

RNA secondary structures are a discrete, graphical model of the 3D shapes of RNA molecules that capture the dominating part of the energy of structure formation and constitute a key intermediate in the formation of the final 3D structure. The relative simplicity of secondary structures makes it possible to efficiently compute ground states and thermodyanmic parameters for given sequences. This sets the stage for exploring the evolution of RNA shapes in response to variations of the underling sequences. At the same time, the same model can be used to study the dynamical process of folding, i.e., structure formation, for a given sequence. The sequence-shape map of RNA has a number of unusual properties, in particular a high degree of neutrality combined with a the proximity of of very different shapes. These properties together explain key features of RNA evolution.