Abstract
We focus on a coarse-grained description of the coupling between ribose pucker discommensuration and base swinging in a standard A-RNA helix. We view this coupling as an actual entrainment where the sugar conformation is regarded as the enslaving variable in the dynamics. Thus, we provide a semiempirical model for the relatively slow dynamics of helix opening reflecting the intermittent exposure of titratable groups to the solvent and consistent with proton exchange kinetics. Our description of bubble formation in the helix is built upon a Φ 4-type model
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