  Nowadays different experimental techniques, such as single molecule or
relaxation experiments, can provide dynamic properties of biomolecular systems,
but the amount of detail obtainable with these methods is often limited in
terms of time or spatial resolution. Here we use state-of-the-art computational
techniques, namely atomistic molecular dynamics and Markov state models, to
provide insight into the rapid dynamics of short RNA oligonucleotides, in order
to elucidate the kinetics of stacking interactions. Analysis of multiple
microsecond-long simulations indicates that the main relaxation modes of such
molecules can consist of transitions between alternative folded states, rather
than between random coils and native structures. After properly removing
structures that are artificially stabilized by known inaccuracies of the
current RNA AMBER force field, the kinetic properties predicted are consistent
with the timescales of previously reported relaxation experiments.
