  The intricate network of interactions observed in RNA three-dimensional
structures is often described in terms of a multitude of geometrical
properties, including helical parameters, base pairing/stacking, hydrogen
bonding and backbone conformation. We show that a simple molecular
representation consisting in one oriented bead per nucleotide can account for
the fundamental structural properties of RNA. In this framework, canonical
Watson-Crick, non-Watson-Crick base-pairing and base-stacking interactions can
be unambiguously identified within a well-defined interaction shell. We
validate this representation by performing two independent, complementary
tests. First, we use it to construct a sequence-independent, knowledge-based
scoring function for RNA structural prediction, which compares favorably to
fully atomistic, state-of-the-art techniques. Second, we define a metric to
measure deviation between RNA structures that directly reports on the
differences in the base-base interaction network. The effectiveness of this
metric is tested with respect to the ability to discriminate between
structurally and kinetically distant RNA conformations, performing better
compared to standard techniques. Taken together, our results suggest that this
minimalist, nucleobase-centric representation captures the main interactions
that are relevant for describing RNA structure and dynamics.
