  The folding of RNA and DNA strands plays crucial roles in biological systems
and bionanotechnology. However, studying these processes with high-resolution
numerical models is beyond current computational capabilities due to the
timescales and system sizes involved. In this article, we present a new
coarse-grained model for investigating the folding dynamics of nucleic acids.
Our model represents 3 nucleotides with a patchy particle and is parametrized
using well-established nearest-neighbor models. Thanks to the reduction of
degrees of freedom and to a bond-swapping mechanism, our model allows for
simulations at timescales and length scales that are currently inaccessible to
more detailed models. To validate the performance of our model, we conducted
extensive simulations of various systems: We examined the thermodynamics of DNA
hairpins, capturing their stability and structural transitions, the folding of
an MMTV pseudoknot, a complex RNA structure involved in viral replication, and
also explored the folding of an RNA tile containing a k-type pseudoknot.
Finally, we evaluated the performance of the new model in reproducing the
melting temperatures of oligomers and the dependence on the toehold length of
the displacement rate in toehold-mediated displacement processes, a key
reaction used in molecular computing. All in all, the successful reproduction
of experimental data and favorable comparisons with existing coarse-grained
models validate the effectiveness of the new model.
