nNxB: a new coarse-grained model for RNA and DNA nanotechnology

The folding processes of RNA and DNA play crucial roles in biological systems and nanotechnology. However, studying these processes with high-resolution models is beyond current computational capabilities. In this article, we present a new coarse-grained model for investigating the folding dynamics of nucleic acids. Our model represents n nucleotides using a single patchy particle and is parametrized using well-established nearest-neighbor models. By simplifying the system and interactions, 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 single-stranded systems. We examined the thermodynamics of DNA hairpins, capturing their stability and structural transitions. We also investigated the folding of an MMTV pseudoknot, a complex RNA structure involved in viral replication. Furthermore, we explored the folding of a challenging RNA tile containing a k-type pseudoknot. The new coarse-grained model accurately captures the folding behavior of diverse nucleic acid structures, providing insights into their thermodynamics. The successful reproduction of experimental data and favorable comparisons with existing coarse-grained models validate the effectiveness of our approach.