Using the SIRAH Force-Field to Model Interactions Between Short DNA Duplexes

Background/Objectives: In recent years, short DNA duplexes have been studied as promising self-assembling systems and versatile building blocks for DNA-based nanotechnologies. Numerical simulations of colloidal systems incorporating such components require, as an input ingredient, simplified but reliable force-fields that capture the essential features of duplex-duplex interactions. Methods: We employed the coarse-grained SIRAH force field under an implicit solvent approximation to in-vestigate the interactions between two short, rigid double-stranded DNA (dsDNA) duplexes. Results: Using this realistic coarse-grained model, we obtained detailed in-sights into how the force field depends on the relative positions, orientations and salt concentration. Calculations were performed for duplexes of 8 and 20 base pairs in length. Conclusions: Our findings represent a foundational step toward the systematic development of simplified, yet qualitatively accurate, model potentials for DNA-based colloidal systems. Beyond nanotechnology, the short-range interaction features cap-tured here are also relevant to biological contexts, including chromatin compaction, homologous recombination, and DNA repair.