Tailoring the mechanical properties of DNA origami nanostructures through nanocomponent design: a coarse-grained molecular dynamics

New abstract: This study explores the impact of structural modifications in wireframe DNA origami nanostructures on their mechanical properties using coarse-grained oxDNA2 simulations. A large wireframe DNA origami nanostructure was selected to enable a detailed examination of how alterations in its nanocomponents affect its stiffness. The structural components were modified using the updated version of the DAEDALUS software. Following the design process and initial relaxation stages, oxDNA2-based force applications were performed to evaluate their mechanical behaviour. The results demonstrate a significant relationship between the number of staple crossovers and the mechanical stiffness of the nanostructures. Specifically, an inverse correlation was observed, where an increase in staple crossovers leads to a reduction in stiffness. Conversely, reducing these crossovers enhances the structural stiffness. The removal of poly-T bulges was also found to decrease the stiffness, highlighting the influence of specific nanocomponent features on the overall mechanical behaviour. These findings suggest that optimising the design of individual nanocomponents can effectively improve the mechanical properties of DNA origami structures, offering insights for applications requiring enhanced mechanical stability. The study emphasises the importance of tailoring the nanocomponent arrangement to achieve desired structural rigidity in DNA-based nanostructures.