Structural stability of wireframe DNA origami: The role of nanocomponent modifications

Abstract

Wireframe DNA origami nanostructures hold immense potential for diverse applications in nanotechnology. The design of wireframe DNA origami structures traditionally follows a top–down approach. This study introduces a complementary bottom–up approach to investigate the nano-components constituting these nanostructures and their impact on structural stability. To this end, modifications to edge staple crossovers, poly-T bulges, and staple sequences were examined through coarse-grained molecular dynamics. The results reveal that reducing the number of edge staple crossovers slightly alters the distance between the two double-stranded DNA helices forming the edges but maintains adequate structural stability. The removal of poly-T bulges, however, leads to edge opening under specific thermal conditions, whereas structures containing poly-T bulges remain intact, highlighting their critical role in edge stability. Furthermore, changes to the staple sequences, achieved by repositioning the scaffold nick, showed negligible effects on the overall stability of the wireframe DNA origami structures. The incorporation of a bottom–up approach in designing wireframe DNA origami structures can enable the creation of nanostructures with tailored properties for specific applications. These modifications can be adapted for a variety of wireframe DNA origami structures, broadening their potential uses in nanotechnology.