DNA origami nanotechnology allows us to rationally design molecular devices with arbitrary shapes and properties through programming the sequence of DNA bases for their directed self-assembly. Despite its remarkable shape programmability, it has not been fully explored yet how to precisely control the twisted shape of DNA origami structures shown to be important in controlling the physical properties of DNA devices, building DNA superstructures, and synthesizing macroscopic soft materials with targeted properties. Here, we demonstrate that designing the spatial configuration of mechanical strain energies induced by base pair (BP) insertions and deletions can effectively modulate the twist rate of DNA origami structures with a fine resolution. To illustrate, various six-helix bundles (6HB) were successfully constructed whose twist rate was precisely tuned with a mean increment of 1.8° per 21-BP-long unit block. We also show that locally relaxing the strain energy via engineered gaps, short unpaired nucleotides (NTs), can widen the range of achievable twist rate with fine controllability. The proposed configurational design approach is expected to expand the feasible design space of twisted DNA origami structures for their various potential applications with target functionalities.
Keywords: DNA nanotechnology; DNA origami; finite element model; mechanical perturbation design; molecular dynamics simulations; twisted bundles.