Precise placement of DNA origami on patterned surfaces

DNA origami is a powerful platform for organizing nanoscale components to create advanced nano devices. However, scaling this technology requires the development of strategies for precise positioning of DNA origami in 3D space or on surfaces. In this work, we investigate potential approaches for surface placement, focusing on orientation control and the simultaneous positioning of multiple origami species. For orientation control, prior studies have shown that the interaction energy between an origami and a patterned surface patch is proportional to their overlapping area. Consequently, minimizing the energy is equivalent to maximizing the overlap. By carefully designing the surface pattern and origami geometry to yield an energy landscape with only a single minimum, the orientation of the origami can be uniquely defined, eliminating degeneracy in alignment. To address the more challenging problem of multispecies placement, we adapted a signal processing algorithm to generate orthogonal patterns with oppositely charged domains on the origami and substrate. Simulations demonstrated that this approach enables simultaneous placement of multiple origami species without misplacement, validating the feasibility of the method. These results highlight the potential of combining energy landscape engineering with charge-based encoding to achieve deterministic placement of DNA origami.