Positioning and Controlling DNA Origami–Gold Dimer Hybrid Nanostructures on Surfaces

Surface nanofabrication is crucial in nanoscience, enabling precise control over nanoscale material properties essential for modifying quantum effects, device miniaturization, and tuning optical characteristics. This thesis combines top-down and bottom-up methods to achieve precise positioning of gold nanoparticle dimers on surfaces. DNA origami techniques assemble dimers, while adsorption sites are created through surface chemical modifications structured via electron beam lithography (EBL). The thesis focuses on controlling the positioning of DNA-nanoparticle hybrid nanostructures on pre-structured silicon surfaces. By limiting the active site size to match the DNA origami dimensions, positional control of the hybrid nanostructures in two-, one-, and zero-dimensional patterns is achieved through simple drop casting. The study examines how diffusion in liquids and nanostructure concentration affect site occupation and proposes a diffusion model that highlights the role of surface diffusion in two- and one-dimensional adsorption. Results demonstrate selective adsorption with high efficiency and precise control over the nanostructures' position and orientation, promising applications for large-scale nanoarrays with nanometer precision. The ability to create multiple folds from a single DNA origami structure increases design flexibility. This research uncovers a unique folding process of DNA origami on small adsorption sites, enabling manipulation of the spatial position of nano-objects. By systematically adjusting adsorption patterns, controllable deformation of DNA origami is achieved, allowing for tuning of the center-to-center distance between gold dimers. This results in the creation of a tunable plasmonic dimer nanoarray on silicon. Efficiency is validated through Raman signal analysis of dye molecules on the gold surfaces, confirming the potential of DNA origami-based plasmonic nanostructures for various applications. Moreover, the thesis explores direct EBL on a molecule monolayer, rather than traditional photoresist, and investigates the adsorption efficiency of hybrid nanostructures on various surfaces, expanding the applicability of this approach.