DNA origami1 are a powerful building block to create nanoelectronic or nanomagnetic circuits. However, in order to achieve the necessary synthetic control to align non-DNA components on the surface, controlling the orientation of the underlying DNA origami is required. One simple strategy is using single stranded linkers to align the rectangular DNA origami.
However, non-specific π-stacking interactions are strong enough to disturb the desired alignment. I compared several strategies to prevent π-stacking and investigated optimal annealing conditions for the oligomerization of DNA origami. I tested i) inclusion of T-bumpers, ii) omission of staple strands on the edge of the DNA origami, iii) varying the number of linking sites and the stoichiometry of linking strands, and iv) optimization of annealing time and temperature. The DNA origami chains were characterized both on mica and cationic SAMs on silicon  by tapping mode atomic force microscopy (AFM) in the air. Orientations were verified by observation of loop regions on the DNA origami and an intentionally designed notch that makes the origami structure chiral on the surface. Streptavidin or gold nanoparticle attachment was also used to reveal the up/down alignments of the origami. AFM images show that inclusion of T- bumpers fails to block π-stacking interactions. On the other hand, elimination of staple strands from the edge of the DNA origami formed short oligomers with controlled alignment. I investigated the optimal annealing temperature and time with quenching experiments and observed stepwise condensation, origami formation, and oligomerization at different stages of the annealing process. Aligned DNA origami chains were selectively deposited on 60 nm wide lithographically patterned lines of cationic SAMs on silicon chips, Preliminary studies were done to show that DNA origami could be deposited on hydrogen silsesquioxane (HSQ); this work establishes a pathway towards multilevel patterning of DNA origami.