Comparison of methods for orienting and aligning DNA origami

Abstract

DNA origami are self-assembling units that can themselves undergo further self-assembly to form oligomers. These oligomers have potential applications for assembly of nanoelectronic or nanophotonic circuitry or for assembly of biological components. However, there are a variety of assembly defects that must be controlled. These include defects in alignment between the origami (origami that are offset from each other), defects in relative orientation (origami that are rotated relative to one another), and defects in up/down orientation (neighboring origami that are not both face up or face down). Four strategies for controlling the oligomerization of DNA origami were compared. We tested (i) inclusion of T-bumpers, (ii) omission of staple strands on the edge of the DNA origami, (iii) varying numbers and lengths of single-stranded linkers 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 [100] by tapping mode 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. AFM images showed that inclusion of T-bumpers failed to block π-stacking interactions, and that inclusion of single stranded linkers greatly reduced alignment defects but did not control defects in relative orientation. On the other hand, single stranded linkers in conjunction with elimination of staple strands from the edge of the DNA origami formed short oligomers with good alignment and good relative orientation. We investigated the optimal annealing temperature and time with quenching experiments and observed stepwise origami formation and oligomerization.