Physical Properties of Single-Sheet DNA Origami Nanotiles

Central to DNA origami is the need to have oligomeric DNA bind adjacent DNA helices,
whose spacing is dependent on the spatial offset between the helices. In square-based
origami, this spacing must be an odd-number of half-turns, requiring a non-integer
number as B-form DNA has a helical pitch of 10.50 bp. The inability to have non-integer
spacings creates a phasing mismatch, leading to curvature of origami. This work
explores how cationic concentration and species affect this curvature.
Asymmetric single-sheet DNA origami with varying crossover spacings, said to be
overwound, planar and underwound, were imaged under bulk aqueous solution with
AFM, where the adsorption orientation served as a metric to infer the magnitude and
direction of curvature. The combination of these three designs demonstrated how the
effective Mg2+ concentration affects both DNA helicity as well as the electrostatic
repulsion between the tightly packed helices. Low Mg2+ concentrations caused helix
destabilisation; leading to flatter origami, whilst elevated Mg2+ concentrations appeared
to shield electrostatic repulsions, causing a decrease in curvature. These results
highlight the importance of Mg2+ concentration and its effect on origami curvature.
Exposure to UV radiation induced unwinding of DNA through the formation of
photoproducts, causing the overwound origami to experience a decrease in adsorption
bias whereas the planar and underwound origami experienced an increase in bias.
These results aid the idea that the direction of curvature is independent of crossover
spacing. The combination of tiles in varying Mg2+ and those exposed to UV radiation
served as a baseline to determine the effects that Ba2+ has on the DNA helix. Ba2+
appeared to induce over-winding of the DNA helix, whilst remaining in an overall
destabilised state, compared to that of Mg2+. This caused the underwound origami to
exhibit more curvature compared to those of the overwound and planar origami.