Dynamics of DNA Origami Lattice Formation at Solid–Liquid Interfaces

Abstract

The self-organized formation of regular patterns is not only a fascinating topic encountered in a multitude of natural and artificial systems, but also presents a versatile and powerful route toward large-scale nanostructure assembly and materials synthesis. The hierarchical, interface-assisted assembly of DNA origami nanostructures into regular, 2D lattices represents a particularly promising example, as the resulting lattices may exhibit an astonishing degree of order and can be further utilized as masks in molecular lithography. Here, we thus investigate the development of order in such 2D DNA origami lattices assembled on mica surfaces by employing in situ high-speed atomic force microscopy imaging. DNA origami lattice formation is found to resemble thin-film growth in several aspects. In particular, the Na+/Mg2+ ratio controls DNA origami adsorption, surface diffusion, and desorption, and is thus equivalent in its effects to substrate temperature which controls adatom dynamics in thin-film deposition. Consequently, we observe a pronounced dependence of lattice order on Na+ concentration. At low Na+ concentrations, lattice formation resembles random deposition and results in unordered monolayers, whereas very high Na+ concentrations are accompanied by rapid diffusion and especially DNA origami desorption, which prevent lattice formation. At intermediate Na+ concentrations, highly ordered DNA origami lattices are obtained that display an intricate symmetry, stemming from the complex shape of the employed Rothemund triangle. Nevertheless, even under such optimized conditions, the lattices display a considerable number of defects, including grain boundaries, point and line defects, and screw-like dislocations. By monitoring the dynamics of selected lattice defects, we identify mechanisms that limit the obtainable degree of lattice order. Possible routes toward further increasing lattice order by postassembly annealing are discussed.

Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability

“…Compared to liquid imaging, the triangular shapes appear less defined. This can be attributed both to drying-induced conformational alterations of the DNA duplexes in the DNA origami, such as B-A transitions, and minor shape distortions resulting from the removal of Mg 2+ ions from the mica-DNA interface, which leads to a reduced strength of the interaction [54]. The latter is manifested, for example, in the decreased width of the trapezoids composing the triangles, which appear somewhat contracted or rolled up.…”

In situ Surface Charge Density Visualization of Self‐assembled DNA Nanostructures after Ion Exchange

“…Especially the continued adsorption of DNA origami in the presence of K + and Cs + ions is interesting and has to the best of our knowledge not been reported elsewhere. Supplementary Table 1 provides a comparison of selected literature examining ionic species used initial attachment and continued attachment/diffusion of DNA origami [43–45] . Based on the clear differences in DNA origami attachment under the different ionic conditions, we propose a likely pathway (Figure 2B) due to ion exchange phenomenon in the lattice sites of mica.…”

Constructing Large 2D Lattices Out of DNA-Tiles

“…The direct observation of the processes such as the adsorption/desorption of the DNA and its diffusion on the surface would deepen the understanding of kinetics at the solid-liquid interface. High-speed AFM is a method of choice to investigate the morphology and dynamics of lattice formation [113,114]. Despite relatively straightforward assembly protocol, the real challenge remains in understanding the requirements and precise condition in regulating the self-assembly of the DNA-tiles leading to the large single-layer patterns.…”