Cation-dependent assembly of hexagonal DNA origami lattices on SiO₂ surfaces

DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO₂ surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca²⁺ is found to be superior to Mg²⁺ in promoting the assembly of ordered lattices, while the presence of Mg²⁺ rather results in DNA origami aggregation and multilayer formation at the comparably high Na⁺ concentrations of 200 to 600 mM. Furthermore, Na⁺ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na⁺ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO₂ surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.