Scaling Up DNA Origami Lattice Assembly

Abstract

The surface‐assisted hierarchical assembly of DNA origami nanostructures is a promising route to fabricate regular nanoscale lattices. In this work, the scalability of this approach is explored and the formation of a homogeneous polycrystalline DNA origami lattice at the mica‐electrolyte interface over a total surface area of 18.75 cm2 is demonstrated. The topological analysis of more than 50 individual AFM images recorded at random locations over the sample surface showed only minuscule and random variations in the quality and order of the assembled lattice. The analysis of more than 450 fluorescence microscopy images of a quantum dot‐decorated DNA origami lattice further revealed a very homogeneous surface coverage over cm2 areas with only minor boundary effects at the substrate edges. At total DNA costs of € 0.12 per cm2, this large‐scale nanopatterning technique holds great promise for the fabrication of functional surfaces.

Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy

“…Ni 2+ ions undergo stronger binding to the mica surface than Mg 2+ . Therefore, mica surfaces pretreated with Ni 2+ have previously been used for immobilizing genomic DNA molecules [ 41 , 42 , 43 , 44 ], while the displacement of Mg 2+ ions at the mica–DNA interface by Ni 2+ ions has been employed for the fixation of self-assembled DON lattices [ 45 , 46 ]. Figure 3 a shows an AFM image of a mica surface after incubation in 10 mM NiCl 2 solution.…”

“…Mica substrates (Ted Pella, Inc., Redding, CA, USA) were pretreated with NiCl 2 (Sigma-Aldrich Chemie GmbH, Steinheim, Germany), PLL hydrobromide (molecular weight 1000–5000, Sigma-Aldrich Chemie GmbH, Steinheim, Germany), and Spdn (Alfa Aesar, Thermo Fisher (Kandel) GmbH, Kandel, Germany), respectively. NiCl 2 pretreatment: 10 mM NiCl 2 aqueous solution was deposited onto a freshly cleaved mica surface and incubated for 1 h. An incubation time of 1 h was chosen based on our previous work [ 45 ]. It should be noted, however, that equivalent results as reported here were also obtained with shorter incubation times, i.e., 1 min to 30 min.…”

“…NiCl 2 pretreatment: 10 mM NiCl 2 aqueous solution was deposited onto a freshly cleaved mica surface and incubated for 1 h. An incubation time of 1 h was chosen based on our previous work [ 45 ]. It should be noted, however, that equivalent results as reported here were also obtained with shorter incubation times, i.e., 1 min to 30 min.…”

DNA nanostructure-based nucleic acid probes: construction and biological applications

“…Compared to the canonical DNA origami structures which usually have a molecular weight of a few MDa, this new structure has a 1000-fold increase in size thus reaching the GDa-scale. On a macroscopic surface area, Xin et al 86 recently obtained the biggest DNA origami lattice. They reported that they have fabricated fairly homogeneous DNA origami lattices with an area of ∼20 cm 2 , consisting of approximately one trillion origami structures.…”

Hybrid Nanoassemblies from Viruses and DNA Nanostructures

“…Recently, DNA nanostructure assembly toolbox has been expanded with wireframe structures [13,14], automated design methods [15,16], GDa-scale objects [17], micrometer-scale fractal assemblies [18] and constructs with up to 10,000 individual and unique strand components [19], thus lowering the barriers for synthesizing objects at the size range of viruses and cellular organelles. Besides the discrete objects, well-ordered DNA origami-based 2D lattices can reach~10 cm 2 surface areas [20] and 3D DNA crystals millimeter scale dimensions [21,22]. So far, these versatile DNA nanoshapes have found applications in biomedicine, diagnostics and therapeutics [23,24], nanofabrication [25,26], molecular electronics [27,28] and super-resolution imaging [29], and as nanorulers [30], plasmonic or photonic apparatuses [31,32], precise nanoscopic measurement tools [33], tunable nanopores [34,35] and dynamic/robotic devices [36,37].…”