Dynamics of DNA Origami Lattices

Abstract

Hierarchical assembly of programmable DNA frameworkssuch as DNA origamipaves the way for versatile nanometer-precise parallel nanopatterning up to macroscopic scales. As of now, the rapid evolution of the DNA nanostructure design techniques and the accessibility of these methods provide a feasible platform for building highly ordered DNA-based assemblies for various purposes. So far, a plethora of different building blocks based on DNA tiles and DNA origami have been introduced, but the dynamics of the large-scale lattice assembly of such modules is still poorly understood. Here, we focus on the dynamics of two-dimensional surface-assisted DNA origami lattice assembly at mica and lipid substrates and the techniques for prospective three-dimensional assemblies, and finally, we summarize the potential applications of such systems.

Large-Scale Formation of DNA Origami Lattices on Silicon

“…Based on wide literature, , increasing the surface mobility (μ) of the DNA origami should lead to improved lattice formation on a substrate and thus favor larger lattices. For the deposition, we used commonly utilized 1× TAE + 12.5 mM MgCl 2 (Mg 2+ ) buffer with varied concentrations ( C Na ) of NaCl (Na + ).…”

“…Assembling large DNA origami lattices on surfaces creates new ways to craft metamaterial surfaces for nano-optics applications. , Especially, the recently introduced DNA-assisted lithography (DALI) enables direct transformation of the DNA origami shapes into metallic structures on different substrates. , This could offer a straightforward way to create plasmonic metasurfaces such as the fishnet-type metallic lattice, which has unique properties like a negative refractive index . One example of a self-assembled fishnet-type lattice has been achieved using the cross-shaped Seeman tile (ST) DNA origami.…”

“…3 One example of a self-assembled fishnet-type lattice has been achieved using the cross-shaped Seeman tile (ST) DNA origami. However, this has been realized only on a mica surface via direct formation of the lattice on the surface, 17 i.e., surfaceassisted assembly, 12,13 or with lattices formed within bulk solution and then deposited on mica. 16 To fully employ DALI or any other pattern transfer method 27 to obtain metasurfaces, the formation of the lattice needs to be extended to a silicon substrate, a feat that so far has not been fully realized.…”

“…A particularly interesting method to fabricate hierarchical supramolecular structures is DNA origami since it allows folding of arbitrarily shaped nanostructures that can be further designed to organize into larger entities via different interactions like DNA hybridization or blunt end stacking under certain user-defined conditions. , In the past, different kinds of DNA origami, like rectangles, , cross-shapes, the so-called Seeman tiles, , and triangles, − have been arranged into two-dimensional (2D) lattices. Also, 3D lattices , or assemblies like tubes and gears , have been realized, either in solution or on a surface.…”

Reconfigurable pH-Responsive DNA Origami Lattices

“…Nevertheless, the library of already demonstrated small dynamic DNA-based devices 31,32 suggests the DNA origami method could also be harnessed in building larger dynamic lattices and other highly ordered assemblies. 33 In this work, we created a dynamic 2D DNA origami lattice that changes its configuration in response to the pH of the surrounding solution. For that, we designed a pliers-like DNA origami unit that serves as the basic building block of the lattice and that can be readily switched between an open "+"-shaped and a closed "X"-shaped state upon a pH change.…”