Increasing Complexity in Wireframe DNA Nanostructures

Abstract

Structural DNA nanotechnology has recently gained significant momentum, as diverse design tools for producing custom DNA shapes have become more and more accessible to numerous laboratories worldwide. Most commonly, researchers are employing a scaffolded DNA origami technique by “sculpting” a desired shape from a given lattice composed of packed adjacent DNA helices. Albeit relatively straightforward to implement, this approach contains its own apparent restrictions. First, the designs are limited to certain lattice types. Second, the long scaffold strand that runs through the entire structure has to be manually routed. Third, the technique does not support trouble-free fabrication of hollow single-layer structures that may have more favorable features and properties compared to objects with closely packed helices, especially in biological research such as drug delivery. In this focused review, we discuss the recent development of wireframe DNA nanostructures—methods relying on meshing and rendering DNA—that may overcome these obstacles. In addition, we describe each available technique and the possible shapes that can be generated. Overall, the remarkable evolution in wireframe DNA structure design methods has not only induced an increase in their complexity and thus expanded the prevalent shape space, but also already reached a state at which the whole design process of a chosen shape can be carried out automatically. We believe that by combining cost-effective biotechnological mass production of DNA strands with top-down processes that decrease human input in the design procedure to minimum, this progress will lead us to a new era of DNA nanotechnology with potential applications coming increasingly into view.

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

“…Therefore, advanced wireframe-like DNA structures have attracted great attention. 83 Another programming platform called vHelix provides an intuitive top-down design and thus models the platform for wireframe DNA replication of user-defined 2D and 3D objects. 84 Using an applicable meshing tool to transform the designed model into a triangular, polyhedral wireframe mesh, the scaffold strand was folded into the wireframe DNA nanostructure in the design after further algorithms and optimizations.…”

Construction of Smart Stimuli‐Responsive DNA Nanostructures for Biomedical Applications

“…With the improvement of the DNA origami approach, the wireframe-based construction of hollow or porousD NA conformationsc ould be also achieved by the meshinga nd rendering method. [58] Awide variety of sophisticated 2D and 3D architectures have been thus constructed at the nanoscale and microscale, such as vase, [7] Mona Lisa, [59] and atomic models [60] ( Figure 2C). Moreover,d ynamic DNA origami can be obtained by rational design, including DNA origami nanocapsules, [61] nanorobots, [62] and DNA vaults [63] ( Figure 2D).…”

“…In addition, the space of DNA shapes hasb een expanded through the wireframe-based meshedm ethod to construct hollow nanostructures with improvedstability in biological environments. [58] DNA nanotubes were designedt hrough the regulation of concatenated capsule structures to selectively trap and responsively releaset he encapsulated gold nanoparticlesw ith proper sizes. DNA triangles of different sizes were assembled longitudinally with two different-sized cavitiesb yc onnecting these linking strands together.…”

Chiral 3D DNA origami structures for ordered heterologous arrays

“…Numerous wireframe structures have been demonstrated and allow increases of both size and complexity of the DNA structures with lower packing density. Advantages over parallel packing include rapid folding and increased stability at low cation concentrations and physiological ion conditions 24 . The wireframe approach is particularly useful for formation of convex polyhedra themselves having potential as cargo carrying nanostructures and even as artificial vaccines if their exterior is decorated with antigens 25 .…”