Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components

Abstract

Nucleic acids (DNA and RNA) are widely used to construct nanoscale structures with ever increasing complexity1–14 for possible applications in fields as diverse as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early examples typically containing on the order of 10 unique DNA strands. The introduction of DNA origami4, which uses many staple strands to fold one long scaffold strand into a desired structure, gave access to kilo- to mega-dalton nanostructures containing about 102 unique DNA strands6,7,10,13 . Aiming for even larger DNA origami structures is in principle possible15,16, but faces the challenge of having to manufacture and route an increasingly long scaffold strand. An alternative and in principle more readily scalable approach uses DNA brick assembly8,9, which doesn’t need a scaffold and instead uses hundreds of short DNA brick strands that self-assemble according to specific inter-brick interactions. First-generation bricks used to create 3D structures are 32-nt long with four 8-nt binding domains that directed 102 distinct bricks into well-formed assemblies, but attempts to create larger structures encountered practical challenges and had limited success.9 Here we show that a new generation of DNA bricks with longer binding domains makes it possible to self-assemble 0.1 – 1 giga-dalton three-dimensional nanostructures from 104 unique components, including a 0.5 giga-dalton cuboid containing 30,000 unique bricks and a 1 giga-dalton rotationally symmetric tetramer. We also assemble a cuboid containing 10,000 bricks and 20,000 uniquely addressable ‘nano-voxels’ that serves as a molecular canvas for three-dimensional sculpting, with introduction of sophisticated user-prescribed 3D cavities yielding structures such as letters, a complex helicoid and a teddy bear. We anticipate that, with further optimization, even larger assemblies might be accessible and prove useful as scaffolds or for positioning functional components.

DNA self-assembly scaled up

“…This grouping offers several advantages for this type of analysis. For instance, the authors could solve the problem of finding consistent regional ancient environmental data because the height of these mammals' teeth correlates strongly with characteristics of their environment, including precipitation levels 3 and the amount of plant material in the ecosystem 4 . Without this measure, the authors would have had to rely on standard global measurements of environmental change, an approach that can mask substantial regional-level variation.…”

“…Scientists have long aspired to construct artificial objects using self-assembly to reach the dimensions and complexity of cells or organelles, with the aim of building synthetic cellular machines for research, engineering and medical applications. Four papers [2][3][4][5] in this issue address this goal by reporting methods for scaling up the sizes and production of self-assembling, designer nanostructures made from DNA.…”

“…Ong et al 4 (page 72) report a method that allows 3D SST DNA constructs to be made at the micrometre scale (Fig. 1c).…”

“…b, Wagenbauer et al 3 prepared a 3D, V-shaped building block using DNA origami, and assembled this hierarchically into polyhedra. c, Ong et al 4 built on a method known as single-stranded tile assembly to prepare DNA bricks that form one strand that contains 52 nucleotides. Each strand contains four binding domains that enable the bricks to assemble into larger constructions.…”

Bigger and cheaper

“…But the translation of DNA nanotechnology from an academic concept to a practical tool is still in its infancy. Now a series of papers showcasing micrometresized two-dimensional DNA arrays and gigadalton three-dimensional origami structures might move the field a little bit closer to this goal, proving that bigger and more complex architectures can be built with high yields and low error rates [3][4][5] . Notably, a smart one-pot biotechnological approach published alongside these papers also offers a pragmatic route to cut DNA origami production costs 6 .…”