Source: Nature Chemistry, University of Arizona

The new meta-DNA self-assembly concept may totally transform the microscopic world of structural DNA nanotechnology. Decades ago a huge milestone in DNA technology was the invention of DNA origami, where a long single-stranded DNA is folded into designated shapes with the help of hundreds of short DNA staple strands. DNA nanotechnology had challenges assembling larger (micron to millimeter) sized DNA architectures. The new micron-size structures are on the order of the width of a human hair, which is 1,000 times larger than the original DNA nanostructures.

In the future, more complicated circuits, molecular motors and nanodevices could be rationally designed using M-DNA and used in applications related to biosensing and molecular computation. This research will make the creation of dynamic micron-scale DNA structures, that are reconfigurable upon stimulation, significantly more feasible.

These structures may be used as a scaffold for patterning complex functional components that are larger and more complex than previously thought possible. This discovery may also lead to more sophisticated and complex behaviors that mimic cell or cellular components with a combination of different M-DNA-based hierarchical strand displacement reactions.

The Meta-DNA’ (M-DNA) strategy allows various submicrometer- to micrometer-size DNA structures to self-assemble in a manner similar to how simple short DNA strands self-assemble at the nanoscale level. The group demonstrated that a six-helix bundle DNA origami nanostructure in the submicrometer scale (meta-DNA) could be used as a magnified analog of single-stranded DNA, and that two meta-DNAs containing complementary “meta-base pairs” could form double helices with programmed handedness and helical pitches.

Using meta-DNA building blocks, they have constructed a series of submicrometer- to micrometer-scale DNA architectures, including meta-multi-arm junctions, 3D polyhedrons, and various 2D/3D lattices. They also demonstrated a hierarchical strand-displacement reaction on meta-DNA to transfer the dynamic features of DNA to the meta-DNA.

They used a coarse-grained computational model of the DNA to simulate the double-stranded M-DNA structure and to understand the different yields of left-handed and right-handed structures that were obtained.

Changing the local flexibility of the individual M-DNA and their interactions, they were able to build a series of submicrometer- or micron-scale DNA structures from 1D to 3D with a wide variety of geometric shapes, including meta-junctions, meta-double crossover tiles, tetrahedrons, octahedrons, prisms and six types of closely packed lattices.


Models and transmission electron microscopy images of various 3D polyhedra that were constructed by connecting the self-linked triangular M-DNA and rectangular M-DNA. From left to right: a tetrahedron, triangular bipyramid, octahedron, pentagonal bipyramid, triangular prism, rectangular prism, pentagonal prism and hexagonal prism.

Nature Chemistry – Meta-DNA structures

Abstract
DNA origami has emerged as a highly programmable method to construct customized objects and functional devices in the 10–100 nm scale. Scaling up the size of the DNA origami would enable many potential applications, which include metamaterial construction and surface-based biophysical assays. Here we demonstrate that a six-helix bundle DNA origami nanostructure in the submicrometre scale (meta-DNA) could be used as a magnified analogue of single-stranded DNA, and that two meta-DNAs that contain complementary ‘meta-base pairs’ can form double helices with programmed handedness and helical pitches. By mimicking the molecular behaviours of DNA strands and their assembly strategies, we used meta-DNA building blocks to form diverse and complex structures on the micrometre scale. Using meta-DNA building blocks, we constructed a series of DNA architectures on a submicrometre-to-micrometre scale, which include meta-multi-arm junctions, three-dimensional (3D) polyhedrons, and various 2D/3D lattices. We also demonstrated a hierarchical strand-displacement reaction on meta-DNA to transfer the dynamic features of DNA into the meta-DNA. This meta-DNA self-assembly concept may transform the microscopic world of structural DNA nanotechnology.