DNA origami make sturdier polyhedra with struts to get them 400 times larger than DNA bricks

Scientists at the Harvard’s Wyss Institute have built a set of self-assembling DNA cages one-tenth as wide as a bacterium. The structures are some of the largest and most complex structures ever constructed solely from DNA. The cage could be modified with chemical hooks that could be used to hang other components such as proteins or gold nanoparticles. With sides of 100 nm length, and a volume one one thousandth that of a typical bacterial cell, these ‘closets’ should be large enough to precisely assemble fairly complex assortments of nanoscale functional elements.

The scientists visualized them using a DNA-based super-resolution microscopy method — and obtained the first sharp 3D optical images of intact synthetic DNA nanostructures in solution.

In the future, scientists could potentially coat the DNA cages to enclose their contents, packaging drugs for delivery to tissues. And, like a roomy closet, the cage could be modified with chemical hooks that could be used to hang other components such as proteins or gold nanoparticles. This could help scientists build a variety of technologies, including tiny power plants, miniscule factories that produce specialty chemicals, or high-sensitivity photonic sensors that diagnose disease by detecting molecules produced by abnormal tissue.

The five cage-shaped DNA polyhedra here have struts stabilizing their legs, and this innovation allowed a Wyss Institute team to build by far the largest and sturdiest DNA cages yet. The largest, a hexagonal prism (right), is one-tenth the size of an average bacterium. Credit: Yonggang Ke/Harvard’s Wyss Institute

Science – Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-PAINT

Yin and his colleagues first used DNA origami to create extra-large building blocks the shape of a photographer’s tripod. The plan was to engineer those tripod legs to attach end-to-end to form polyhedra — objects with many flat faces that are themselves triangles, rectangles, or other polygons.

But when Yin and the paper’s three lead authors, Ryosuke Iinuma, a former Wyss Institute Visiting Fellow, Yonggang Ke, Ph.D., a former Wyss Postdoctoral Fellow who is now an Assistant Professor of Biomedical Engineering at Georgia Institute of Technology and Emory University, and Ralf Jungman, Ph.D, a Wyss Postdoctoral Fellow, built bigger tripods and tried to assemble them into polyhedra, the large tripods’ legs would splay and wobble, which kept them from making polyhedra at all.

The researchers got around that problem by building in a horizontal strut to stabilize each pair of legs, just as a furniture maker would use a piece of wood to bridge legs of a wobbly chair.

To glue the tripod legs together end-to-end, they took advantage of the fact that matching DNA strands pair up and adhere to each other. They left a tag of DNA hanging off a tripod leg, and a matching tag on the leg of a different tripod that they wanted it to pair with.

The team programmed DNA to fold into sturdy tripods 60 times larger than previous DNA tripod-like building blocks and 400 times larger than DNA bricks. Those tripods then self-assembled into a specific type of three-dimensional polyhedron — all in a single test tube.

By adjusting the length of the strut, they built tripods that ranged from upright to splay-legged. More upright tripods formed polyhedra with fewer faces and sharper angles, such as a tetrahedron, which has four triangular faces. More splay-legged tripods formed polyhedra with more faces, such as a hexagonal prism, which is shaped like a wheel of cheese and has eight faces, including its top and bottom.

In all, they created five polyhedra: a tetrahedron, a triangular prism, a cube, a pentagonal prism, and a hexagonal prism.

Ultrasharp snapshots

After building the cages, the scientists visualized them using a DNA-based microscopy method Jungmann had helped developed called DNA-PAINT. In DNA-PAINT, short strands of modified DNA cause points on a structure to blink, and data from the blinking images reveal structures too small to be seen with a conventional light microscope. DNA-PAINT produced ultrasharp snapshots of the researchers’ DNA cages – the first 3D snapshots ever of single DNA structures in their native, watery environment.

ABSTRACT

DNA self-assembly has produced diverse synthetic three-dimensional polyhedra. These structures typically have a molecular weight no greater than 5 megadaltons (MD). We report a simple, general strategy for one-step self-assembly of wireframe DNA polyhedra that are more massive than most previous structures. A stiff three-arm-junction DNA origami tile motif with precisely controlled angles and arm lengths was used for hierarchical assembly of polyhedra. We experimentally constructed a tetrahedron (20 MD), a triangular prism (30 MD), a cube (40 MD), a pentagonal prism (50 MD), and a hexagonal prism (60 MD) with edge widths of 100 nanometers. The structures were visualized by transmission electron microscopy and by three-dimensional DNA-PAINT super-resolution fluorescent microscopy of single molecules in solution.

53 pages of supplemental information

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