Blue octahedra and pink decahedra cram together in a roundish cluster, which is just a cross section of a larger structure. In some places, the pink particles line up well with the blue particles along the outer surface of the structure. More internal layers are visible based on the pink particles. In these layers, the faces of the blue particles don't perfectly align, creating some black, empty space.

Flexible DNA linkers enable “impossible” nanostructures

Nanoparticles that couldn’t fit together with conventional DNA “glue” may now be created with the help of joints added to the rigid DNA.

By:

Michigan Chemical Engineering

Written by Derek Smith in collaboration with Seth Zimmerman.

Using DNA to guide the self-assembly of nanoparticles has been limited by the stiffness of DNA molecules, but pliant spacers added to the DNA can enable previously impossible shape combinations, researchers from Northwestern University and the University of Michigan have shown.

Blue octahedra and pink decahedra cram together in a roundish cluster, which is just a cross section of a larger structure. In some places, the pink particles line up well with the blue particles along the outer surface of the structure. More internal layers are visible based on the pink particles. In these layers, the faces of the blue particles don't perfectly align, creating some black, empty space.
This composite material is made from nanoparticles with two different shapes: octahedra (particles with eight triangular faces, shown in blue) and decahedra (particles with ten triangular faces, shown in pink). The different shapes could be linked together, even though they don’t perfectly fill space inside the material, thanks to flexible DNA linkers designed by researchers at the University of Michigan and Northwestern University. The image shows a simulated cross section of the larger composite material, which the researchers can use to study the internal structure of the material. Image credit: Glotzer Group, University of Michigan, published in Science.

Such materials may be designed to interact with light in new ways, potentially leading to technologies like “invisibility cloaks” and ultra high-speed optical computing systems, the researchers say.

“Creating structures from nanoparticles could lead to materials with interesting optical effects because the spacing between the particles can be at the scale of light waves,” said Sharon Glotzer, the Anthony C. Lembke Department Chair of Chemical Engineering and co-corresponding author of the study published today in Science.

“In most of the studies out there, there’s one particle shape that is linked together to make something cool. Now, we can start to think about mixing and matching different shapes,” added Glotzer.

The team’s flexible ligands significantly expand the design space for nanotechnology.

“We’ve enabled the creation of highly ordered colloidal crystals with shapes and sizes previously deemed impossible to make,” said Wenjie Zhou, a PhD graduate from Northwestern University and one of the study’s lead authors.

The team managed to pack together shapes that don’t normally fill space well and combine two variations on the octahedron (a particle with eight faces) into a honeycomb-like structure. Such feats bring the team closer to combining different nanoparticle properties in ways that currently don’t exist within a single material.

Nanoparticles are like bricks that engineers use to build larger structures, but these blocks are too small to be picked up and placed. Instead, engineers need to convince the particles to assemble themselves into the desired structures.

our crystal structures are shown side-by-side in two separate rows. Each row represents a unique view of the crystals. Pictures generated with computer models are in the top row, the crystals look like blue, bulky diamond squeezed together. A white box surrounds a group of the crystals to show it constitutes a repeating unit in a larger structure. The leftmost blue diamonds are closer together and aligned at their faces while the rightmost diamonds are further apart and aligned at their pointy ends. The bottom row shows microscopy images of the crystals, which look like gray, jagged stones.
Controlling the length of the DNA linkers relative to the nanoparticles’ size changes how the nanoparticles assemble. Longer DNA linkers congregate at the vertices – or pointy ends – of the nanoparticles, causing them to glue together vertex-to-vertex (like the bcc structures on the right). Short DNA linkers cause the particles to bind facet-to-facet (like the sh structures shown on the left). The Minkowski and I-43d structures are created with intermediate DNA length to particle size ratios. The top row shows computer simulations of the crystal structure while the bottom row shows scanning electron microscopy images of the structures. The white square represents the boundaries of the unit cells, or the repeating units in the larger crystal structure. Image credit: Glotzer Group, University of Michigan and Mirkin Lab, Northwestern University, published in Science.

Because single strands of DNA bind only with complementary strands, Mirkin’s group has been using them as programmable adhesives that tell nanoparticles how to stick together. The problem is, DNA molecules are like stiff rods, and that prevents all of the DNA molecules from binding when the shapes of the nanoparticles prevent their faces from perfectly aligning. 

To overcome this downside, the team inserted flexible molecules into the DNA, which act like the accordion part of a bendy straw. This added flexibility allows the DNA to glue together nanoparticles that don’t perfectly align. 

At the top of the image is a conventional, rigid DNA linker, which looks like the usual DNA double helix. Beneath the rigid linker is a green arrow, which points to a modified, flexible linker. The flexible linker looks like a jagged tube (which represents the spacer molecule) was placed inside the double helix at two locations. Parentheses mark the boundaries of the spacer molecule. The letter n follows each closing parenthesis and indicates that the spacer molecule can be repeated several times.
The research team created more flexible DNA linkers by inserting spacer molecules into the DNA. The spacer molecules give the DNA more freedom to wiggle, allowing them to glue together nanoparticles that don’t perfectly align, and can be repeated several times to tune the linker’s length and flexibility. Image credit: Mirkin Lab, Northwestern University, published in Science.

“DNA and nanoparticles have dimensions on the same length scale and we can chemically encode particles with DNA so they can be designed to recognize complementary particles, and therefore the DNA effectively becomes our hands,” said Chad Mirkin, the George B. Rathmann Professor of Chemistry at the Weinberg College of Arts and Sciences and co-corresponding author on the study.

This extra flexibility also causes the DNA to settle onto areas of the particles where they have more freedom to wiggle. For longer pieces of DNA, this tends to be at the nanoparticles’ vertices, or pointy ends. This arrangement of the DNA linkers causes the nanoparticles to glue together vertex-to-vertex. Shorter DNA molecules, on the other hand, tend to uniformly coat the particle surfaces, leading to structures that bind facet-to-facet.

“If the DNA linkers are flexible enough, we can control the types of structures that form by controlling the DNA length relative to the nanoparticle’s overall size,” said Kwanghwi Je, a PhD graduate from the Department of Chemical Engineering at the University of Michigan and the co-author of the study who performed simulations that predicted how the particles would arrange in space. “The beauty of this is that we can tune the length of the DNA linkers to guide the nanoparticles into specific structures.”

Controlling how the composite materials assemble into new structures could potentially yield materials with different properties, even when using the same building blocks.

The research was funded by the Air Force Office of Scientific Research, the US Department of Energy, the Simons Foundation, Northwestern University and the University of Michigan. The study used resources at NU’s Electron Probe Instrumentation Center, the NSF’s Extreme Science and Engineering Discovery Environment and U-M’s Advanced Research Computing. Sharon Glotzer is also the John Werner Cahn Distinguished University Professor of Engineering, the Stuart W. Churchill Collegiate Professor of Chemical Engineering and a professor of materials science and engineering, macromolecular science and engineering and physics.

related links

Study: “Space-tiled colloidal crystals from DNA-forced shape-complementary polyhedra pairing” DOI: 10.1126/science.adj1021

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