Esoteric news

Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory have developed the capability of creating dynamic nanomaterials — ones whose structure and associated properties can be switched, on-demand. In a paper appearing in Nature Materials, they describe a way to selectively rearrange nanoparticles in three-dimensional arrays to produce different configurations, or “phases,” from the same nano-components.

“One of the goals in nanoparticle self-assembly has been to create structures by design,” said Oleg Gang, who led the work at Brookhaven’s Center for Functional Nanomaterials (CFN), a DOE Office of Science User Facility. “Until now, most of the structures we’ve built have been static.” KurzweilAI covered that development in a previous article, “Creating complex structures using DNA origami and nanoparticles.”

The new advance in nanoscale engineering builds on that previous work in developing ways to get nanoparticles to self-assemble into complex composite arrays, including linking them together with tethers constructed of complementary strands of synthetic DNA.

“We know that properties of materials built from nanoparticles are strongly dependent on their arrangements,” said Gang. “Previously, we’ve even been able to manipulate optical properties by shortening or lengthening the DNA tethers. But that approach does not permit us to achieve a global reorganization of the entire structure once it’s already built.”

DNA-directed rearrangement

“Now we are trying to achieve an even more ambitious goal,” reveal Gang: “Making materials that can transform so we can take advantage of properties that emerge with the particles’ rearrangements.”

The ability to direct particle rearrangements, or phase changes, will allow the scientists to choose the desired properties — say, the material’s response to light or a magnetic field — and switch them whenever needed. Such phase-changing materials could lead to radical new applications, such as dynamic energy-harvesting or responsive optical materials.

In the new approach, the reprogramming DNA strands adhere to open binding sites on the already assembled nanoparticles. These strands exert additional forces on the linked-up nanoparticles.

“By introducing different types of reprogramming DNA strands, we modify the DNA shells surrounding the nanoparticles,” explained CFN postdoctoral fellow Yugang Zhang, the lead author on the paper. “Altering these shells can selectively shift the particle-particle interactions, either by increasing both attraction and repulsion, or by separately increasing only attraction or only repulsion. These reprogrammed interactions impose new constraints on the particles, forcing them to achieve a new structural organization to satisfy those constraints.”

Using their method, the team demonstrated that they could switch their original nanoparticle array, the “mother” phase, into multiple different daughter phases with precision control.

DNA-based matter reprogramming

This is quite different from phase changes driven by external physical conditions such as pressure or temperature, Gang said, which typically result in single phase shifts, or sometimes sequential ones. “In those cases, to go from phase A to phase C, you first have to shift from A to B and then B to C,” said Gang. “Our method allows us to pick which daughter phase we want and go right to that one because the daughter phase is completely determined by the type of DNA reprogramming strands we use.”

The scientists were able to observe the structural transformations to various daughter phases using a technique called in situ small-angle x-ray scattering at the National Synchrotron Light Source, a DOE Office of Science User Facility that operated at Brookhaven Lab from 1982 until last September (now replaced by NSLS-II, which produces x-ray beams 10,000 times brighter). The team also used computational modeling to calculate how different kinds of reprogramming strands would alter the interparticle interactions, and found their calculations agreed well with their experimental observations.

“The ability to dynamically switch the phase of an entire superlattice array will allow the creation of reprogrammable and switchable materials wherein multiple, different functions can be activated on demand,” said Gang. “Our experimental work and accompanying theoretical analysis confirm that reprogramming DNA-mediated interactions among nanoparticles is a viable way to achieve this goal.”

This research was done in collaboration with scientists from Columbia University’s School of Engineering and Applied Science and the Indian Institute of Technology Gandhinagar. The work was funded by the DOE Office of Science.

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Abstract of Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions

The rapid development of self-assembly approaches has enabled the creation of materials with desired organization of nanoscale components. However, achieving dynamic control, wherein the system can be transformed on demand into multiple entirely different states, is typically absent in atomic and molecular systems and has remained elusive in designed nanoparticle systems. Here, we demonstrate with in situ small-angle X-ray scattering that, by using DNA strands as inputs, the structure of a three-dimensional lattice of DNA-coated nanoparticles can be switched from an initial ‘mother’ phase into one of multiple ‘daughter’ phases. The introduction of different types of reprogramming DNA strands modifies the DNA shells of the nanoparticles within the superlattice, thereby shifting interparticle interactions to drive the transformation into a particular daughter phase. Moreover, we mapped quantitatively with free-energy calculations the selective reprogramming of interactions onto the observed daughter phases.

Scientists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and collaborators have developed a method using DNA for designing new customized materials with complex structures for applications in energy, optics, and medicine.

They used ropelike configurations of DNA to form a rigid geometrical framework and then added dangling pieces of single-stranded DNA to glue nanoparticles in place.

The method, described in the journal Nature Nanotechnology, produced predictable geometric configurations that are somewhat analogous to molecules made of atoms, according to Brookhaven physicist Oleg Gang, who led the project at the Lab’s Center for Functional Nanomaterials (CFN).

“While atoms form molecules based on the nature of their chemical bonds, there has been no easy way to impose such a specific spatial binding scheme on nanoparticles, he said. “This is exactly the problem that our method addresses.

“We may be able to design materials that mimic nature’s machinery to harvest solar energy, or manipulate light for telecommunications applications, or design novel catalysts for speeding up a variety of chemical reactions,” Gang said.

As a demonstration, the researchers used an octahedral (eight-sided) scaffold (structure) with particles positioned in precise locations on the scaffold according to specific DNA coding. They also used the geometrical clusters as building blocks for larger arrays, including linear chains and two-dimensional planar sheets.

“Our work demonstrates the versatility of this approach and opens up numerous exciting opportunities for high-yield precision assembly of tailored 3D building blocks in which multiple nanoparticles of different structures and functions can be integrated,” said CFN scientist Ye Tian, one of the lead authors on the paper.

A new DNA “origami” kit

This nanoscale construction approach takes advantage of two key characteristics of the DNA molecule: the twisted-ladder double helix shape, and the natural tendency of strands with complementary bases (the A, T, G, and C letters of the genetic code) to pair up in a precise way.

Here’s how the scientists built a complex structure with this “DNA origami” kit:

1. They created bundles of six double-helix DNA molecules.

2. They put four of these bundles together to make a stable, somewhat rigid building material — similar to the way individual fibrous strands are woven together to make a very strong rope.

3. They used these ropelike girders to form the frame of three-dimensional octahedrons, “stapling” the linear DNA chains together with hundreds of short complementary DNA strands. (“We refer to these as DNA origami octahedrons,” Gang said.)

4. To make it possible to “glue” nanoparticles to the 3D frames, the scientists engineered each of the original six-helix bundles to have one helix with an extra single-stranded piece of DNA sticking out from both ends.

5. When assembled into the 3D octahedrons, each vertex of the frame had a few of these “sticky end” tethers available for binding with objects coated with complementary DNA strands.

“When nanoparticles coated with single strand tethers are mixed with the DNA origami octahedrons, the ‘free’ pieces of DNA find one another so the bases can pair up according to the rules of the DNA complementarity code. Thus the specifically DNA-encoded particles can find their correspondingly designed place on the octahedron vertices,” Gang explained.

The scientists can also change what binds to each vertex by changing the DNA sequences encoded on the tethers. In one experiment, they encoded the same sequence on all the octahedron’s tethers, and attached strands with a complementary sequence to gold nanoparticles. The result: One gold nanoparticle attached to each of octahedron’s six vertices.

In additional experiments,the scientists changed the sequence of some vertices and used complementary strands on different kinds of particles, illustrating that they could direct the assembly and arrangement of the particles in a very precise way.

In one case, they made two different arrangements of the same three pairs of particles of different sizes, producing products with different optical properties. They were even able to use DNA tethers on selected vertices to link octahedrons end-to-end, forming chains, and in 2D arrays, forming sheets.

Visualizing the structures

Confirming the particle arrangements and structures was a major challenge because the nanoparticles and the DNA molecules making up the frames have very different densities. Certain microscopy techniques would reveal only the particles, while others would distort the 3D structures.

To see both the particles and origami frames, the scientists used cryo-electron microscopy (cryo-EM), led by Brookhaven Lab and Stony Brook University biologist Huilin Li, an expert in this technique, and Tong Wang, the paper’s other lead co-author, who works in Brookhaven’s Biosciences department with Li.

They had to subtract information from the images to “see” the different density components separately, then combine the information using single particle 3D reconstruction and tomography to produce the final images.

This research was supported by the DOE Office of Science.

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Abstract of Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames

Three-dimensional mesoscale clusters that are formed from nanoparticles spatially arranged in pre-determined positions
can be thought of as mesoscale analogues of molecules. These nanoparticle architectures could offer tailored properties
due to collective effects, but developing a general platform for fabricating such clusters is a significant challenge. Here, we
report a strategy for assembling three-dimensional nanoparticle clusters that uses a molecular frame designed with
encoded vertices for particle placement. The frame is a DNA origami octahedron and can be used to fabricate clusters
with various symmetries and particle compositions. Cryo-electron microscopy is used to uncover the structure of the DNA
frame and to reveal that the nanoparticles are spatially coordinated in the prescribed manner. We show that the DNA
frame and one set of nanoparticles can be used to create nanoclusters with different chiroptical activities. We also show
that the octahedra can serve as programmable interparticle linkers, allowing one- and two-dimensional arrays to be
assembled with designed particle arrangements.