DNA double helix does double duty in assembling arrays of nanoparticles

In a new twist on the use of DNA in nanoscale construction, scientists at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory and collaborators put synthetic strands of the biological material to work in two ways: They used ropelike configurations of the DNA double helix to form a rigid geometrical framework, and added dangling pieces of single-stranded DNA to glue nanoparticles in place. The method, described in the journal ("Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames"), produced predictable clusters and arrays of nanoparticles--an important step toward the design of materials with tailored structures and functions for applications in energy, optics, and medicine. octahedrons using ropelike structures made of bundles of DNA double-helix molecules to form the frames Scientists built octahedrons using ropelike structures made of bundles of DNA double-helix molecules to form the frames (a). Single strands of DNA attached at the vertices (numbered in red) can be used to attach nanoparticles coated with complementary strands. This approach can yield a variety of structures, including ones with the same type of particle at each vertex (b), arrangements with particles placed only on certain vertices (c), and structures with different particles placed strategically on different vertices (d). "These arrays of nanoparticles with predictable geometric configurations are somewhat analogous to molecules made of atoms," said Brookhaven physicist Oleg Gang, who led the project at the Lab's Center for Functional Nanomaterials (CFN, http://www.bnl.gov/cfn/), a DOE Office of Science User Facility. "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. This is exactly the problem that our method addresses." Using the new method, the scientists say they can potentially orchestrate the arrangements of different types of nanoparticles to take advantage of collective or synergistic effects. Examples could include materials that regulate energy flow, rotate light, or deliver biomolecules. "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. The scientists demonstrated the technique to engineer nanoparticle architectures using an octahedral scaffold with particles positioned in precise locations on the scaffold according to the specificity of DNA coding. The designs included two different arrangements of the same set of particles, where each configuration had different optical characteristics. 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 combination cryo-electron microscopy image of an octahedral frame with one gold nanoparticle bound to each of the six vertices, shown from three different angles A combination cryo-electron microscopy image of an octahedral frame with one gold nanoparticle bound to each of the six vertices, shown from three different angles. Details of assembly 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. First, the scientists created bundles of six double-helix molecules, then 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. The scientists then 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. 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. 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 said. The scientists can 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. using octahedrons to link nanoparticles into one-dimensional chainlike arrays (left) and two-dimensional square sheets By strategically placing tethers on particular vertices, the scientists used the octahedrons to link nanoparticles into one-dimensional chainlike arrays (left) and two-dimensional square sheets (right). Visualization of arrays 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. "Cryo-EM preserves samples in their near-native states and provides close to nanometer resolution," Wang said. "We show that cryo-EM can be successfully applied to probe the 3D structure of DNA-nanoparticle clusters." These images confirm that this approach to direct the placement of nanoparticles on DNA-encoded vertices of molecular frames could be a successful strategy for fabricating novel nanomaterials.
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Engineering phase changes in nanoparticle arrays

Scientists at the U.S. Department of Energy's Brookhaven National Laboratory have just taken a big step toward the goal of engineering dynamic nanomaterials whose structure and associated properties can be switched on demand. In a paper appearing in ("Selective transformations between nanoparticle superlattices via the reprogramming of DNA-mediated interactions"), they describe a way to selectively rearrange the nanoparticles in three-dimensional arrays to produce different configurations, or phases, from the same nano-components. Engineering Phase Changes in Nanoparticle Arrays Introducing "reprogramming" DNA strands into an already assembled nanoparticle array triggers a transition from a "mother phase," where particles occupy the corners and center of a cube (left), to a more compact "daughter phase" (right). The change represented in the schematic diagrams is revealed by the associated small-angle x-ray scattering patterns. Such phase-changes could potentially be used to switch a material's properties on demand. "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, a DOE Office of Science User Facility. "Until now, most of the structures we've built have been static. Now we are trying to achieve an even more ambitious goal: 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 as needed. Such phase-changing materials could lead to new applications, such as dynamic energy-harvesting or responsive optical materials. DNA-directed rearrangement This latest advance in nanoscale engineering builds on the team's previous work 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. In this case, they started with an assembly of nanoparticles already linked in a regular array by the complementary binding of the A, T, G, and C bases on single stranded DNA tethers, then added "reprogramming" DNA strands to alter the interparticle interactions. "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." 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. Injecting different kinds of reprogramming DNA strands can change the interparticle interactions Injecting different kinds of reprogramming DNA strands can change the interparticle interactions in different ways depending on whether the new strands increase attraction, repulsion, or a combination of these forces between particles. "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. 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." reprogrammin strands Various types of reprogramming strands can be used to selectively trigger the transformation to different phases, or configurations, of the same particle combinations. 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 (http://www.bnl.gov/ps/), another 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."
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Table-top extreme UV laser system heralds imaging at the nanoscale

Researchers at Swinburne University of Technology have discovered a new way to generate bright beams of coherent extreme UV radiation using a table-top setup that could be used to produce high resolution images of tiny structures at the nanoscale. “The ability to image nano-scale features with a conventional optical microscope is limited by the wavelength of the light used to illuminate the sample, Professor Lap van Dao, who led the research, said. “One way to achieve higher spatial resolution is to use radiation with shorter wavelengths such as extreme UV radiation or ‘soft’ x-rays.” The new table-top system may offer a cost-effective and convenient alternative to large-scale, multi-million-dollar facilities such as synchrotrons or free-electron lasers, which, until now, were the only way to generate bright coherent beams of extreme UV radiation. Table-top extreme UV laser system The researchers from the Centre for Quantum and Optical Science used their table-top laser setup to illuminate a gas cell of argon with two intense beams of ultrashort laser pulses at different wavelengths. One beam generates ‘high-order harmonics’ in the extreme UV, while the effect of the second overlapping beam is to amplify the extreme UV radiation by a process known as optical parametric amplification. These bright coherent beams of extreme UV radiation will be used for high resolution imaging based on a ‘lensless’ imaging technique called coherent diffractive imaging, in which images are reconstructed by a computer. “This research paves the way for the generation of intense radiation at still shorter wavelengths and ultimately to apply coherent diffractive imaging techniques to nano-scale structures and to biological samples in the water window region (2-4 nanometres),” Emeritus Professor Peter Hannaford said. The new research has been published in the prestigious journal ("Perturbative optical parametric amplification in the extreme ultraviolet").
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