ScienceDaily (Mar. 20, 2010) — The self-assembling properties of the DNA molecule have allowed for the construction of an intriguing range of nanoscale forms. Such nanoarchitectures may eventually find their way into a new generation of microelectronics, semiconductors, biological and chemical sensing devices and a host of biomedical applications. Now Hao Yan and Yan Liu, professors at the Biodesign Institute's Center for Single Molecule Biophysics and their collaborators have introduced a new method to deterministically and precisely position silver nanoparticles onto self-assembling DNA scaffolds.

In their latest research, the group used a long single-strand of DNA, which had been folded into a triangular building platform through a process known as DNA origami. This architectural foundation was then 'decorated' with one, two or three silver nanoparticles, which self-assembled at pre-determined locations on the DNA nanostructure. The group's experimental results, which appear in the advanced online edition of the journal Angewandte Chemie, demonstrate for the first time the viability of using silver, rather than the gold nanoparticles traditionally applied to DNA-tile or origami based architectures. The study was co-authored by Suchetan Pal, Zhengtao Deng, Baoquan Ding.

One of many applications for DNA scaffolds studded with nanoparticles is to perform precise sensing operations at the molecular scale. Sensitive detection of single molecules with high specificity is of great scientific interest for chemists, biologists, pharmacologists, medical researchers and those involved in environmental areas where trace analysis is required. The detailed study of human genes is but one area where improved single-molecule detection could be of enormous benefit.

In their current effort, the group sought to exploit the properties of the silver nanoparticles to increase the surface plasmon resonance -- a vibration of electrons that can give researchers clues regarding the molecular nature of the sample they are studying. "Theoretically, people predicted that a local surface plasmon resonance can be much stronger if you use silver particles compared to gold," said Yan. These locally enhanced areas between nanoparticles are referred to as electrical hot spots.

The group however, had to overcome significant obstacles to the use of silver nanoparticles. Silver tends to be much less stable than gold and can easily oxidize in its normal state. To counter this tendency, Yan and Liu's team attached multiple sulfur atoms to the backbone of the DNA strand used to make the platform for the nanoparticles. Each silver nanoparticle is then firmly held in place by nine sulfur atoms, once it is mounted on the DNA origami shape.

The new study paves the way for creating a more functional DNA architecture. "I believe this work will open doors to implement and study distance-dependent plasmonic interaction between noble nanoparticles at the single particle level," Yan said, adding that the first critical steps to creating hierarchically organized silver nanoparticle structures have now been taken.

Story Source:

Adapted from materials provided by Arizona State University. Original article written by Richard Harth.

Journal Reference:

1. Suchetan Pal, Zhengtao Deng, Baoquan Ding, Hao Yan, Yan Liu. DNA-Origami-Directed Self-Assembly of Discrete Silver-Nanoparticle Architectures. Angewandte Chemie International Edition, 2010; DOI: 10.1002/anie.201000330

ScienceDaily (Mar. 20, 2010) — Composites are combinations of materials that produce properties inaccessible in any one material. A classic example of a composite is fiberglass -- plastic fibers woven with glass to add strength to hockey sticks or the hull of a boat. Unlike the well-established techniques for producing fiberglass and other macroscale composites, however, there aren't general schemes available for making nanoscale composites.

Now, researchers at Berkeley Lab's Molecular Foundry, in collaboration with researcher at the University of California, Berkeley, have shown how nanocomposites with desired properties can be designed and fabricated by first assembling nanocrystals and nanorods coated with short organic molecules, called ligands. These ligands are then replaced with clusters of metal chalcogenides, such as copper sulfide. As a result, the clusters link to the nanocrystal or nanorod building blocks and help create a stable nanocomposite. The team has applied this scheme to more than 20 different combinations of materials, including close-packed nanocrystal spheres for thermoelectric materials and vertically aligned nanorods for solar cells.

"We're just starting to understand how combining materials on the nanoscale can open up new possibilities for electronic properties and efficient energy technologies," said Delia Milliron, Director of the Inorganic Nanostructures Facility at the Molecular Foundry. "This new process for fabricating inorganic nanocomposites gives us unprecedented ability to tune composition and control morphology."

The researchers anticipate demand from users seeking this latest addition to the Foundry's arsenal of materials synthesis capabilities, as this mix-and-match approach to nanocomposites could be used in an infinite list of applications, including materials for such popular uses as battery electrodes, photovoltaics and electronic data storage.

"The beauty of our method is not just the flexibility of compositions that can be achieved, but the ease with which this can be done. No specialized equipment is required, a variety of substrates can be used and the process is scalable," said Ravisubhash Tangirala, a Foundry post-doctoral researcher working with Milliron.

A paper reporting this research, titled "Modular inorganic nanocomposites by conversion of nanocrystal superlattices," appears in the journal Angewandte Chemie (International Edition). Co-authoring the paper with Milliron and Tangirala were Jessy Baker and Paul Alivisatos.

Portions of this work at the Molecular Foundry were supported by DOE's Office of Science.

The Molecular Foundry is one of the five DOE Nanoscale Science Research Centers (NSRCs), premier national user facilities for interdisciplinary research at the nanoscale. Together the NSRCs comprise a suite of complementary facilities that provide researchers with state-of-the-art capabilities to fabricate, process, characterize and model nanoscale materials, and constitute the largest infrastructure investment of the National Nanotechnology Initiative. The NSRCs are located at DOE's Argonne, Brookhaven, Lawrence Berkeley, Oak Ridge and Sandia and Los Alamos National Laboratories. For more information about the DOE NSRCs, please visit http://nano.energy.gov.

For more about Berkeley Lab's Molecular Foundry visit the Website at http://foundry.lbl.gov/

Story Source:

Adapted from materials provided by DOE/Lawrence Berkeley National Laboratory.

Journal Reference:

1. Ravisubhash Tangirala, Jessy L. Baker, A. Paul Alivisatos, Delia J. Milliron. Modular inorganic nanocomposites by conversion of nanocrystal superlattices. Angewandte Chemie International Edition, 2010; DOI: 10.1002/anie.200906642

ScienceDaily (Mar. 19, 2010) — Centuries ago, scientists began reducing the physics of the universe into a few, key laws described by a handful of parameters. Such simple descriptions have remained elusive for complex biological systems -- until now.

Emory biophysicist Ilya Nemenman has identified parameters for several biochemical networks that distill the entire behavior of these systems into simple equivalent dynamics. The discovery may hold the potential to streamline the development of drugs and diagnostic tools, by simplifying the research models.

The resulting paper, now available online, will be published in the March issue of Physical Biology.

"It appears that the details of the complexity of these biological systems don't matter, as long as some aggregate property, which we've calculated, remains the same," says Nemenman, associate professor of physics and biology. He conducted the analysis with Golan Bel and Brian Munsky of the Los Alamos National Laboratory.

The simplicity of the discovery makes it "a beautiful result," Nemenman says. "We hope that this theoretical finding will also have practical applications."

He cites the air molecules moving about his office: "All of the crazy interactions of these molecules hitting each other boils down to a simple behavior: An ideal gas law. You could take the painstaking route of studying the dynamics of every molecule, or you could simply measure the temperature, volume and pressure of the air in the room. The second method is clearly easier, and it gives you just as much information."

Nemenman wanted to find similar parameters for the incredibly complex dynamics of cellular networks, involving hundreds, or even thousands, of variables among different interacting molecules. Among the key questions: What determines which features in these networks are relevant? And if they have simple equivalent dynamics, did nature choose to make them so complex in order to fulfill a specific biological function? Or is the unnecessary complexity a "fossil record" of the evolutionary heritage?

For the Physical Biology paper, Nemenman and co-authors investigated these questions in the context of a kinetic proofreading (KPR) scheme.

KPR is the mechanism a cell uses for optimal quality control as it makes protein. KPR was predicted during the 1970s and it applies to most cellular assembly processes. It involves hundreds of steps, and each step may have different parameters.

Nemenman and his colleagues wondered if the KPR scheme could be described more simply. "Our calculations confirmed that there is, in fact, a key aggregate rate," he says. "The whole behavior of the system boils down to just one parameter."

That means that, instead of painstakingly testing or measuring every rate in the process, you can predict the error and completion rate of a system by looking at a single aggregate parameter.

Charted on a graph, the aggregate behavior appears as a straight line amid a tangle of curving ones. "The larger and more complex the system gets, the more the aggregate behavior is visible," Nemenman says. "The completion time gets simpler and simpler as the system size goes up."

Nemenman is now collaborating with Emory theoretical biologist Rustom Antia, to see if the discovery can shed light on the processes of immune cells. In particular, they are interested in the malfunction of certain immune receptors involved in most allergic reactions.

"We may be able to simplify the model for these immune receptors from about 3,000 steps to three steps," Nemenman says. "You wouldn't need a supercomputer to test different chemical compounds on the receptors, because you don't need to simulate every single step -- just the aggregate."

Just as the discovery of an ideal gas law led to the creation of engines and automobiles, Nemenman believes that such simple biochemical aggregates could drive advancements in health.

Story Source:

Adapted from materials provided by Emory University.

Journal Reference:

1. Golan Bel, Brian Munsky, Ilya Nemenman. The simplicity of completion time distributions for common complex biochemical processes. Physical Biology, 2009; 7 (1): 016003 DOI: 10.1088/1478-3975/7/1/016003

ScienceDaily (Mar. 19, 2010) — In findings that took the experimenters three years to believe, University of Michigan engineers and their collaborators have demonstrated that light itself can twist ribbons of nanoparticles.

The results are published in the current edition of Science.

Matter readily bends and twists light. That's the mechanism behind optical lenses and polarizing 3-D movie glasses. But the opposite interaction has rarely been observed, said Nicholas Kotov, principal investigator on the project. Kotov is a professor in the departments of Chemical Engineering, Biomedical Engineering and Materials Science and Engineering.

While light has been known to affect matter on the molecular scale -- bending or twisting molecules a few nanometers in size -- it has not been observed causing such drastic mechanical twisting to larger particles. The nanoparticle ribbons in this study were between one and four micrometers long. A micrometer is one-millionth of a meter.

"I didn't believe it at the beginning," Kotov said. "To be honest, it took us three and a half years to really figure out how photons of light can lead to such a remarkable change in rigid structures a thousand times bigger than molecules."

Kotov and his colleagues had set out in this study to create "superchiral" particles -- spirals of nano-scale mixed metals that could theoretically focus visible light to specks smaller than its wavelength. Materials with this unique "negative refractive index" could be capable of producing Klingon-like invisibility cloaks, said Sharon Glotzer, a professor in the departments of Chemical Engineering and Materials Science and Engineering who was also involved in the experiments. The twisted nanoparticle ribbons are likely to lead to the superchiral materials, the professors say.

To begin the experiment, the researchers dispersed nanoparticles of cadmium telluride in a water-based solution. They checked on them intermittently with powerful microscopes. After about 24 hours under light, the nanoparticles had assembled themselves into flat ribbons. After 72 hours, they had twisted and bunched together in the process.

But when the nanoparticles were left in the dark, distinct, long, straight ribbons formed.

"We discovered that if we make flat ribbons in the dark and then illuminate them, we see a gradual twisting, twisting that increases as we shine more light," Kotov said. "This is very unusual in many ways."

The light twists the ribbons by causing a stronger repulsion between nanoparticles in them.

The twisted ribbon is a new shape in nanotechnology, Kotov said. Besides superchiral materials, he envisions clever applications for the shape and the technique used to create I it. Sudhanshu Srivastava, a postdoctoral researcher in his lab, is trying to make the spirals rotate.

"He's making very small propellers to move through fluid -- nanoscale submarines, if you will," Kotov said. "You often see this motif of twisted structures in mobility organs of bacteria and cells."

The nanoscale submarines could conceivably be used for drug-delivery and in microfluidic systems that mimic the body for experiments.

This newly-discovered twisting effect could also lead to microelectromechanical systems that are controlled by light. And it could be utilized in lithography, or microchip production.

Glotzer and Aaron Santos, a postdoctoral researcher in her lab, performed computer simulations that helped Kotov and his team better understand how the ribbons form. The simulations showed that under certain circumstances, the complex combination of forces between the tetrahedrally-shaped nanoparticles could conspire to produce ribbons of just the width observed in the experiments. A tetrahedron is a pyramid-shaped, three-dimensional polyhedron.

"The precise balance of forces leading to the self-assembly of ribbons is very revealing," Glotzer said. "It could be used to stabilize other nanostructures made of non-spherical particles. It's all about how the particles want to pack themselves."

Other collaborators include researchers from the University of Leeds in the UK, Chungju National University in Korea, Argonne National Laboratory, Pusan National University in Korea and Jiangnan University in China.

The research is funded by the Air Force Office of Scientific Research, the Korea Science and Engineering Foundation and the U.S. Department of Energy.

Story Source:

Adapted from materials provided by University of Michigan.

Journal Reference:

1. Sudhanshu Srivastava, Aaron Santos, Kevin Critchley, Ki-Sub Kim, Paul Podsiadlo, Kai Sun, Jaebeom Lee, Chuanlai Xu, G. Daniel Lilly, Sharon C. Glotzer, Nicholas A. Kotov. Light-Controlled Self-Assembly of Semiconductor Nanoparticles into Twisted Ribbons. Science, 2010; 327 (5971): 1355 DOI: 10.1126/science.1177218

ScienceDaily (Mar. 19, 2010) — Alternative approaches to medicine are stock-in-trade in the ASU laboratory of microbiologist Shelley Haydel.

So when ASU senior Jenny Koehl joined Haydel's investigative team seeking firsthand knowledge of how basic research is done, how drugs are tested and potential cures produced, she found it and much more.

With the guidance of Tanya Cunningham, a graduate student mentor, Koehl has helped advance understanding about the antibacterial activity of clay minerals and their ability to kill what the best antibiotics on the market can't touch.

Haydel's group, part of the School of Life Sciences, in the College of Liberals Arts and Sciences, and the Biodesign Institute at ASU, did the work in collaboration with Jack Summers, an inorganic chemist at Western Carolina University. They uncovered two factors that control the antibacterial activity. Their article "pH-dependent metal ion toxicity influences the antibacterial activity of two natural mineral mixtures" was published March 1 in the journal PLoS ONE, published by the Public Library of Science.

"This work sets a baseline from which to look for potential mechanisms of antibacterial action," said Cunningham, lead author, who is now a research technician with the Fred Hutchinson Cancer Research Center in Seattle.

"We need helpful alternatives, natural approaches to antibacterial cures, because there is bacterial resistance to drugs," Koehl said. "Knowing the mechanisms of action will help us develop our own topical treatments."

Clay has had a role in human health as ancient as man. However, specific identification of the mechanisms underlying this antibacterial activity has been elusive, until now.

The Haydel-Summers collaborative has added clarity to these distinctly muddy waters by screening more than 50 mineral mixtures (and aqueous extractions from them, known as leachates) marketed as health and cosmetic products using pathogens Escherichia coli, Salmonella enterica serovar Typhimurium, Staphylococcus aureus, methicillin-resistant S. aureus (MRSA), and Pseudomonas aeruginosa. Only two mineral mixtures of significantly different compositions (and their leachates) were discovered to possess antibacterial traits.

Clay minerals often are recognized as the slimy slurry of minerals that slicks rivers' banks. Understanding clay's structure is integral to answering questions about the mechanisms behind its antibacterial activity. Negatively charged surfaces attract positively charged elements, such as iron, copper, silver and other metals. In turn, water is absorbed between layers of the crystal structure creating a cation sandwich with aqueous filling or interlayer.

Antibacterial activity in leachates, extracted from the mineral mixtures, confirm that the antibacterial activity is chemically-based, rather than a result of physical interactions with microbes.

Because of the tendency of clay to attract multivalent ions, particularly metals, the scientists next examined the leachates' chemistry and antibacterial activity in the presence of chelators, which bind metals. The researchers also used thiourea, a hydroxyl radical scavenger, at various pH levels. Chelation of the minerals with ethylenediaminetetraacetic acid (EDTA) or desferrioxamine eliminated or reduced toxicity, respectively.

Further testing of the mineral leachates confirmed that there are higher concentrations of chemically-accessible metal ions in leachates from antibacterial samples than from non-bactericidal mineral samples.

In addition, acidic conditions were found to increase the availability of metal ions and their toxicity. Overall, these findings suggest a role of an acid soluble metal species, particularly iron or other sequestered metal cations, in mineral toxicity.

However, whatever advances the study puts forward also present researchers with further challenges. Acidity may complicate development of topical treatments, if neutral pH, least damaging to skin and tissue, also reduces the mineral's antibacterial action.

Another complicating factor, accentuated by the PLoS ONE study, is that chemical environments under which any particular clay can emerge can greatly influence its toxicity, adsorptive qualities and, according to their findings, its antibacterial effects.

"Because natural mineral mixtures can be variable, both mineralogically and chemically, we must continue to define specific chemical properties that influence the antibacterial effectiveness," Haydel said. "Our goal is to understand the details, so we can, in the future, perhaps generate mineral mixtures that mimic the chemical compositions and environment, so that the antibacterial activity can be controlled and ensured."

This work is about eliminating the unknowns," Koehl said. "We have more analysis to do, looking at the leachate composition, the action of the chelators and activity of the iron scavengers."

Koehl, who is working with Haydel as part of the School of Life Sciences Undergraduate Research (SOLUR) program, said of her experience: "Science is like an obstacle course. I've learned that when you come across problems in the laboratory, you have to be creative to work them out. This process has helped me be more critical, to be a thinking scientist, because I've had to analyze my own experiments and figure them out. This isn't just something that someone handed to me on paper in a classroom."

Studies are moving forward in other laboratories to develop structured clays for slow-release topical medical treatments, but there may be chemical schemes that come from Haydel's research, supported by the National Institutes of Health, that enhance their effectiveness.

"This study has given me an idea of how things move from idea to shelf," Koehl said. "One day, when I am a pharmacist, maybe I'll be selling this!"

Story Source:

Adapted from materials provided by Arizona State University.

Journal Reference:

1. Tanya M. Cunningham, Jennifer L. Koehl, Jack S. Summers, Shelley E. Haydel. pH-Dependent Metal Ion Toxicity Influences the Antibacterial Activity of Two Natural Mineral Mixtures. PLoS ONE, 2010; 5 (3): e9456 DOI: 10.1371/journal.pone.0009456