Researchers turn photons into work using DNA

(Left) An illustration of the DNA-based molecular motor. The molecule is extended in its soft cis mode, and then contracted back to its original size in its stiffer trans mode, when work is extracted. (Right) An illustration of the DNA?s structure. Image credit: McCullagh, et al. ?2011 American Chemical Society.

(PhysOrg.com) -- By using light to change the elasticity of a DNA molecule, scientists have designed a molecular motor that can turn light into mechanical work. Unlike most previously reported molecular motors, the proposed setup involves an atomic force microscope, which acts as an interface with the outside world and enables the work to be extracted.

The researchers, Martin McCullagh, Ignacio Franco, Mark A. Ratner, and George C. Schatz, from the Department of Chemistry and the Non-equilibrium Energy Research Center (NERC) at Northwestern University, have published their study in a recent issue of the Journal of the American Chemical Society.

The molecule that the scientists propose using as the central component of the motor is a DNA hairpin that includes two guanine-cytosine base pairs capped by an azobenzene compound. The scientists designed a computational model of the system including the attachment of one end of the DNA hairpin to a surface and the other end to an atomic force microscope coupled to a cantilever.

“The greatest significance of this work is showing how the structure of DNA can be exploited to amplify the transduction ability of azobenzene in a setup in which the work can be extracted,” Schatz told PhysOrg.com. “To our knowledge, this is the first proposed DNA-based molecular motor with an interface to the outside world.”

In their molecular dynamics simulations, the researchers used light to change the structure of the azobenzene. In this process, called “isomerization,” the DNA-motor reversibly changes between the cis isomer and the trans isomer. Although this photoinduced isomerization is only a structural change, it has important implications, such as changing the length of the molecule (the trans isomer is longer) and altering the stability of the bonds between the guanine and cytosine bases (the trans isomer’s intra base pair interactions are stable across a greater range of lengths).

As the chemists showed, these two differences between the cis and trans isomers alter the molecule’s elasticity, and can be exploited to extract work from the system. For modest extensions, the trans isomer of the DNA hairpin is stiffer because it has a geometry that favors DNA base pairing, which makes it more difficult to extend the DNA hairpin.

To extract work from the system, the scientists proposed using a single-molecule analog of a thermodynamic cycle (a Stirling cycle). In this cycle, the molecule in its soft cis mode is first extended using the AFM setup. Next, light transforms the cis isomer into the stiffer trans isomer. The trans structure is then contracted to the motor’s original extension. Finally, a second light source is used to isomerize the molecule back to the cis state to close the cycle. Since the molecule is stiffer during contraction, the work extracted during contraction is larger than the work invested during extension, leading to net work extraction.

“The basis of this motor is the photoinduced change in elasticity of the azobenzene-DNA molecule,” Schatz said. “Because of the setup, the AFM is an integral part of the DNA motor. Work must be done on the molecule and cantilever to extend it, and work is extracted from the composite system during contraction. If the molecule is stiffer during contraction, then net work can be extracted.”

The scientists estimated a maximum of 3.4 kcal/mol of extractable work per cycle with an estimated maximum efficiency of 2.4%. This amount of work is comparable to the 7.3 kcal/mol of free energy output in ATP hydrolysis, which is the main energy source in biological processes.

“While the amount of extractable work from this motor is promising, the focus of this study is on investigating novel concepts in energy conversion,” Schatz said. “The proposed DNA-based motor provides a platform upon which further improvements can be made. We would like to highlight that the explored setup provides a means to quantify the transduction abilities of single molecules. Such quantification is a pivotal step in transforming single-molecule machines from scientific curiosity to actual power supplies for nanoscale processes.”

In the future, the scientists plan to use these insights regarding the relationship between a molecule’s structure and its function to improve the DNA-based motor design. They hope to find more optimal azobenzene-capped structures, as well as investigate the effect of temperature on the motor’s performance.

More information: Martin McCullagh, et al. “DNA-Based Optomechanical Molecular Motor.” Journal of the American Chemical Society. DOI:10.1021/ja109071a

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Opalinus Clay as a potential host rock for nuclear waste repositories

Scientists at Johannes Gutenberg University Mainz (JGU, Germany) have studied natural claystone in the laboratory for more than four years in order to determine how the radioactive elements plutonium and neptunium react with this rock. The experiments have been performed as part of a Germany-wide project sponsored by the Federal Ministry of Economics and Technology (BMWi) to find a suitable geological repository for radioactive waste. Geological configurations that could play a role for the permanent disposal of nuclear waste include not only salt and granite formations, but also claystone. The results obtained by the team of nuclear chemists under the supervision of Professor Tobias Reich confirm that natural clay has certain useful properties that counteract the migration of radioactive materials. Professor Reich, director of the Institute of Nuclear Chemistry at Mainz University, summarizes the results obtained so far as follows: "It does seem that clay could be suitable as host rock, although we still need to wait for the outcome of long-term investigations."

The cylinders of clay used by the Mainz team of nuclear chemists have come a long way: Cores of Opalinus Clay were obtained by drilling in the Underground Rock Laboratory Mont Terri in the Swiss Jura mountains. This clay formation was deposited some 180 million years ago. In Switzerland, Opalinus Clay is being considered as a rock formation for the storage of radioactive waste. The bore cores were first transferred to the Institute for Nuclear Waste Disposal (INE) in Karlsruhe, Germany, where they were cut in small round disks with a thickness of 11 millimeters. At the Institute of Nuclear Chemistry in Mainz, these clay disks were packed in diffusion cells and contacted with pore water containing radioactive neptunium or plutonium. Other samples of clay were transferred to test tubes where a suspension of this material with pore water and the radioactive elements was agitated and centrifuged and then analyzed by highly sensitive mass spectrometers in order to determine the sorption characteristics of the clay material. Afterwards, the samples were transported to the particle accelerators in Grenoble, Karlsruhe, and at the Paul Scherrer Institute in Switzerland, where they were investigated by beams of synchrotron radiation with a width of only 0.0015 millimeters. "This provides us with detailed information on the distribution of the elements, and where and how the elements are sorbed on the clay material," explains Reich.

The batch experiments show that radioactive plutonium in the oxidation state IV is nearly totally sorbed on Opalinus Clay, leaving almost no plutonium in the aqueous solution. In the case of neptunium(V), the corresponding ratio is 60:40. However, if neptunium is reduced to neptunium(IV) by iron minerals present in the clay, a near 100 percent sorption of neptunium on the clay is observed. The diffusion experiments using “radioactive” water have demonstrated that water passes through a clay cylinder with a thickness of 1.1 centimeters within a week. Neptunium, on the other hand, hardly diffuses through the clay, and even after a month it is still almost where it started.

Thin, millimeter-wide sections of the clay disks also show which chemical reactions of the radioactive elements occur as they pass through the clay material: Plutonium(VI) is reduced during its passage through the clay cylinder and is recovered as plutonium(IV). "This is a great advantage, as plutonium(IV) stays where it is put." Professor Reich and his research team also discovered what is responsible for the sorption of the radioactive substances: It is predominantly the clay minerals, while the iron minerals responsible for the reduction process are only of minor importance in this connection.

Opalinus Clay, which occurs not only in Switzerland but also in Southern Germany, thus appears to be an excellent candidate for further investigation on the migration of long-lived radionuclides - neptunium, for example, has a half-life of 2.14 million years. The Mainz team of nuclear chemists had previously reported similar results using the clay mineral kaolinite from the United States of America. "In the meantime we have developed the necessary equipments and have defined the experimental processes required," Reich summarizes the outcome of the experiments with Opalinus Clay. Over the coming three years, he and his team plan to investigate the behavior of clay in the presence of higher salt concentrations.

The studies are being conducted as part of a project initiated by the German Federal Ministry of Economics and Technology in 1995 to find a suitable location for a nuclear waste repository. Eight research institutions are participating in the joint project entitled "Interaction and transport of actinides in natural claystone, under consideration of humic substances and organic clay materials" to investigate to what extent Opalinus Clay could be a suitable host rock for the permanent disposal of highly radioactive waste.

Provided by Johannes Gutenberg University Mainz

Study clarifies the role of cocoa bean handling on flavanol levels

As evidence regarding the health benefits of consuming dark chocolate and cocoa mounts, there has been an increasing debate about which cocoa and chocolate products deliver the most beneficial compounds, known as flavanols, and if steps in cocoa and chocolate production diminish the levels of cocoa flavanols.

In a recently published paper, scientists reported on the effect of conventional production methods of cocoa beans on the levels of flavanols, natural antioxidants. The study, conducted by researchers at the Hershey Center for Health & Nutrition®, investigated cocoa beans and cocoa powders and described production steps that retain naturally occurring flavanols and reported that alkali processing causes a loss of up to 98% of one important flavanol, epicatechin, in the final product.

The study, published in the Journal of Agricultural and Food Chemistry, compared the effects of various common production methods on freshly harvested unfermented and naturally farm-fermented beans. Levels of epicatechin and catechin, a less active flavanol antioxidant, were compared in beans that were unfermented and in beans that underwent medium (about 5 days) and long fermentation (about 10 days). Long fermentation previously has been shown to impact the level of epicatechin in cocoa beans, and the authors reported loss of both flavanols as fermentation time increased. Beans were roasted to temperatures of 120oC and the researchers found that temperatures of 70°C or higher caused some loss (up to 88% at 120oC) of epicatechin. Catechin levels, however, increased as roasting temperature increased. Additionally, natural cocoa powders and powders that had been treated with different levels of alkali also were measured. The study found that by far the greatest flavanol losses occurred during alkali processing. The results also suggested that epicatechin may be converted to catechin by alkali processing.

"This study is meant to address the impact of processing on the level of beneficial flavanol antioxidants found in cocoa beans" said Dr. Mark Payne, lead author of the paper. "We found that the processing step which causes the most loss in the flavanol epicatechin is the alkali processing step. Here the epicatechin, which is thought to be most beneficial, appears to be converted to catechin which has been shown to be less active in the body."

"Most of the world's cocoa beans undergo a natural, field fermentation on the farm and then roasting," said Dr. David A. Stuart, co-director of the Hershey Center. "Both steps are critical to the flavor development for chocolate and cocoa powder. It is important that we understand the balance in creating the wonderful flavor of chocolate with the health benefits of cocoa powder and dark chocolate. This study has gone a long way in furthering that understanding and is the first systematic study of the whole process, from bean to powder, that we are aware of."

Provided by The Hershey Company

Newly identified spider toxin may help uncover novel ways of treating pain and human diseases

Spider venom toxins are useful tools for exploring how ion channels operate in the body. These channels control the flow of ions across cell membranes, and are key components in a wide variety of biological processes and human diseases.

A newly identified toxin from the American Funnel Web spider acts on T-type and N-type calcium channels, researchers from the University of California at Riverside have discovered. The toxin offers a new target for studying T-type channels, which play a role in congestive heart failure, hypertension, epilepsy and pain.

"The blocking mechanism of the toxin is different from classical pore blocker toxins and voltage modifier toxins," says lead researcher Xiao Zhang, a postdoc at the Del Webb Center for Neuroscience in La Jolla, Calif. "It indicates a new toxin blocking mechanism on voltage-gated ion channels."

Zhang purified the toxin and created a recombinant version as part of his doctoral research at the University of California, Riverside. "If we can develop a calcium-channel blocker based on this toxin, we could have a new way to identify how these channels work and develop drugs for treating pain and disease," says Zhang.

More information: The presentation, "A Spider Toxin and its Recombinant Isoform Block T-type and N-type Calcium Channels with High Affinity" by Xiao Zhang, Li Dai, and Michael E. Adams is at 1:00 p.m. on Wednesday, March 9, 2011 in the Baltimore Convention Center, Room 307. ABSTRACT: http://tinyurl.com/4nhp7m6

Provided by American Institute of Physics

Molecular tug-of-war could lead to new materials

Tug-of-war isn't just for play. In the chemistry world, the game could identify a Saran-wrap-like material that instantly heals microscopic tears in its own structure.

Duke scientists are testing this idea using atomic forceps to tug on individual molecules. They’ve already discovered that a slight pull can pop open rare, triangle-shaped molecular structures in milliseconds.

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The usual way to open these molecules is to heat them at high temperatures – overnight, said chemist Stephen Craig, who described his research at a colloquium on March 3. With the molecular tug-of-war, Craig foresees a microscopic world where scientists could almost instantly move molecules and atoms to create new materials and even new chemistry.

Craig and his colleagues recently explored how molecule chains, called polymers, can snap back to structures smaller than their original forms. The team also trapped a molecule in the middle of the reaction that made it shrink. Typically that halfway point, called a “transition state,” lasts for less than one millionth of a millionth of a second, but Craig’s team succeeded in “catching lightning in a bottle,” which may be useful in understanding the electronic properties of the transition state.

To quantify the tug-of-war at the molecular level requires an atomic force microscope. Craig sees the tool like a diving board. When a particularly heavy person or tough molecule is on the end, the board bends way down. Measuring the bend of the microscope’s board, the team can put a number to the force or strength of the molecule being tugged.

The microscope can pull harder and harder on the chain until it breaks, which shows the polymers that can endure the “heaviest diver” or most force. His team can also use the tool to watch if specific molecules change their shapes, such as opening and closing their triangle structures, as the polymer starts to break apart.

By seeing this new chemistry as it happens, Craig and other scientists could learn how to move atoms and molecules where they need them. The manipulation provides scientists with another way to create new materials for applications from longer-lasting coatings on artificial hips to plastic wrapping that never gets holes.

Provided by Duke University (news : web)

Fluorescent tail tags TB

 A new way of detecting tuberculosis (TB) inside cells has been developed by scientists from Oxford University and NIH in the US.

Methods for diagnosing TB haven’t changed much in a century, still relying on the staining of tissue sections and chest X-rays.

In a recent issue of Nature Chemical Biology Ben Davis, from Oxford University’s Department of Chemistry, and colleagues describe a new method which can, for the first time, detect TB inside cells using a small molecule.

"We designed and created a fluorescent sugar that we discovered is a substrate for an enzyme, Ag85, found on the surface of TB bacteria," Ben told us.

"The sugar is a variant of one that TB uses but is not used at all in mammalian biology. The Ag85 enzyme takes this and attaches a greasy lipid tail - this greasy product then becomes buried on the greasy surface of TB. The result is that the cell surface of the bug is fluorescently 'painted'."

Ben explains that the net result is a selective labelling of TB even when the bugs are found inside mammalian macrophages, where it normally lies dormant in infected hosts. Other bugs are not labelled and other sugars do not work, so it's very selective.

He adds: "We've been able to use this here to map out aspects of TB cell biology but the implications for diagnosing and monitoring TB as a disease are clearly much broader."

Provided by Oxford University (news : web)

Battling the bedbug epidemic

"Sleep tight, don't let the bedbugs bite" -- is becoming an impossible dream for millions of people as the world experiences a resurgence of an ancient scourge that is fostering human misery, financial burdens and the risk of exposure to potentially toxic materials. That's the message from the cover story of the current edition of Chemical & Engineering News (C&EN), ACS' weekly newsmagazine.

In the article, C&EN News Editor William G. Schulz points out that bedbugs represent a growing epidemic that is difficult to control. The bugs hide in mattresses, box springs, nightstands, and other areas, emerging at night to dine on human blood. Their bites can cause allergic skin reactions, mental anguish, and loss of sleep. Infestations can be a financial burden, with professional extermination sometimes costing thousands of dollars and taking eight weeks or more. Some chemicals that were once effective against the pests, such as DDT, have been banned due to threats to human health and the environment, leaving exterminators with few effective options for controlling the pests, which have developed the ability to shrug-off some pesticides.

But the fight against bedbugs is intensifying. Scientists are looking for new substances to fight bedbugs that are safe and effective. Officials in Ohio — "bedbug ground zero' — are seeking Federal government permission to resume use of a pesticide called propoxur that can quickly halt infestations. Propoxur was pulled from the market by its manufacturer after EPA raised safety and efficacy concerns. For now, a combination of pesticides and preventive measures, such as regular inspection, laundering, vacuuming, removing clutter, and sealing up cracks in walls and baseboards, are among the best ways to control the bugs, the article notes.

More information: "Battling the Bedbug Epidemic" http://pubs.acs.or … 10cover.html

Provided by American Chemical Society (news : web)