The structural DNA path toward productive nanosystems has achieved another step forward with the demonstration that a DNA origami scaffolding can be used to program a DNA motor to navigate a network of tracks. A hat tip to PhysOrg.com for reprinting this news release from Kyoto University “ DNA Motor Programmed to Navigate a Network of Tracks “: Kyoto, Japan — Expanding on previous work with engines traveling on straight tracks, a team of researchers at Kyoto University and the University of Oxford have successfully used DNA building blocks to construct a motor capable of navigating a programmable network of tracks with multiple switches. The findings, published in the January 22 online edition of the journal Nature Nanotechnology [ abstract ], are expected to lead to further developments in the field of nanoengineering. The research utilizes the technology of DNA origami, where strands of DNA molecules are sequenced in a way that will cause them to self-assemble into desired 2D and even 3D structures. In this latest effort, the scientists built a network of tracks and switches atop DNA origami tiles, which made it possible for motor molecules to travel along these rail systems. “We have demonstrated that it is not only possible to build nanoscale devices that function autonomously,” explained Dr. Masayuki Endo of Kyoto University’s Institute for Integrated Cell-Material Sciences (iCeMS), “but that we can cause such devices to produce predictable outputs based on different, controllable starting conditions.” The team, including lead author Dr. Shelley Wickham at Oxford, expects that the work may lead to the development of even more complex systems, such as programmable molecular assembly lines and sophisticated sensors. “We are really still at an early stage in designing DNA origami-based engineering systems,” elaborated iCeMS Prof. Hiroshi Sugiyama. “The promise is great, but at the same time there are still many technical hurdles to overcome in order to improve the quality of the output. This is just the beginning for this new and exciting field.” Courtesy Sugiyama Lab, Kyoto University iCeMS A depiction of a DNA origami tile with a built-in network of tracks. The DNA engine or motor, in red, can be programmed to navigate a series of junctions to reach one of four desired end points. Perhaps the next step is to have multiple addressable DNA motors bring different components together to be joined? —James Lewis
Posts Tagged ‘Development’
Targeted proteins for diabetes drug design
Type 2 diabetes mellitus is a common metabolism disorder characterized by high glucose in the bloodstream, especially in the case of insulin resistance and relative insulin deficiency. Nowadays, it is very common in middle-aged people and involves such dangerous symptoms as increasing risk of stroke, obesity and heart failure. In Vietnam, besides the common treatment of insulin injection, some herbal medication is used but no unified optimum remedy for the disease yet exists and there is no production of antidiabetic drugs in the domestic market yet. In the development of nanomedicine at the present time, drug design is considered as an innovative tool for researchers to study the mechanisms of diseases at the molecular level. The aim of this article is to review some common protein targets involved in type 2 diabetes, offering a new idea for designing new drug candidates to produce antidiabetic drugs against type 2 diabetes for Vietnamese people.
Mechanical pressure produces atomically-precise, multifunctional 2D sheets
A few months ago the use of designed peptides to build supramolecular structures on surfaces was reported. Another group has now reported making two-dimensional atomically precise sheets using peptoids, a class of peptide mimetics in which the side chain is attached to the backbone nitrogen atom instead of to the alpha carbon atom. Such sheets might be useful as templates for assembling other nanostructures. A hat tip to Science Daily for reprinting this news release from the Lawrence Berkeley National Laboratory (Berkeley Lab) “ Shaken, not stirred: Berkeley Lab scientists spy molecular maneuvers “: Stir this clear liquid in a glass vial and nothing happens. Shake this liquid, and free-floating sheets of protein-like structures emerge, ready to detect molecules or catalyze a reaction. This isn’t the latest gadget from James Bond’s arsenal—rather, the latest research from the U. S. Department of Energy (DOE)’s Lawrence Berkeley National Laboratory (Berkeley Lab) scientists unveiling how slim sheets of protein-like structures self-assemble. This “shaken, not stirred” mechanism provides a way to scale up production of these two-dimensional nanosheets for a wide range of applications, such as platforms for sensing, filtration and templating growth of other nanostructures. “Our findings tell us how to engineer two-dimensional, biomimetic materials with atomic precision in water,” said Ron Zuckermann, Director of the Biological Nanostructures Facility at the Molecular Foundry, a DOE nanoscience user facility at Berkeley Lab. “What’s more, we can produce these materials for specific applications, such as a platform for sensing molecules or a membrane for filtration.” Zuckermann, who is also a senior scientist at Berkeley Lab, is a pioneer in the development of peptoids, synthetic polymers that behave like naturally occurring proteins without degrading. His group previously discovered peptoids capable of self-assembling into nanoscale ropes, sheets and jaws, accelerating mineral growth and serving as a platform for detecting misfolded proteins. In this latest study, the team employed a Langmuir-Blodgett trough — a bath of water with Teflon-coated paddles at either end — to study how peptoid nanosheets assemble at the surface of the bath, called the air-water interface. By compressing a single layer of peptoid molecules on the surface of water with these paddles, said Babak Sanii, a post-doctoral researcher working with Zuckermann, “we can squeeze this layer to a critical pressure and watch it collapse into a sheet.” “Knowing the mechanism of sheet formation gives us a set of design rules for making these nanomaterials on a much larger scale,” added Sanii. … The research was published in the Journal of the American Chemical Society (JACS) [ abstract ]. It will be interesting to see if these peptoid nanosheets can be developed to provide atomically precise surfaces on which other components can be assembled in a defined atomically precise arrangement, as can be done with DNA origami .
RNA CAD tool for synthetic biology may facilitate RNA nanotechnology
New computer assisted design (CAD) tools for engineering RNA components have been developed for the growing field of synthetic biology. The knowledge of RNA folding and RNA catalytic and binding functions incorporated into these CAD tools may also prove useful for RNA nanotechnology. A hat tip to Science Daily for reprinting this news release from the Lawrence Berkeley National Laboratory (Berkeley Lab) “ CAD for RNA “: The computer assisted design (CAD) tools that made it possible to fabricate integrated circuits with millions of transistors may soon be coming to the biological sciences. Researchers at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) have developed CAD-type models and simulations for RNA molecules that make it possible to engineer biological components or “RNA devices” for controlling genetic expression in microbes. This holds enormous potential for microbial-based sustainable production of advanced biofuels, biodegradable plastics, therapeutic drugs and a host of other goods now derived from petrochemicals. “Because biological systems exhibit functional complexity at multiple scales, a big question has been whether effective design tools can be created to increase the sizes and complexities of the microbial systems we engineer to meet specific needs,” says Jay Keasling, director of JBEI and a world authority on synthetic biology and metabolic engineering. “Our work establishes a foundation for developing CAD platforms to engineer complex RNA-based control systems that can process cellular information and program the expression of very large numbers of genes. Perhaps even more importantly, we have provided a framework for studying RNA functions and demonstrated the potential of using biochemical and biophysical modeling to develop rigorous design-driven engineering strategies for biology.” … The ressearch was published in Science [ abstract ]. To test their CAD tools, the researchers engineered 28 molecular devices to regulate metabolic pathways in bacteria via RNA-controlled gene expression, and verified that expected levels of expression were obtained. From the abstract, “… More broadly, we provide a framework for studying RNA functions and illustrate the potential for the use of biochemical and biophysical modeling to develop biological design methods.” The news release continues: … As with other engineering disciplines, CAD tools for simulating and designing global functions based upon local component behaviors are essential for constructing complex biological devices and systems. However, until this work, CAD-type models and simulation tools for biology have been very limited. Identifying the relevant design parameters and defining the domains over which expected component behaviors are exerted have been key steps in the development of CAD tools for other engineering disciplines,” says Carothers, a bioengineer and lead author of the Science paper who is a member of Keasling’s research groups with both JBEI and the California Institute for Quantitative Biosciences. “We’ve applied generalizable engineering strategies for managing functional complexity to develop CAD-type simulation and modeling tools for designing RNA-based genetic control systems. Ultimately we’d like to develop CAD platforms for synthetic biology that rival the tools found in more established engineering disciplines, and we see this work as an important technical and conceptual step in that direction.” … RNA nanotechnology has a unique set of advantages as a pathway technology toward atomically precise productive nanosystems that reflect its central role in biological systems. Unlike the simple Watson-Crick base-pair molecular recognition code that underlies DNA nanotechnology, the more complex rules of base-pairing involved in RNA folding allow RNA to fold into compact complex three-dimensional shapes. These shapes are somewhat reminiscent of the complex folds of protein structures, yet the folding rules are considerably simpler than those of proteins. These RNA CAD tools may be an important step toward powerful design tools for folded polymer paths toward molecular machine systems.
Crowd-sourced protein design a promising path to advanced nanotechnology
Less than four years ago we asked here whether online gamers playing Foldit could help perfect the de novo design of proteins that do not exist in nature. Four months ago we reported that Foldit players had succeeded where scientists had failed in solving the structure of an important viral enzyme. Now Scientific American reports that Foldit players have topped scientists in redesigning a protein—the challenge we suggested less than four years ago. From “ Online gamers achieve first crowd-sourced redesign of protein “: Obsessive gamers’ hours at the computer have now topped scientists’ efforts to improve a model enzyme, in what researchers say is the first crowdsourced redesign of a protein. The online game Foldit, developed by teams led by Zoran Popovic, director of the Center for Game Science, and biochemist David Baker, both at the University of Washington in Seattle, allows players to fiddle at folding proteins on their home computers in search of the best-scoring (lowest-energy) configurations. The researchers have previously reported successes by Foldit players in folding proteins, but the latest work moves into the realm of protein design, a more open-ended problem. By posing a series of puzzles to Foldit players and then testing variations on the players’ best designs in the lab, researchers have created an enzyme with more than 18-fold higher activity than the original. The work was published January 22 in Nature Biotechnology [ abstract ]. “I worked for two years to make these enzymes better and I couldn’t do it,” says Justin Siegel, a post-doctoral researcher working in biophysics in Baker’s group. “Foldit players were able to make a large jump in structural space and I still don’t fully understand how they did it.” … The latest effort involved an enzyme that catalyses one of a family of workhorse reactions in synthetic chemistry called Diels-Alder reactions. Members of this huge family of reactions are used throughout industry to synthesize everything from drugs to pesticides, but enzymes that catalyze Diels-Alder reactions have been elusive. In 2010, Baker and his team reported that they had designed a functional Diels–Alderase computationally from scratch [ abstract ], but, says Baker, “it wasn’t such a good enzyme”. The binding pocket for the pair of reactants was too open and activity was low. After their attempts to improve the enzyme plateaued, the team turned to Foldit. In one puzzle, the researchers asked users to remodel one of four amino-acid loops on the enzyme to increase contact with the reactants. In another puzzle, players were asked for a design that would stabilize the new loop. The researchers got back nearly 70,000 designs for the first puzzle and 110,000 for the second, then synthesized a number of test enzymes based on the best designs, ultimately resulting in the final, 18-fold-more-active enzyme.… The article was written by Jessica Marshall and reprinted in Scientific American with permission from Nature , where it was originally published as “ Victory for crowdsourced biomolecule design: Players of the online game Foldit guide researchers to a better enzyme. ” The article does an excellent job of describing how researchers and game players collaborated to achieve the final result. The gamers explored much more radical changes to the protein than can be done by conventional molecular biology techniques such as directed evolution, which typic[a]lly explores only single amino acid substitutions. The researchers then physically constructed and characterized the enzyme designed by the gamers. The choice as design target of an enzyme to catalyze Diels-Alder reactions is particularly interesting from the standpoint of developing advanced nanotechnology, also referred to as molecular manufacturing. As noted in the 2010 Science paper, this reaction is a “cornerstone” in organic synthesis, and no naturally occurring enzymes are known to catalyze this reaction. As early as 1994 Markus Krummenacker proposed the use of Diels-Alder cycloaddition in a strategy to develop molecular building blocks for molecular manufacturing (“ Steps towards molecular manufacturing “). What roles crowd-sourcing, citizen science, and de novo protein design will play in the development of molecular manufacturing, or productive nanosystems, remains to be seen, but this latest result looks like an important step alog the way. —James Lewis
Will new piezoelectric materials lead to new tools for nanotechnology?
One of the key technologies in the development of nanotechnology has been scanning probe microscopy, and one of the key technologies that has made scanning probe microscopies possible is piezoelectric materials. Researchers have now integrated a single-crystal material with “giant” piezoelectric properties onto silicon. Improved actuators for nanopositioning devices are listed among the several possible applications of improved piezoelectric materials. Will these actuators be used to integrate scanning probe microscopes on a chip and would such instruments be useful for atomically precise manufacturing? ScienceDaily reprints the University of Wisconsin-Madison news release : Integrating a complex, single-crystal material with “giant” piezoelectric properties onto silicon, University of Wisconsin-Madison engineers and physicists can fabricate low-voltage, near-nanoscale electromechanical devices that could lead to improvements in high-resolution 3-D imaging, signal processing, communications, energy harvesting, sensing, and actuators for nanopositioning devices, among others. Led by Chang-Beom Eom, a UW-Madison professor of materials science and engineering and physics, the multi-institutional team published its results in the November 18 issue of the journal Science [ abstract ]. … Eom studies the advanced piezoelectric material lead magnesium niobate-lead titanate, or PMN-PT. Such materials exhibit a “giant” piezoelectric response that can deliver much greater mechanical displacement with the same amount of electric field as traditional piezoelectric materials. They also can act as both actuators and sensors. For example, they use electricity to deliver an ultrasound wave that penetrates deeply into the body and returns data capable of displaying a high-quality 3-D image. Currently, a major limitation of these advanced materials is that to incorporate them into very small-scale devices, researchers start with a bulk material and grind, cut and polish it to the size they desire. It’s an imprecise, error-prone process that’s intrinsically ill-suited for nanoelectromechanical systems (NEMS) or microelectromechanical systems (MEMS). Until now, the complexity of PMN-PT has thwarted researchers’ efforts to develop simple, reproducable microscale fabrication techniques. Applying microscale fabrication techniques such as those used in computer electronics, Eom’s team has overcome that barrier. He and his colleagues worked from the ground up to integrate PMN-PT seamlessly onto silicon. Because of potential chemical reactions among the components, they layered materials and carefully planned the locations of individual atoms. “You have to lay down the right element first,” says Eom. Onto a silicon “platform,” his team adds a very thin layer of strontium titanate, which acts as a template and mimics the structure of silicon. Next comes a layer of strontium ruthenate, an electrode Eom developed some years ago, and finally, the single-crystal piezoelectric material PMN-PT. The researchers have characterized the material’s piezoelectric response, which correlates with theoretical predictions. “The properties of the single crystal we integrated on silicon are as good as the bulk single crystal,” says Eom. His team calls devices fabricated from this giant piezoelectric material “hyper-active MEMS” for their potential to offer researchers a high level of active control. Using the material, his team also developed a process for fabricating piezoelectric MEMS. We will have to watch to see if the use of this material in fabricating piezoelectric MEMS leads to improvements in the use of scanning probes for atomically precise manufacturing.
Holiday Greetings from Foresight!
This holiday season, you’re invited to join with us in celebrating the following events: Foresight Announces Election of New President Larry Millstein Meet The President: Dinner Reception Monday 12/12, 6:30pm @ Don Giovanni’s in Mountain View, CA Annual Challenge Grant Kickoff: Donate this month for double the value to Foresight! I. Foresight Announces Election of our New President Foresight is proud to announce that Larry S. Millstein, Ph.D., J.D. has been elected President of the Institute by the Board of Directors. Larry has been a Foresight member since 1998. He was instrumental in establishing the Foresight Communication Prize in 2000 and in ensuring its funding since then; he has been a member of the Board of Directors since 2009. He has been interested in atomically and molecularly precise technologies for many years – since reading Nanosystems over a decade ago and strengthened by the development of mechanochemistry and the recent commercialization of single molecule DNA sequencing instruments. “We are thrilled to have persuaded such a technically accomplished and experienced leader to be President of Foresight and to take on the task of accelerating the development of transformative nanotechnologies and their beneficial uses,” said Foresight co-founder and current President Christine Peterson, who will continue to be a member of the Board and active advisor to the Institute and will collaborate closely with senior staff in making the transition. “I look forward to forging new tools for Foresight to catalyze the development of truly transformative technologies,” Larry says. “Foresight has a key role to play in forcefully communicating the power and potential of atomically precise technologies to transform the world in remarkably beneficial ways, and its activities will be a seminal catalyst for ideas and actions that will — by harnessing the power of atomic precision — realize some of humankind’s most fervently wished for goals.” Larry has been very active for some time in educating and evangelizing the public on the beauty and power of science, arranging dozens of dinners and lectures with scientists and technologists in the Washington, DC area, particularly at the Cosmos Club . He founded and supports the Zimm Prize in Physical Chemistry at UCSD. He teaches on biotechnology (and on law) at Georgetown University . He developed the Emerging Technologies course there, which recently has been directed to NexGen DNA Sequencing Technologies and Personalized Genomics, and will soon turn to DNA Machines and Synthetic Genomics. He also teaches an introduction to Intellectual Property law to graduate students in the Biotechnology Program at Georgetown. He is an author of a variety of scientific research articles and an inventor of several nucleic acid amplification methods and of inventions relating to molecular arrays and their manufacture. He has worked with inventors and written and prosecuted many patent applications on inventions in biotechnology and nanotechnology, and he has served in an in-house role for several start up companies. Larry is a partner in Millen, White, Zelano & Branigan, PC , and Adjunct Professor of Biochemistry, Molecular & Cellular Biology and Chair of the Biotechnology Program Advisory Board at Georgetown University. He also is Treasurer and a member of the Board of the Washington Academy of Sciences and Program Chair, Past President and member of the Board of the Philosophical Society of Washington . Larry earned his BS at CCNY-CUNY (Chemistry), his MS and PhD at the University of California-San Diego ( Chemistry / Molecular Biology) and the Scripps Research Institute (where he did his graduate research with Joel Gottesfeld ). He earned his JD at George Mason University , and is a graduate of the GMU Patent Law Specialty Track Program. He was a research professor at the University of Rochester before turning to law. And, as a lawyer, he was an associate at Foley & Lardner , served as Senior Patent Counsel at Human Genome Sciences , founded Millstein & Taylor and merged it a decade later with Holland & Knight , where he was a partner and led the biotechnology practice. He joined Millen White as a partner in 2008. II. Meet The President: Dinner Reception Monday 12/12, 6:30pm @ Don Giovanni’s in Mountain View, CA When: Monday December 12th, 2011, drinks/reception at 6:30, Dinner at 7:15pm Where: Don Giovanni’s, 235 Castro Street, Mountain View, CA, 94041 RSVP: $40 to foresight@foresight.org via Paypal.com by midnight Saturday, 12/10/11 Meal options: List fish, chicken or vegetarian in your Paypal note! Join us for an informal celebration reception and dinner with incoming Foresight Institute President Larry S. Millstein in Mountain View on Monday, 12 December 2011. We will be welcoming Larry on his first visit to our offices and chatting with him about his experiences, Foresight’s future and the power in transformative nanotechnology. He is looking forward to meeting members old, new, and prospective while he is here, especially Senior Associates. Please join us as we celebrate this year’s progress, present our thoughts on Foresight’s program for next year — and bring your own ideas and your enthusiasm for Foresight! III. Annual Challenge Grant Kickoff: Donate this month for double the value to Foresight This year, Foresight has again received a generous $30,000 Challenge Grant, where every dollar you donate between now and December 31st is matched and doubled. Do you believe in Foresight’s vision of transformative nanotechnology? Did you enjoy the quality of this year’s conference and dinner lectures? Would you like to see us expand our youth outreach? If you would like to see these re-energized programs take off, now is a great time to support us by making your annual donation, or upgrade your membership. Please send in your check, dated by Dec 31 to the address below, or donate online at: http://www.foresight.org/challenge Foresight Institute PO Box 61058 Palo Alto, CA 94306 USA main: 650-289-0860 fax: 650-289-0863 Or to find out more on how to help, contact Desiree Dudley at 650-289-0860, x259 or desiree@foresight.org . We are excited about our coming year. We hope you are, too! Come help us create the future. Christine Peterson, Co-Founder/President Larry Millstein, President-Elect Desiree Dudley, Director of Development and Outreach
Nose Power: Electricity From Human Respiration
The same piezoelectric effect that ignites your gas grill with the push of a button could one day power sensors in your body via the respiration in your nose. Researchers at the University of Wisconsin–Madison have created a polyvinylidene fluoride ( PVDF ) strip that vibrates when passed by low-speed airflow such as human respiration, generating an electric charge. The researchers engineered the PVDF to generate sufficient piezoelectric energy from respiration to operate small electronic devices. “Basically, we are harvesting mechanical energy from biological systems. The airflow of normal human respiration is typically below about two meters per second,” says Xudong Wang. “We calculated that if we could make this material thin enough, small vibrations could produce a microwatt of electrical energy that could be useful for sensors or other devices implanted in the face.” Researchers are taking advantage of advances in nanotechnology and miniaturized electronics to develop a host of biomedical devices that could monitor blood glucose for diabetics or keep a pacemaker battery charged so that it would not need replacing. What’s needed to run these tiny devices is a miniscule power supply. Waste energy in the form or blood flow, motion, heat, or in this case respiration, offers a consistent source of power. The team used an ion-etching process to carefully thin material while preserving its piezoelectric properties. With improvements, Wang believes the thickness can be controlled down to the submicron level. Because PVDF is biocompatible, he says the development represents a significant advance toward creating a practical micro-scale device for harvesting energy from respiration. Read More Paper Movie (.wmv)



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