Posts Tagged ‘Nanobiotechnology’

Nanoparticles reduce tumors in clinical trial

An artist’s rendering of BIND-014. Image credit: Digizyme, Inc. We have often reported here that targeted nanoparticles to treat cancer have shown great promise in animal studies. An MIT news release written by Anne Trafton now informs us that “ Targeted nanoparticles show success in clinical trials “: Targeted therapeutic nanoparticles that accumulate in tumors while bypassing healthy cells have shown promising results in an ongoing clinical trial, according to a new paper. The nanoparticles feature a homing molecule that allows them to specifically attack cancer cells, and are the first such targeted particles to enter human clinical studies. Originally developed by researchers at MIT and Brigham and Women’s Hospital in Boston, the particles are designed to carry the chemotherapy drug docetaxel, used to treat lung, prostate and breast cancers, among others. In the study, which appears April 4 in the journal Science Translational Medicine [ abstract ], the researchers demonstrate the particles’ ability to target a receptor found on cancer cells and accumulate at tumor sites. The particles were also shown to be safe and effective: Many of the patients’ tumors shrank as a result of the treatment, even when they received lower doses than those usually administered. “The initial clinical results of tumor regression even at low doses of the drug validates our preclinical findings that actively targeted nanoparticles preferentially accumulate in tumors,” says Robert Langer, the David H. Koch Institute Professor in MIT’s Department of Chemical Engineering and a senior author of the paper. “Previous attempts to develop targeted nanoparticles have not successfully translated into human clinical studies because of the inherent difficulty of designing and scaling up a particle capable of targeting tumors, evading the immune system and releasing drugs in a controlled way.” The Phase I clinical trial was performed by researchers at BIND Biosciences, a company cofounded by Langer and Omid Farokhzad in 2007. “This study demonstrates for the first time that it is possible to generate medicines with both targeted and programmable properties that can concentrate the therapeutic effect directly at the site of disease, potentially revolutionizing how complex diseases such as cancer are treated,” says Farokhzad, director of the Laboratory of Nanomedicine and Biomaterials at Brigham and Women’s Hospital, associate professor of anesthesia at Harvard Medical School and a senior author of the paper. … The news release goes on to detail several features of these nanoparticles that may be useful in evaluating other types of nanoparticles that are currently at earlier stages of development and have only been tested in animal models. First of all, nanoparticles of many different compositions have been developed, from gold to DNA. These, called AccurinsTM , use clinically validated biocompatible polymers and incorporate a “stealth” layer to avoid removal by the immune system. As explained in the news release: One of the challenges in developing effective drug-delivery nanoparticles, Langer says, is designing them so they can perform two critical functions: evading the body’s normal immune response and reaching their intended targets. “You need exactly the right combination of these properties, because if they don’t have the right concentration of targeting molecules, they won’t get to the cells you want, and if they don’t have the right stealth properties, they’ll get taken up by macrophages,” says Langer, also a member of the David H. Koch Institute for Integrative Cancer Research at MIT. The BIND-014 nanoparticles have three components: one that carries the drug, one that targets PSMA, and one that helps evade macrophages and other immune-system cells. A few years ago, Langer and Farokhzad developed a way to manipulate these properties very precisely, creating large collections of diverse particles that could then be tested for the ideal composition. “They systematically made a set of materials that varied in the properties they thought would matter, and developed a way to screen them. That’s not been done in this kind of setting before,” says Mark Saltzman, a professor of biomedical engineering at Yale University who was not involved in this study. “They’ve taken the concept from the lab into clinical trials, which is quite impressive.” The systematic way in which these researchers addressed multiple variables and issues gives us some indication of what will be required to move nanoparticles and other nanotherapeutics from laboratory studies into clinical trials. —James Lewis, PhD

Faster, less expensive medical diagnostics through nanotechnology

Image courtesy of Oregon State University Artistic representation of a carbon nanotube and two protein molecules. Nanomedicine will make major contributions to health care not only by providing new and improved therapies, but by providing new diagnostic methods that will be faster and less expensive than currently available procedures. A hat tip to KurzweilAI News for reprinting this news release from Oregon State University “ Nanotube technology leading to fast, lower-cost medical diagnostics “: Researchers at Oregon State University have tapped into the extraordinary power of carbon “nanotubes” to increase the speed of biological sensors, a technology that might one day allow a doctor to routinely perform lab tests in minutes, speeding diagnosis and treatment while reducing costs. The new findings have almost tripled the speed of prototype nano-biosensors, and should find applications not only in medicine but in toxicology, environmental monitoring, new drug development and other fields. The research was just reported in Lab on a Chip [ abstract ], a professional journal. More refinements are necessary before the systems are ready for commercial production, scientists say, but they hold great potential. “With these types of sensors, it should be possible to do many medical lab tests in minutes, allowing the doctor to make a diagnosis during a single office visit,” said Ethan Minot, an OSU assistant professor of physics. “Many existing tests take days, cost quite a bit and require trained laboratory technicians. “This approach should accomplish the same thing with a hand-held sensor, and might cut the cost of an existing $50 lab test to about $1,” he said. The key to the new technology, the researchers say, is the unusual capability of carbon nanotubes. An outgrowth of nanotechnology, which deals with extraordinarily small particles near the molecular level, these nanotubes are long, hollow structures that have unique mechanical, optical and electronic properties, and are finding many applications. In this case, carbon nanotubes can be used to detect a protein on the surface of a sensor. The nanotubes change their electrical resistance when a protein lands on them, and the extent of this change can be measured to determine the presence of a particular protein – such as serum and ductal protein biomarkers that may be indicators of breast cancer. The newest advance was the creation of a way to keep proteins from sticking to other surfaces, like fluid sticking to the wall of a pipe. By finding a way to essentially “grease the pipe,” OSU researchers were able to speed the sensing process by 2.5 times. Further work is needed to improve the selective binding of proteins, the scientists said, before it is ready to develop into commercial biosensors. “Electronic detection of blood-borne biomarker proteins offers the exciting possibility of point-of-care medical diagnostics,” the researchers wrote in their study. “Ideally such electronic biosensor devices would be low-cost and would quantify multiple biomarkers within a few minutes.” The above news item indicates not only how nanotechnology is going to improve medical care, but it hints at the future economic impact of widespread nanotechnology. If a five-minute test using a handheld biosensor in the doctor’s office replaces several expensive lab tests performed by skilled technicians, what happens to the jobs of those technicians? Historically technological innovation has created more and better jobs than those that were lost, and in this case the expanding nanotechnology industry may create jobs for the displaced medical lab technicians. But it is not at all clear that this trend will persist with the more radical displacements that will occur as nanotechnology advances toward productive nanosystems and atomically precise manufacturing. As early as 1986 in Engines of Creation Eric Drexler described how advanced nanotechnology and artificial intelligence could produce a world of abundance with no need of human labor and proposed an Inheritance Day to distribute the wealth. Three years ago here on Nanodot J Storrs Hall described how artificial general intelligence could produce an “early retirement” for the human race (see “ Early retirement ” and “ Early retirement — how soon? “). Perhaps the issue of how transformative technologies will affect jobs, employment, and the distribution of wealth deserves more attention. —James Lewis, PhD

Novel RNA structural motifs expand tool kit for RNA nanotechnology

RNA structural motif identification is essential in understanding the RNA architecture and functionalities. The illustration shows a novel RNA structural motif, named ‘rope sling motif’, identified by a newly developed computational framework … – Credit: C. Zhong and S. Zhang, Nucleic Acids Res. , 2012, 40: 1307–1317 As we pointed out recently , a unique advantage of RNA nanotechnology compared to DNA nanotechnology is that the more complex rules of base pairing involved in RNA folding allow the formation of a variety of compact, complex three-dimensional shapes. Although one principal function of RNA molecules in cells is as messenger RNA, carrying a copy of the information in a DNA gene to the ribosomes where that message is translated to make a protein, a large number of other RNA molecules, including those comprising the ribosomes themselves, have complex three-dimensional shapes and embody various functional properties dependent on those shapes, as do proteins. Taking advantage of the rapid increase in available high resolution, three-dimensional structures for various non-coding RNA molecules, a new computational method has uncovered many new RNA structural motifs, revealing the tool kit of RNA nanotechnology to be even more diverse than thought. A hat tip to Science Daily for reprinting this news release from the University of Central Florida “ Computer Sleuthing Helps Unravel RNA’s Role in Cellular Function “: … University of Central Florida Engineering Assistant Professor Shaojie Zhang used a complex computer program to analyze RNA motifs – the subunits that make up RNA (ribonucleic acid). … The units that make up RNA fold like a long accordion and vary in structure. Many have been identified in the past, but finding a quick automatic way to determine patterns in the varying types of units has been elusive until now. “We have discovered many new RNA structural motifs using our new computational method,” Zhang said. “This breakthrough can largely increase our current knowledge of RNA structural motifs. And newly discovered motifs may also help us develop possible treatment of certain diseases.” Zhang’s work is this month’s cover story in Nucleic Acids Research [ abstract , Open Access Full Text ], an academic journal. Using computers, Zhang and his team have been able to view these RNA accordion-like structures and how they fold in a 3-D scale. The program can quickly go through many RNA samples and discover units that are distinct and form patterns. That information gives researchers clues about their function. … The newly identified structural motifs contain variations in base-pairing rules. As the authors conclude: These new motifs may lead to the discovery of unknown structure–function relationships and define new building blocks for the RNA architecture, significantly improving our understanding of the RNA structural motifs. … The next test will be to see if these new insights into RNA structure will enable the design of new RNA machines with novel functions, and eventually artificial RNA molecular machines. —James Lewis

DNA nanotechnology-based nanorobot delivers cell suicide message to cancer cells

Image courtesy of the Wyss Institute “ The nanosized robot was created in the form of an open barrel whose two halves are connected by a hinge. The DNA barrel, which acts as a container, is held shut by special DNA latches that can recognize and seek out combinations of cell-surface proteins, including disease markers. This image was created by Campbell Strong, Shawn Douglas, and Gaël McGill using Molecular Maya and cadnano. “ DNA nanotechnology is not only a very promising path toward productive nanosystems and atomically precise manufacturing, but also a path to increasingly sophisticated DNA molecular machines for near-term drug delivery applications in nanomedicine. A recent advance comprises an autonomous DNA nanorobot incorporating a DNA origami chasis and DNA aptamer locks functioning as logical AND gates that are unlocked after the aptamers bind a protein target on the target cell, allowing the nanorobot to discharge its therapeutic cargo. A hat tip to KurzweilAI.net for reprinting this Harvard Gazette news release written by Twig Mowatt “ Sending DNA robot to do the job: Technology has potential to seek out cancer cells, cause them to self-destruct “: Researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University have developed a robotic device made from DNA that could potentially seek out specific cell targets within a complex mixture of cell types and deliver important molecular instructions, such as telling cancer cells to self-destruct. Inspired by the mechanics of the body’s own immune system, the technology might one day be used to program immune responses to treat various diseases. The research findings appear today in Science ["A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads" abstract ; full text available for fair use on Church lab web site]. Using the DNA origami method, in which complex 3-D shapes and objects are constructed by folding strands of DNA, Shawn Douglas, a Wyss Technology Development Fellow, and Ido Bachelet, a former Wyss postdoctoral fellow who is now an assistant professor in the Faculty of Life Sciences and the Nano-Center at Bar-Ilan University in Israel, created a nanosized robot in the form of an open barrel whose two halves are connected by a hinge. The DNA barrel, which acts as a container, is held shut by special DNA latches that can recognize and seek out combinations of cell-surface proteins, including disease markers. When the latches find their targets, they reconfigure, causing the two halves of the barrel to swing open and expose its contents, or payload. The container can hold various types of payloads, including specific molecules with encoded instructions that can interact with specific cell surface signaling receptors. Douglas and Bachelet used this system to deliver instructions, which were encoded in antibody fragments, to two different types of cancer cells — leukemia and lymphoma. In each case, the message to the cell was to activate its “suicide switch” — a standard feature that allows aging or abnormal cells to be eliminated. And because leukemia and lymphoma cells speak different languages, the messages were written in different antibody combinations. … “We can finally integrate sensing and logical computing functions via complex, yet predictable, nanostructures — some of the first hybrids of structural DNA, antibodies, aptamers, and metal atomic clusters — aimed at useful, very specific targeting of human cancers and T-cells,” said George Church, a Wyss core faculty member and professor of genetics at Harvard Medical School, who is principal investigator on the project. … A key feature of this work is that the DNA aptamer changes structure upon binding its target so it releases its hold on the complementary part of the DNA latch. Since two DNA latches hold the nanorobot in a closed configuration, the latches can be programmed to both respond to the same cell surface target, or to each respond to a different target so that both targets would need to be on the cell to activate the nanorobot to open and allow the payload molecules to bind their targets. This logical AND function allows for much greater specificity in recognizing target cells. As the authors conclude, “These findings demonstrate that the robots can induce a variety of tunable changes in cell behavior.” Conceivably a similar mechanism could be used in an atomically precise manufacturing operation in which DNA nanorobots could add a payload molecule to a workpiece depending on whether both of two specific molecular signals on the workpiece were present. —James Lewis

DNA motor navigates network of DNA tracks

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

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.

First Master’s of Science in Nanomedicine degree program in US announced

We received this announcement of the new M.S. in Nanomedicine program from Radiological Technologies University – VT : Radiological Technologies University VT, located in South Bend, Indiana is pleased to announce the approval of the first Master’s of Science in Nanomedicine degree program in the country. The formal approval was granted today through the Indiana Commission for Postsecondary Proprietary Education. Nanomedicine is the medical application of Nanotechnology which focuses its work at the cellular level to do everything from repairing tissue, to cleaning arteries, to attacking cancer cells and viruses like AIDS. The RTU Nanomedicine program is the first of its kind in the country by combining Nanotechnology with an emphasis on Medical Physics. Radiological Technologies University offers degree programs ranging from a Bachelor’s degree in Medical Dosimetry to Master’s of Science degrees in Medical Dosimetry, Medical Physics, Medical Health Physics, and Nanomedicine. Although Foresight has no information about the details of this nanomedicine program, just one item from the NCI Alliance for Nanotechnology in Cancer news archive highlights the potential of nanomedicine, specifically the application of nanoparticles to cancer therapy. From “ Nanoparticles seek and destroy drug-resistant glioblastoma “: Glioblastoma is one of the most aggressive forms of brain cancer. Rather than presenting as a well-defined tumor, glioblastoma will often infiltrate the surrounding brain tissue, making it extremely difficult to treat surgically or with chemotherapy or radiation. Likewise, several mouse models of glioblastoma have proven completely resistant to all treatment attempts. In a new study, a team led by scientists at Sanford-Burnham Medical Research Institute (SBMRI) and the Salk Institute for Biological Studies developed a method to combine a tumor-homing peptide, a cell-killing peptide, and a nanoparticle that both enhances tumor cell death and allows the researchers to image the tumors. When used to treat mice with glioblastoma, this new nanosystem eradicated most tumors in one model and significantly delayed tumor development in another. These findings were published in the Proceedings of the National Academy of Sciences of the USA [ abstract ]. “This is a unique nanosystem for two reasons,” said project leader Erkki Ruoslahti of the SBMRI. “First, linking the cell-killing peptide to nanoparticles made it possible for us to deliver it specifically to tumors, virtually eliminating the killer peptide’s toxicity to normal tissues. Second, ordinarily researchers and clinicians are happy if they are able to deliver more drugs to a tumor than to normal tissues. We not only accomplished that, but were able to design our nanoparticles to deliver the killer peptide right where it acts, at the mitochondria, the cell’s energy-generating center.” The nanosystem developed in this study is made up of three elements. First, a nanoparticle acts as the carrier framework for an imaging agent and for two peptides. One of these peptides guides the nanoparticle and its payload specifically to cancer cells and the blood vessels that feed them by binding cell surface markers that distinguish them from normal cells. This same peptide also drives the whole system inside these target cells, where the second peptide wreaks havoc on the mitochondria, triggering cellular suicide through a process known as apoptosis. Together, these peptides and nanoparticles proved extremely effective at treating two different mouse models of glioblastoma. In the first model, treated mice survived significantly longer than untreated mice. In the second model, untreated mice survived for only eight to nine weeks. In sharp contrast, treatment with this nanosystem cured all but one of ten mice. What’s more, in addition to providing therapy, the nanoparticles could aid in diagnosing glioblastoma; they are made of iron oxide, which makes them and the tumors they target visible by magnetic resonance imaging. In a final twist, the researchers made the whole nanosystem even more effective by administering it to the mice in conjunction with a third peptide. Ruoslahti and his team previously showed that this peptide, known as iRGD, helps co-administered drugs penetrate deeply into tumor tissue. iRGD has been shown to substantially increase treatment efficacy of various drugs against human breast, prostate, and pancreatic cancers in mice, achieving the same therapeutic effect as a normal dose with one-third as much of the drug. Here, iRGD enhanced nanoparticle penetration and therapeutic efficacy. In this study, the researchers tested their nanoparticles on mice that developed glioblastomas with the same characteristics as observed in humans with the disease. Once the nanoparticles reached the tumors’ blood vessels, they delivered their payload directly to the cell’s power producer, the mitochondria. By destroying the blood vessels and also some surrounding tumor cells, the investigators found they were able to cure some mice and extend the lifespan of the rest.”

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

Geometry of DNA nanostructures used to program molecular recognition

The wide assortment of nanostructures and nanomachines made possible by structural DNA nanotechnology are all based upon the molecular recognition code of the familiar DNA double helix. Initially this code was exploited to build atomically precise structures on the order of 20 nmm in size. Since the publication of the DNA origami technique by Paul W. K. Rothemund in 2006 it has been possible to fold a long single strand of DNA with the help of numerous short DNA ‘staples’ into larger and more complex two-dimensional and three-dimensional nanostructures on the order of 100 nm in size. In a recent publication [ abstract ], Rothemund and Sungwook Woo use a different type of molecular coding derived from DNA—blunt-end stacking interactions at the ends of DNA helices—to create molecular shape complementarity on a larger scale. Rothemund’s earlier work making rectangular DNA tiles using DNA origami had revealed that the rectangles tended to form chains due to the blunt-end stacking interactions of the helix ends exposed at the edges of the tiles. In their current work Woo and Rothemund tested methods of making these blunt-end interactions specific so that multiple origami tiles could be assembled in a programmed fashion to make well-defined nanostructures. Through matching patterns of projecting and recessed ends at the edges of tiles, discrete segments could be made to assemble in a particular order to form larger structures approaching micrometer scale. The stacking interactions are weaker than base pairing interactions but permit building loser structures on a ten-times-larger scale. The researchers speculate that it might be possible to design larger nanomachines in which parts can be programmed to both self-assemble and slide freely past each other in a programmed way. The Caltech DNA computation group has made three PDFs available on their web site describing the research in detail: the full text of the Nature Chemistry research paper “ Programmable molecular recognition based on the geometry of DNA nanostructures “, a Nature Chemistry commentary by Andrew J. Turberfield, and a report on the work by Michael Eisenstein published in Nature Methods .