Posts Tagged ‘dna’

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.

Arrays of artificial molecular machines could lead to atomically precise nanotechnology

A few weeks ago we noted the publication of a tutorial review that asks whether artificial molecular machines can deliver the performance that visionaries expect. Upon learning that the full text is available after a free registration, I downloaded the review to learn what the authors think about the prospects of eventually doing atomically precise manufacturing with artificial molecular machine systems. The authors begin with the observation that, despite “remarkable progress” in synthesizing molecular switches, there have been only few and very rudimentary examples of harvesting useful work from such molecular switches. They then ask whether only incremental progress will be necessary for artificial molecular machines to achieve the levels of function so elegantly achieved by biological molecular machines, or whether some paradigm shift in thinking will be necessary (they believe the latter). The fundamental theory of molecular machines is applied to two questions. (1) Can artificial molecular machines be developed to manipulate or chemically transform other molecular or nanoscale structures? (2) Can artificial molecular machines be assembled into integrated systems that work together to manipulate or fabricate structures at the meso- and macroscopic levels? The overall conclusion of these authors with respect to these two questions is optimistic: Indeed, nanoscale-based machinery has been envisaged ever since the days of Feynman and today the Feynman’s Grand Prize offers a $250,000 reward to the first persons to create a nanoscale robotic arm, capable of precise positional control. While, in pursuit of this goal, the “top-down” fabrication strategies have so far failed rather dismally, we are convinced that a “bottom-up” approach, utilizing AMMs [artificial molecular machines], can deliver. Engineering a macromolecular architecture capable of robotic function will no doubt be a considerable synthetic challenge. We feel, however, that the time is ripe for such an undertaking—for instance, by combining AMMs with the DNA-origami materials, such that the former would provide the actuation within precisely folded DNA nanoscaffolds of the latter. A major focus of this tutorial review is to describe the recently developed theoretical concepts “that distinguish simple molecular switches from fully fledged molecular machines.” Simple molecular switches differ from familiar macroscopic switches in that the switching between the states of the switch is driven by thermal noise. To advance from simple molecular switches to molecular machines, it must be possible to drive chemical reactions uphill, away from equilibrium, as do biological motor molecules. This can be accomplished by using molecular switches to alter the energy profile of the reaction by first lowering the energy of the intermediate to be less than the energy of the starting material, and then switching again to raise the energy of the intermediate above that of the product, and finally switching again to reset the system to the original energy profile. Switching makes each molecular transformation along the way spontaneous, but the end result is shifted way from the equilibrium without switching. The authors give the example of doubly stable bistable rotaxanes—dumbbell-shaped molecules in which an electrochemical input can move reactants to different positions along the central part of the dumbbell to alter an energy profile and drive a reaction uphill. An example is given of a molecule that can be switched by an oxidation-reduction event between contracted and extended states. If such a molecule is attached to a molecular spring, then the extended form of the molecule could store energy in the spring molecule. If the architecture of the device as a whole allows the spring to be detached from the oxidation-reduction switch, then the energy stored in the spring can be harvested to do external work. Thus an oxidation-reduction switch becomes part of a simple molecular motor. Having considered how to extract external work from externally switchable molecules, the authors consider how sufficient energy to perform macroscopic work could be harvested from mesoscopic arrays of AMMs. They note that in biological systems molecular motors are organized spatially and synchronized to act together, and consider approaches to fabricate such arrays through self-assembly. They cite metal oxide frameworks as one potentially promising type of scaffolding that might be used to array AMMs. The brief roadmap presented in this tutorial review outlines the challenges and opportunities involved in transforming simple molecular switches into AMMs. The authors are optimistic: On the horizon lie new types of “mechanized” enzyme-like mimicks, addressable nanomaterials, nanorobots, and possibly more into the bargain.

Advanced nanofactories in twenty years?

The potential of advanced nanotechnology is getting some attention from mainstream media. Late last year The Guardian web site posted a brief article on the prospects for nanofactories and atomically precise manufacturing, featuring quotes from Christine Peterson and Robert Freitas. From “ Nanofactories – a future vision ” by Penny Sarchet: Mimicking nature is a recurring theme in nanotechnology and molecular nanotechnology, inspired by the natural nanostructures found in our own bodies, offers many exciting potential outcomes. “Molecular nanotechnology is the expected ability to build our products with molecular-level precision, as nature can do,” says Christine Peterson, president of the Foresight Nanotech Institute in California. “It will bring unprecedented quality, energy efficiency and environmental sustainability”. The recent development of an electron-powered molecular “nanocar”, by a team led by chemist Ben Feringa at the University of Groningen in the Netherlands, hints at the potential. Further indications that molecular nanotechnology is achievable are being found in the quest for ever-smaller computing. Many of these efforts attempt to use nature’s own method of storing and transferring information – DNA. “DNA computing is the goal of building devices out of DNA that are able to act like computers, initially doing simple calculations but eventually doing everything that a macroscale computer can do,” says Peterson. … One future prospect for molecular-scale nanotechnology is to build nanofactories. “The nanofactory is a proposed compact molecular manufacturing system that could build a diverse selection of large-scale, atomically precise products,” explains Robert Freitas Jr, senior research fellow at the Institute for Molecular Manufacturing, also in California. “The products of a nanofactory would be atomically precise, with every atom in exactly the right place, offering the ultimate in quality control. It could make products out of the strongest materials known to man – especially diamond, sapphire, and related ultra-strong ceramics. In manufacturing, it’s hard to do better than that.” The first two-dimensional structure to be built atom-by-atom was made from silicon in 2003. However, Freitas says nanofactories are still a long way off. “We expect this will require a 20-year research and development effort and on the order of $1bn (£622m) in funding to achieve.” … If anyone knows someone with a billion dollars they will not need for twenty years, ask them to contact Christine or Robert.

DNA nanosensors profile gene activity to reveal state of cells

A clever use of a simple DNA nanodevice demonstrates how relatively simple present day nanotech can contribute substantially to solving very important problems in biotechnology and medicine. A University of California – Santa Barbara press release available on EurekAlert! explains how. From “ Nanosensors made from DNA may light path to new cancer tests and drugs “: Sensors made from custom DNA molecules could be used to personalize cancer treatments and monitor the quality of stem cells, according to an international team of researchers led by scientists at UC Santa Barbara and the University of Rome Tor Vergata. The new nanosensors can quickly detect a broad class of proteins called transcription factors, which serve as the master control switches of life. The research is described in an article published in Journal of the American Chemical Society [ abstract — includes diagram of how device works]. “The fate of our cells is controlled by thousands of different proteins, called transcription factors,” said Alexis Vallée-Bélisle, a postdoctoral researcher in UCSB’s Department of Chemistry and Biochemistry, who led the study. “The role of these proteins is to read the genome and translate it into instructions for the synthesis of the various molecules that compose and control the cell. Transcription factors act a little bit like the ‘settings’ of our cells, just like the settings on our phones or computers. What our sensors do is read those settings.” When scientists take stem cells and turn them into specialized cells, they do so by changing the levels of a few transcription factors, he explained. This process is called cell reprogramming. “Our sensors monitor transcription factor activities, and could be used to make sure that stem cells have been properly reprogrammed,” said Vallée-Bélisle. “They could also be used to determine which transcription factors are activated or repressed in a patient’s cancer cells, thus enabling physicians to use the right combination of drugs for each patient.” … This international research effort –– organized by senior authors Kevin Plaxco, professor in UCSB’s Department of Chemistry and Biochemistry, and Francesco Ricci, professor at the University of Rome, Tor Vergata –– started when Ricci realized that all of the information necessary to detect transcription factor activities is already encrypted in the human genome, and could be used to build sensors. “Upon activation, these thousands of different transcription factors bind to their own specific target DNA sequence,” said Ricci. “We use these sequences as a starting point to build our new nanosensors.” … Transcription factors function by binding to a short sequence of DNA that regulates the activity of a class of genes, with each factor binding a different DNA sequence. This specific binding was used to turn a small DNA molecule into a specific biosensor. Specifically, the team re-engineered three naturally occurring DNA sequences, each recognizing a different transcription factor, into molecular switches that become fluorescent when they bind to their intended targets. Using these nanometer-scale sensors, the researchers could determine transcription factor activity directly in cellular extracts by simply measuring their fluorescence level. The researchers believe that this strategy will ultimately allow biologists to monitor the activation of thousands of transcription factors, leading to a better understanding of the mechanisms underlying cell division and development. “Alternatively, since these nanosensors work directly in biological samples, we also believe that they could be used to screen and test new drugs that could, for example, inhibit transcription-factor binding activity responsible for the growth of tumor cells,” said Plaxco.

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 .

Darpa seeks nanotechnology defense against novel pathogens

One of the great successes of twentieth century medicine has been the use of antibiotics to treat formerly fatal bacterial infections. This success is now at risk of being reversed by the ability of bacteria to evolve resistance to antibiotics, and by the recently developed ability to engineer particularly lethal new pathogens for military or terrorist purposes. Darpa wants to deploy nanotechnology to maintain the upper hand against both evolving and engineered bacterial threats. Thanks to Glenn Reynolds for passing along this item from Wired written by Katie Drummond “ Darpa: Do Away With Antibiotics, Then Destroy All Pathogens “: …In the military’s latest round of small business solicitations, Darpa is making a long-shot request for an all-out replacement to antibiotics, the decades-old standard for killing or injuring bacteria to demolish a disease. In its place: the emerging field of nanomedicine would be used to fight bacterial threats. The agency’s “Rapidly Adaptable Nanotherapeutics” is after a versatile “platform capable of rapidly synthesizing therapeutic nanoparticles” to target unknown, evolving and even genetically engineered bioweapons.… Darpa wants researchers to use nanoparticles — tiny, autonomous drug delivery systems that can carry molecules of medication anywhere in the body, and get them right into a targeted cell. Darpa would like to see nanoparticles loaded with “small interfering RNA (siRNA)” — a class of molecules that can target and shut down specific genes. If siRNA could be reprogrammed “on-the-fly” and applied to different pathogens, then the nanoparticles could be loaded up with the right siRNA molecules and sent directly to cells responsible for the infection. Replacing a billion dollar industry that’s been a medical mainstay since 1940? Far fetched, sure, but researchers already know how to engineer siRNA and shove it into nanoparticles. They did it last year, during a trial that saw four primates survive infection with a deadly strain of Ebola Virus after injections of Ebola-targeted siRNA nanoparticles. Doing it quickly, and with unprecedented versatility, is another question. It can take decades for a new antibiotic to be studied and approved. Darpa seems to be after a system that can do the same job, in around a week. … Using nanoparticles of various types to deliver therapeutic siRNA molecules is already a hot research area in nanomedicine ( for example ). The challenge here may lie in rapid DNA sequencing and good bioinformatics tools to find the best siRNA molecules to target novel bacterial threats.

Tying Molecular Knots

Molecular knots can be found in DNA , proteins and even in the molecules that make up man-made plastics, where they often play an important role in the substance’s properties; for example, 85% of the elasticity of natural rubber is due to knot-like entanglements in the rubber molecules chains. However, deliberately tying molecules into well-defined knots so that these effects can be studied is extremely difficult. Up to now, only the simplest type of knot – a trefoil knot – had been prepared by scientists. Now A research team from the University of Edinburgh, UK, and the University of Jyväskylä in Finland have made the most complex molecular knot to date. Their complex knot is a pentafoil knot (also known as a cinquefoil knot or a Solomon’s seal knot) that looks like a five-pointed star. Remarkably, the thread that is tied into the star-shaped knot is just 160 atoms in length – that is about 16 nanometers long. The Edinburgh researchers used self-assembly to prepare the knot in a chemical reaction, wherein the building blocks are chemically programmed to spontaneously wrap themselves up into the desired knot. Making knotted structures from simple chemical building blocks in this way should make it easier to understand why entanglements and knots have such important effects on material properties and may also help scientists to make new materials with improved properties based on knotted molecular architectures. Read More Paper

An artificial molecular clock to control artificial molecular machines

One of the challenges in developing advanced nanotechnology, sometimes called molecular manufacturing or productive nanosystems, is learning to control systems of molecular machines by using other molecular systems for timing and turning machines on and off. The more complex the desired output of a molecular machine system, the more different kinds of molecular machines that need to be controlled, and therefore the more complicated the problem of control systems. A molecular system to time molecular motion and production has been demonstrated by a team of scientists that includes Erik Winfree, co-winner of the 2006 Foresight Institute Feynman Prize in both the Theoretical and Experimental categories. The research was published in the Proceedings of the National Academy of Sciences [ abstract , Open Access PDF ]. A description of the research published in Biopolymers is available on Winfree’s web site . Another description is available on the Human Frontier Science Program web site . One of the professed goals of this research was to advance understanding of the complex regulatory networks that need to be constructed in synthetic biology by building simpler regulatory networks, with reduced number of components, using biochemical circuits that work in the test tube. However, this same understanding should prove useful for building control circuits for productive nanosystems as well. The current demonstration is based upon a synthetic transcriptional oscillator [Open Access] published by two of these authors earlier this year. The transcriptional oscillators consist of two enzymes (one that synthesizes RNA and one that degrades RNA, and a number of DNA molecules that serve as genes for producing small RNA molecules that switch those genes either on or off. Consequently, the oscillator is based upon “genelets” that produce regulatory RNA molecules. Three different oscillators exhibiting both positive and negative feedback control were demonstrated. In the current work, the authors use such a transcriptional oscillator as a molecular clock to time two other molecular processes. One of these is a DNA nanomechanical device, a DNA tweezers that gives different fluorescent signals when open and when closed. Different RNA molecules produced by the transcriptional oscillator act to either open or close the tweezers. The other process is the synthesis by the transcriptional oscillator of an RNA molecule that binds the dye molecule Malachite Green, changing its fluorescence. The regulatory circuits worked, but the detailed behavior turned out to be complex. Regulation was found to be improved by the introduction of an additional “insulator circuit” to produce an amplified signal. Many details need to be worked out even for relatively simple systems, but these results are first steps toward designing and implementing controllable molecular machine systems.

On the role of low-energy electrons in the radiosensitization of DNA by gold nanoparticles

Four different gold nanoparticle (GNP) preparations, including naked GNPs and GNPs coated either with thiolated undecane (S-C 11 H 23 ), or with dithiolated diethylenetriaminepentaacetic (DTDTPA) or gadolinium (Gd) DTDTPA chelating agents, were synthesized. The average diameters, for each type of nanoparticle, are 5 nm, 10 and 13 nm, respectively. Dry films of plasmid DNA pGEM-3Zf(−), DNA with bound GNPs and DNA with coated GNPs were bombarded with 60 keV electrons. The yields of single and double strand breaks were measured as a function of exposure by electrophoresis. The binding of just one GNP without coating to DNA containing 3197 base pairs increases single and double strand breaks by a factor of 2.3 while for GNPs coated with S-C 11 H 23 this factor is reduced to 1.6. The GNPs coated with DTDTPA and DTDTPA:Gd in the same ratio with the DNA, produce essentially no increment in damage. These results could be explained by the attenuation b…