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Nanotechnology carries gene editing package into cells

Posted by Jim Lewis on October 2nd, 2015

Credit: North Carolina State University

DNA nanotechnology has been used to deliver to a cell, not just drug molecules, but an entire gene editing system. A hat tip to Bioscience Technology for reprinting this news release from North Carolina State University “Researchers Use DNA ‘Clews’ to Shuttle CRISPR-Cas9 Gene-Editing Tool into Cells“:

Researchers from North Carolina State University and the University of North Carolina at Chapel Hill have for the first time created and used a nanoscale vehicle made of DNA to deliver a CRISPR-Cas9 gene-editing tool into cells in both cell culture and an animal model.

The CRISPR-Cas system, which is found in bacteria and archaea, protects bacteria from invaders such as viruses. It does this by creating small strands of RNA called CRISPR RNAs, which match DNA sequences specific to a given invader. When those CRISPR RNAs find a match, they unleash Cas9 proteins that cut the DNA. In recent years, the CRISPR-Cas system has garnered a great deal of attention in the research community for its potential use as a gene editing tool – with the CRISPR RNA identifying the targeted portion of the relevant DNA, and the Cas protein cleaving it.

But for Cas9 to do its work, it must first find its way into the cell. This work focused on demonstrating the potential of a new vehicle for directly introducing the CRISPR-Cas9 complex – the entire gene-editing tool – into a cell.

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DNA nanotechnology guides assembling cells into 'Organoids'

Posted by Jim Lewis on September 30th, 2015

Credit: Todhunter et al. and Nature Methods

Our principal interest in DNA nanotechnology is based on using the easily coded molecular recognition properties of DNA to arrange molecules and other nanometer scale structures; however, DNA is also proving useful for arranging whole cells for a new branch of nanomedicine: the three-dimensional printing of human tissue. A hat tip to Bioscience Technology for reprinting this University of California at San Francisco news release written by Nicholas Weiler “DNA-Guided 3-D Printing of Human Tissue is Unveiled“:

Technique Produces ‘Organoids’ Useful in Cancer Research, Drug Screening

A UCSF-led team has developed a technique to build tiny models of human tissues, called organoids, more precisely than ever before using a process that turns human cells into a biological equivalent of LEGO bricks. These mini-tissues in a dish can be used to study how particular structural features of tissue affect normal growth or go awry in cancer. They could be used for therapeutic drug screening and to help teach researchers how to grow whole human organs.

The new technique — called DNA Programmed Assembly of Cells (DPAC) and reported in the journal Nature Methods [abstract, PDF courtesy of Prof. Gartner's publications page] — allows researchers to create arrays of thousands of custom-designed organoids, such as models of human mammary glands containing several hundred cells each, which can be built in a matter of hours.

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Catalytic micromotors demonstrate carbon dioxide removal from water

Posted by Jim Lewis on September 29th, 2015

Image credit: Laboratory for Nanobioelectronics, UC San Diego Jacobs School of Engineering.

Visionary proposals for advanced medical nanorobots often picture µm scale submarine-like devices navigating the bloodstream. Those are probably still a couple decades away, but prototypes of conceptually much simpler six µm scale motors that could someday navigate the oceans to sequester carbon dioxide have been demonstrated. A hat tip to Science Daily for reprinting this news release from the University of California at San Diego Jacobs School of Engineering”Tiny carbon-capturing motors may help tackle rising carbon dioxide levels“:

Machines that are much smaller than the width of a human hair could one day help clean up carbon dioxide pollution in the oceans. Nanoengineers at the University of California, San Diego have designed enzyme-functionalized micromotors that rapidly zoom around in water, remove carbon dioxide and convert it into a usable solid form.

The proof of concept study represents a promising route to mitigate the buildup of carbon dioxide, a major greenhouse gas in the environment, said researchers. The team, led by distinguished nanoengineering professor and chair Joseph Wang, published the work this month in the journal Angewandte Chemie [abstract].

“We’re excited about the possibility of using these micromotors to combat ocean acidification and global warming,” said Virendra V. Singh, a postdoctoral scientist in Wang’s research group and a co-first author of this study.

In their experiments, nanoengineers demonstrated that the micromotors rapidly decarbonated water solutions that were saturated with carbon dioxide. Within five minutes, the micromotors removed 90 percent of the carbon dioxide from a solution of deionized water. The micromotors were just as effective in a sea water solution and removed 88 percent of the carbon dioxide in the same timeframe.

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Atomically precise boron doping of graphene nanoribbons

Posted by Jim Lewis on September 28th, 2015

Graphene nanoribbon under the microscope. Credit: University of Basel

Even without a general method for high throughput atomically precise manufacturing, atomic precision in nanotechnology is proving increasingly useful across a range of technologies. One recent example is the atomically controlled boron-doping of graphene nanoribbons. A hat tip to Science Daily for reprinting this University of Basel news release “Successful Boron-Doping of Graphene Nanoribbon“:

Physicists at the University of Basel succeed in synthesizing boron-doped graphene nanoribbons and characterizing their structural, electronic and chemical properties. The modified material could potentially be used as a sensor for the ecologically damaging nitrogen oxides, scientists report in the latest issue of Nature Communications ["Atomically controlled substitutional boron-doping of graphene nanoribbons" OPEN ACCESS].

Graphene is one of the most promising materials for improving electronic devices. The two-dimensional carbon sheet exhibits high electron mobility and accordingly has excellent conductivity. Other than usual semiconductors, the material lacks the so-called band gap, an energy range in a solid where no electron states can exist. Therefore, it avoids a situation in which the device is electronically switched off. However, in order to fabricate efficient electronic switches from graphene, it is necessary that the material can be switched “on” and “off”.

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Parallel to protein folding improves DNA origami process

Posted by Jim Lewis on September 27th, 2015

Credit: University of Oxford

Frequently we report here the use of DNA origami, a large subset of DNA nanotechnology, as a way to build and organize increasingly complex nanostructures, both to advance specific current applications and to build a path toward atomic precision in manufacturing. Despite the impressive track record of this technology, there may be opportunities to substantially improve it, as reported recently at From “Unfolding the mysteries of DNA origami“:

Experiments performed by a University of York physicist have provided new insights into how DNA assembles into nanostructures, paving the way for more precise use in technology and medicine.

Dr Katherine Dunn, now a Research Associate in the Intelligent Systems Group in the Department of Electronics at York, presents her findings in a paper published in Nature [abstract]. It describes how Dr Dunn’s experiments at Oxford demonstrated that DNA strands could not only self-assemble, but, in doing so, they follow distinct and identifiable pathways.

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Review of artificial molecular machines and their controlled motions

Posted by Jim Lewis on September 18th, 2015

Credit: Leigh research group, University of Manchester

Two weeks ago, a post about a recent overview of molecular machines included this reference:

One of the earliest reviews of artificial molecular machines, and arguably the most comprehensive, titled “Synthetic Molecular Motors and Mechanical Machines” [abstract] was published in December 2006, written by Prof. Leigh in collaboration with Euan R. Kay and Francesco Zerbetto, and was recommended here by Christine Peterson.

A few days after that post, Prof. Leigh and current colleagues Sundus Erbas-Cakmak, Charlie T. McTernan, and Alina L. Nussbaumer published in the American Chemical Society journal Chemical Reviews an updated and comparably comprehensive review titled “Artificial Molecular Machines” [abstract]. Unfortunately, at this writing, it only seems to exist behind a pay wall. At 64 MB and 126 pages, it is more like a small textbook than a review, so the size of the article is at least commensurate with the $35 fee.

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Conference video: Bringing Computational Programmability to Nanostructured Surfaces

Posted by Jim Lewis on September 11th, 2015

Credit: Alex Wissner-Gross

A select set of videos from the 2013 Foresight Technical Conference: Illuminating Atomic Precision, held January 11-13, 2013 in Palo Alto, have been made available on vimeo. Videos have been posted of those presentations for which the speakers have consented. Other presentations contained confidential information and will not be posted.

The first speaker at the Computation and Molecular Nanotechnolgies session, Alex Wissner-Gross, presented “Bringing Computational Programmability to Nanostructured Surfaces” as an effort to close the feedback loop between bits and atoms. – video length 29:14. Dr. Wissner-Gross observed that, looking at the past few decades, the progress on the “bits” side of technology has been unrelenting, and that it is incumbent upon nanotechnologists to make sure that the atoms side of the story is equally compelling. Looking at the progress of civilization over the past several millennia, Dr. Wissner-Gross argued that all of the progress has been defined by our ability to increasingly, finely, and programmably tune the properties of matter in our physical world. Taken to its logical completion, one could say the ultimate form of universal programmability is the substrate for computation. He proposed that exploring the interplay between programmable atoms and programmable bits will ultimately define the critical path toward some of the most interesting technologies likely to appear over the next few decades.

One way of approaching this is to look at a brief history of time. Starting with some natural examples of programmable matter, like ribozymes, ribosomes, polyketides, and immune systems. Starting in the 15th century, artificial forms of programmable matter blend the interface between bits and matter, starting with moveable type, phonographs, universal Turing machines, and transistors. One additional very important development is the transmission of the first Internet packet, which was arguably the official decoupling of bits from atoms. Dr. Wissner-Gross then asked, how do we start to re-couple bits and atoms now that bits have made so much progress? How can we help atoms to catch up?

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Addressable molecular machines arranged in a porous crystal

Posted by Jim Lewis on September 10th, 2015

Schematic of the approach to organizing rotaxanes inside the channels of a metal–organic framework. Credit: (c) 2015 PNAS doi: 10.1073/pnas.1514485112

The artificial molecular machines overview we pointed to last week included several significant recent developments that we had missed, including this about molecular machines organized within a metal-organic framework, from the research group of 2007 Foresight Feynman Prize winner for the Experimental category J. Fraser Stoddart and his collaborators. Two months ago we described here a similar advance by a Canadian group immobilizing a molecular shuttle in a metal organic framework. The difference in the approach taken by the Loeb research group at the University of WIndsor and the Stoddart research group at Northwestern University and their collaborators is very nicely explained in an article by Heather Zeiger at “Solid-state molecular switches using redox active molecules in a porous crystal“:

A group of researchers have provided a proof-of-concept procedure for making a solid-state molecular-sized switch. They combined a mechanically interlocked molecule with a pre-synthetized metal-organic framework (MOF).

Mechanically interlocked molecules have several features that make them ideal candidates for molecular switches. These interlocked molecules, known as rotaxanes or catenanes, typically involve two molecular components that have distinct orientations based on interactions between them. Scientists can control which orientation the interlocked molecules take using stimuli, such as electrochemical potential or light. Redox active interlocked molecules are compelling candidates for a molecular switch. However, in solution, these molecules are unpredictable, and when it comes to designing circuitry, controlling the molecular switch is vital.

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Overview of molecular machines documents recent progress

Posted by Jim Lewis on September 4th, 2015

Credit: Loeb Research Group, University of Windsor. One of a number of types of molecular machines included in a recent Nature overview.

Since advanced nanotechnology will be primarily about complex systems of artificial molecular machines, it is very nice to see the journal Nature begin the month with a very useful overview of molecular machines, presented as a News Feature written by Mark Peplow “The tiniest Lego: a tale of nanoscale motors, rotors, switches and pumps“:

The robot moves slowly along its track, pausing regularly to reach out an arm that carefully scoops up a component. The arm connects the component to an elaborate construction on the robot’s back. Then the robot moves forward and repeats the process — systematically stringing the parts together according to a precise design.

It might be a scene from a high-tech factory — except that this assembly line is just a few nanometres long. The components are amino acids, the product is a small peptide and the robot, created by chemist David Leigh at the University of Manchester, UK, is one of the most complex molecular-scale machines ever devised.

We commented on this advance in January 2013. Returning to the Nature review:

It is not alone. Leigh is part of a growing band of molecular architects who have been inspired to emulate the machine-like biological molecules found in living cells — kinesin proteins that stride along the cell’s microscopic scaffolding, or the ribosome that constructs proteins by reading genetic code. Over the past 25 years, these researchers have devised an impressive array of switches, ratchets, motors, rods, rings, propellers and more — molecular mechanisms that can be plugged together as if they were nanoscale Lego pieces. And progress is accelerating, thanks to improved analytical-chemistry tools and reactions that make it easier to build big organic molecules.…

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Nanotechnology provides sensors for liver-on-chip drug testing

Posted by Jim Lewis on September 2nd, 2015

Hebrew University liver-on-chip device. Photo credit: Yaakov Nahmias / Hebrew University

One of the indirect ways in which nanotechnology is impacting medical research, in synergy with biotechnology, is by enabling a “liver-on-chip” replacement for animal testing. A hat tip to Nanotechnology Now for reprinting this news release from Hebrew University “Israeli-German Partnership Aims To Replace Animal Experiments With Advanced Liver-On-Chip Devices“:

Safety evaluation is a critical part of drug and cosmetic development. In recent years there is a growing understanding that animal experiments fail to predict the human response. This necessitates the development of alternative models to predict drug toxicity.

The recent tightening of European regulations preventing the cosmetic industry from using animals in research and development, blocks companies like L’Oréal and Estée Lauder from developing new products, bringing massive investment into this field.

The main challenge in replacing animal experiments is that human cells seldom survive more than a few days outside the body. To address this challenge, scientists at The Hebrew University of Jerusalem and the Fraunhofer Institute for Cell Therapy and Immunology in Germany partnered to create a liver-on-chip device mimicking human physiology.

“The liver organs we created were less than a millimeter in diameter and survive for more than a month,” said Professor Yaakov Nahmias, the study’s lead author and Director of the Alexander Grass Center for Bioengineering at The Hebrew University.

While other groups showed similar results, the breakthrough came when the groups added nanotechnology-based sensors to the mix. “We realized that because we are building the organs ourselves, we are not limited to biology, and could introduce electronic and optical sensors to the tissue itself. Essentially we are building bionic organs on a chip,” said Nahmias.

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Macroscopic mechanical manipulation controls molecular machine array

Posted by Jim Lewis on September 1st, 2015

Pliers representing amphipathic binaphthyl (left), chemical formula of amphipathic binaphthyl (center), and three-dimensional conformation of amphipathic binaphthyl. Credit: NIMS MANA

Current nanotechnology is about nanomaterials, nanodevices, and simple molecular machines. Advanced nanotechnology will largely be about complex systems of artificial molecular machines, rather as life can be described as complex systems of biological molecular machines. So any new insight about molecular machines is of potential interest as a signpost toward advanced nanotechnology. A hat tip to AZO NANO for reprinting this press release from Japan’s National Institute for Materials Science “Motion of Supramolecular Machines Successfully Controlled through Simple Mechanical Manipulation“:

NIMS MANA researchers found that molecular machines can be easily manipulated using very small mechanical energy, taking advantage of the property that they aggregate on the surface of water. This study was published in the online version of the German Chemical Society’s journal “Angewandte Chemie International Edition” on June 12, 2015. (D. Ishikawa, T. Mori, Y. Yonamine, W. Nakanishi, D. L. Cheung, J. P. Hill, and K. Ariga “Mechanochemical tuning of binaphthyl conformation at the air-water interface” Angew. Chem. Int. Ed., DOI: 10.1002/anie.201503363)

MANA Scientist Waka Nakanishi and other researchers at the Supermolecules Unit (Katsuhiko Ariga, director) of the NIMS International Center for Materials Nanoarchitectonics (MANA), in collaboration with Dr. David Cheung at the University of Strathclyde (UK), found that molecular machines (molecules capable of mechanical movement) can be easily manipulated using very small mechanical energy, taking advantage of the property that they aggregate on the surface of water. Our findings are expected to contribute to the development of basic technology for the operation of various molecular machines that have been studied for their application as sensor and other types of devices.

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Femtosecond imaging with near nanometer spatial resolution

Posted by Jim Lewis on August 31st, 2015

Three-dimensional rendering of surface features imaged by ptychographic coherent diffractive imaging. (Source: University of Colorado). The surface shown is a portion of Fig. 4a. Judging from the scale bar in the scanning electron micrograph of this surface shown in Fig. 1b, the inner diameter of the circle is about 10 µm (10,000 nm).

As we noted back in April, Richard Feynman in his classic 1959 talk challenged his fellow physicists to make the electron microscope 100 times better. A “new super powerful electron microscope that can pinpoint the position of single atoms” had been unveiled at a facility in the UK. While that SuperSTEM is one of only three in the world, a recently demonstrated technology based upon “tabletop extreme-ultraviolet ptychography” brings complementary nanometer-scale resolution to a much smaller (and presumably less expensive) instrument. A hat tip to John Faith for bringing this EETimes article by R Colin Johnson to our attention “EUV Breaks Through to Angstrom“:

The wavelength of visible light — 400-to-700 nanometers — makes it impossible with today’s tools to take photographs of nanoscale objects with any sort of reasonable resolution. The answer has been to use scanning electron microscopy (SEM) and atomic force microscopy (ATM), which yield reasonable images. These tools, however, produce nothing close to the angstrom-level (tenth of a nanometer) resolution of a new type of microscope that uses femtosecond pulses of extreme ultraviolet light (EUV) — the same wavelength light to be used for sub-10 nanometer semiconductor lithography.] …

The claim made here of angstrom-level resolution appears to be a substantial overstatement of the published result (see below). Nevertheless, the technique does appear to offer substantial advantages, and may approach this resolution in the near future.

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A tunable bandgap by doping a few atomic layers of black phosphorous

Posted by Jim Lewis on August 29th, 2015

Phosphorene (with in-situ deposition of potassium (K) atoms to induce doping) – The natural successor to Graphene? Credit: Institute for Basic Science

The process of finding novel arrangements of atoms with interesting and useful properties does not appear to be slowing. A hat tip to ScienceDaily for reprinting this news release from the Institute for Basic Science, Korea “Black Phosphorus (BP) Surges Ahead of Graphene“:

A Korean team of scientists tune BP’s band gap to form a superior conductor, allowing for the application to be mass produced for electronic and optoelectronics devices

The research team operating out of Pohang University of Science and Technology (POSTECH), affiliated with the Institute for Basic Science’s (IBS) Center for Artificial Low Dimensional Electronic Systems (CALDES), reported a tunable band gap in BP, effectively modifying the semiconducting material into a unique state of matter with anisotropic dispersion. This research outcome potentially allows for great flexibility in the design and optimization of electronic and optoelectronic devices like solar panels and telecommunication lasers.

To truly understand the significance of the team’s findings, it’s instrumental to understand the nature of two-dimensional (2-D) materials, and for that one must go back to 2010 when the world of 2-D materials was dominated by a simple thin sheet of carbon, a layered form of carbon atoms constructed to resemble honeycomb, called graphene. Graphene was globally heralded as a wonder-material thanks to the work of two British scientists who won the Nobel Prize for Physics for their research on it.

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Novel wireframe nanostructures from new DNA origami design process

Posted by Jim Lewis on August 18th, 2015

The versatility of the 3D wireframe design technique was demonstrated with the construction of the snub cube, an Archimedean solid with 60 edges, 24 vertices and 38 faces including 6 squares and 32 equilateral triangles. Credit: TED-43 GFDL ( or CC BY 3.0 (, via Wikimedia Commons

The scaffolded DNA origami technique has been extended to build complex, programmable wireframe structures exhibiting precise control of branching and curvature. A hat tip to KurzweilAI for reporting this Arizona State University Biodesign Institute news release “Rare form: novel structures built from DNA emerge“:

… Hao Yan, a researcher at Arizona State University’s Biodesign Institute, has worked for many years to refine [DNA origami]. His aim is to compose new sets of design rules, vastly expanding the range of nanoscale architectures generated by the method. In new research, a variety of innovative nanoforms are described, each displaying unprecedented design control. …

In the current study, complex nano-forms displaying arbitrary wireframe architectures have been created, using a new set of design rules. “Earlier design methods used strategies including parallel arrangement of DNA helices to approximate arbitrary shapes, but precise fine-tuning of DNA wireframe architectures that connect vertices in 3D space has required a new approach,” Yan says.

Yan has long been fascinated with Nature’s seemingly boundless capacity for design innovation. The new study describes wireframe structures of high complexity and programmability, fabricated through the precise control of branching and curvature, using novel organizational principles for the designs. (Wireframes are skeletal three-dimensional models represented purely through lines and vertices.)

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Conference video: Artificial Biochemistry with DNA

Posted by Jim Lewis on August 13th, 2015

DNA as a Universal Substrate for Chemical Kinetics- embedded control circuit to direct molecular events. Credit: David Soloveichik

A select set of videos from the 2013 Foresight Technical Conference: Illuminating Atomic Precision, held January 11-13, 2013 in Palo Alto, have been made available on vimeo. Videos have been posted of those presentations for which the speakers have consented. Other presentations contained confidential information and will not be posted.

The fourth speaker at the Commercial Scale Devices – Part 2 session, the winner of the 2012 Feynman Prize for Theoretical work, David Soloveichik, presented his prize-winning work “Artificial Biochemistry with DNA” – video length 29:14. Dr. Soloveichik began his talk by asking if we could recapitulate the feats of biology, specifically computation with networks of molecular interactions, with de novo engineering. After the basic technology is developed, possible applications could include artificial control modules that could be inserted into cells to create “smart drugs”, or as control modules for completely artificial systems (“wet robots”). Dr. Soloveichik has made the slides from his talk available here.

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Another nanotechnology computer memory breakthrough from Feynman Prize winner

Posted by Jim Lewis on August 12th, 2015

A schematic shows the layered structure of tantalum oxide, multilayer graphene and platinum used for a new type of memory developed at Rice University. The memory device overcomes crosstalk problems that cause read errors in other devices. (Credit: Tour Group/Rice University)

One prominent area in which nanoscale science and technology is providing a rich pipeline feeding current and near-term improvements in technology is computer hardware, and in particular, solid-state computer memories. One year ago, we cited a breakthrough nanoporous silicon oxide technology for resistive random-access memory (RRAM) developed by the research group of James Tour, winner of the 2008 Foresight Institute Feynman Prize in the Experimental category. Now he appears to have topped this memory architecture with another memory breakthrough. A hat tip to KurzweilAI for reporting this Rice University news release “Tantalizing discovery may boost memory technology“:

Scientists at Rice University have created a solid-state memory technology that allows for high-density storage with a minimum incidence of computer errors.

The memories are based on tantalum oxide, a common insulator in electronics. Applying voltage to a 250-nanometer-thick sandwich of graphene, tantalum, nanoporous tantalum oxide and platinum creates addressable bits where the layers meet. Control voltages that shift oxygen ions and vacancies switch the bits between ones and zeroes.

The discovery by the Rice lab of chemist James Tour could allow for crossbar array memories that store up to 162 gigabits, much higher than other oxide-based memory systems under investigation by scientists. (Eight bits equal one byte; a 162-gigabit unit would store about 20 gigabytes of information.)

Details appear online in the American Chemical Society journal Nano Letters [abstract].

Like the Tour lab’s previous discovery of silicon oxide memories, the new devices require only two electrodes per circuit, making them simpler than present-day flash memories that use three. “But this is a new way to make ultradense, nonvolatile computer memory,” Tour said.

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Ribosome subunits tethered to make versatile artificial molecular machine

Posted by Jim Lewis on August 11th, 2015

An engineered ribosome with a permanent connection between its subunits (red) can operate side-by-side with a cell's own protein production machinery. Credit: Erik Carlson

Engineering Nature’s primordial molecular machine—the ribosome—promises a path to unnatural polymers that may expand the set of properties provided by proteins and biomimetic polymers to engineer artificial molecular machine systems. A hat tip to ScienceDaily for reprinting this University of Illinois at Chicago news release written by Sam Hostettler “Researchers design first artificial ribosome“:

Researchers at the University of Illinois at Chicago and Northwestern University have engineered a tethered ribosome that works nearly as well as the authentic cellular component, or organelle, that produces all the proteins and enzymes within the cell.

The engineered ribosome may enable the production of new drugs and next-generation biomaterials and lead to a better understanding of how ribosomes function.

The artificial ribosome, called Ribo-T, was created in the laboratories of Alexander Mankin, director of the UIC College of Pharmacy’s Center for Biomolecular Sciences, and Northwestern’s Michael Jewett, assistant professor of chemical and biological engineering.

The human-made ribosome may be able to be manipulated in the laboratory to do things natural ribosomes cannot do.

When the cell makes a protein, mRNA (messenger RNA) is copied from DNA. The ribosomes’ two subunits, one large and one small, unite on mRNA to form the functional unit that assembles the protein in a process called translation. Once the protein molecule is complete, the ribosome subunits — both of which are themselves made up of RNA and protein — separate from each other.

In a new study in the journal Nature [abstract], the researchers describe the design and properties of Ribo-T, a ribosome with subunits that will not separate. Ribo-T may be able to be tuned to produce unique and functional polymers for exploring ribosome functions or producing designer therapeutics — and perhaps one day even non-biological polymers.

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Automated design of polyhedral meshes for DNA origami

Posted by Jim Lewis on August 7th, 2015

Björn Högberg and Erik Benson with models of their origami 3D meshes. Credit: Ulf Sirborn

Scaffolded DNA origami, one of the mainstays of structural DNA nanotechnology since its invention in 2006, continues to undergo improvement. A press release from Sweden’s Karolinska Institutet “3D ‘printouts’ at the nanoscale using self-assembling DNA structures“:

A novel way of making 3D nanostructures from DNA is described in a study published in the renowned journal Nature [abstract]. The study was led by researchers at Sweden’s Karolinska Institutet who collaborated with a group at Finland’s Aalto University. The new technique makes it possible to synthesize 3D DNA origami structures that are also able to tolerate the low salt concentrations inside the body, which opens the way for completely new biological applications of DNA nanotechnology. The design process is also highly automated, which enables the creation of synthetic DNA nanostructures of remarkable complexity.

The team behind the study likens the new approach to a 3D printer for nanoscale structures. The user draws the desired structure, in the form of a polygon object, in 3D software normally used for computer-aided design or animation. Graph-theoretic algorithms and optimization techniques are then used to calculate the DNA sequences needed to produce the structure.

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Arranging molecular chromophores on DNA brick nanobreadboards

Posted by Jim Lewis on August 6th, 2015

ON-OFF cycling of AND logic gate formed by arrangement of four single-molecule chromophores on a DNA brick nanobreadboard. Credit: Canon et al. ACS Photonics.

The idea of using a DNA framework as a “nanobreadboard” to prototype various nanoscale circuits and device arrays goes back at least to Paul Rothemund’s 2006 invention of scaffolded DNA origami technology. The idea played a central role in the development of the concept of modular molecular composite nanosystems formulated as part of the 2007 Foresight and Battelle Technology Roadmap for Productive Nanosystems. Earlier this year researchers at Boise State University in Idaho published an open access article in the journal ACS PhotonicsExcitonic AND Logic Gates on DNA Brick Nanobreadboards“. However, instead of scaffolded DNA origami, these researchers built their nanobreadboards using an alternate form of structural DNA nanotechnology (see “Arbitrarily complex 3D DNA nanostructures built from DNA bricks“) that has been extended to fabricate micrometer-scale structures that offer unique opportunities as molecular “breadboards”.

To make single-molecule optical devices for computing and other applications, which exploit the interactions between light and matter at much smaller length scales than the free-space wavelength of light, these molecular chromophores must be precisely arranged to enhance non-radiative dipole-dipole coupling between neighboring chromophores. subnanometer resolution. This coupling facilitates an energy transfer process (FRET – Förster Resonance Energy Transfer) that occurs over a distance that is typically 5 nm or less. Molecular orientation also plays a role. Previous studies of multi-chromophore excitonic circuits have positioned the chromophores using single DNA duplexes or multiarm DNA junctions, or DNA origami. With DNA origami, however, it is only practical to conjugate chromophores to selected staple strands; the long scaffold strand can only play a role in the overall structure since conjugation to the scaffold strand is impractical. This restricted role of the scaffold strand limits the feasibility of using DNA origami for the rapid prototyping of excitonic circuits that is essential to achieve complex functionality.

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Facilitating structural DNA nanotechnology with non-aqueous solvents

Posted by Jim Lewis on August 2nd, 2015

Georgia Tech postdoctoral researcher Isaac Gállego prepares a sample DNA nanostructure for imaging in an atomic force microscope. (Credit: Rob Felt)

Not only does structural DNA nanotechnology work in non-aqueous solvents, but in some ways it may work best in non-aqueous solvents. A hat tip to for reprinting this Georgia Tech news release “Who needs water to assemble DNA? Non-aqueous solvent supports DNA nanotechnology“:

Scientists around the world are using the programmability of DNA to assemble complex nanometer-scale structures. Until now, however, production of these artificial structures has been limited to water-based environments, because DNA naturally functions inside the watery environment of living cells.

Researchers at the Georgia Institute of Technology have now shown that they can assemble DNA nanostructures in a solvent containing no water. They also discovered that adding a small amount of water to their solvent increases the assembly rate and provides a new means for controlling the process. The solvent may also facilitate the production of more complex structures by reducing the problem of DNA becoming trapped in unintended structures.

The research could open up new applications for DNA nanotechnology, and help apply DNA technology to the fabrication of nanoscale semiconductor and plasmonic structures. Sponsored by the National Science Foundation and NASA, the research will be published as the cover story in Volume 54, Issue 23 of the journal Angewandte Chemie International Edition [abstract].

“DNA nanotechnology structures are getting more and more complex, and this solvent could help researchers that are working in this growing field,” said Nicholas Hud, a professor in Georgia Tech’s School of Chemistry and Biochemistry. “With this work, we have shown that DNA nanostructures can be assembled in a water-free solvent, and that we can mix water with the same solvent to speed up the assembly. We can also take the structures that were assembled in this solvent mixed with water –remove the water by applying vacuum – and have the DNA structures remain intact in the water-free solvent.”

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