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DNA triplex formation decorates DNA crystals with sub-nanometer precision

Posted by Jim Lewis on May 3rd, 2016

Our previous post focused on the production of high quality macroscopic DNA crystals containing fairly large (on a molecular scale) cavities. This post deals with the challenge of precisely filling those cavities with guest molecules or nanoparticles. In 2014 Seeman and his collaborators reported using triplex forming oligonucleotides to programmably position guest components on the double-helical edges of the tensegrity triangles comprising the crystal: “Functionalizing Designer DNA Crystals with a Triple-Helical Veneer” [OPEN ACCESS]. Citing their earlier work reporting crystals with cavities exceeding 1000 nm3, the authors propose introducing guest molecules into these cavities by targeting a DNA sequence within the tile comprising the crystal, using triplex-forming oligonucleotides that bind in a sequence specific fashion to the major groove of the DNA double helix by forming base triplets. Because triplex formation requires a lower pH, some triplex forming oligonucleotides incorporated triplex stabilizing nucleosides in place of the usual DNA nucleosides C and T. A cyanine dye molecule was attached o he 5`-terminus of each triplex forming oligonucleotide (TFO) to facilitate characterization of the product and to serve as a test guest molecule to be incorporated into the crystal.

A) Base triplets. B) Triplex sequence. C) Cy5-labeled TFOs containing stabilizing analogues. D) Model of the TFO-bound tile. E) Functionalization of DNA crystals. Credit: Rusling et al. Angewandte Chemie

TFOs were shown to bind to the tensegrity triangle tiles as expected. Binding of the TFOs did not affect the formation of crystals from the tiles. Fluorescence of the crystals clearly showed that the dye had been incorporated. Several of the crystals were analyzed by X-ray diffraction, yielding the same results as the previous work.

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Macroscopic DNA crystals from molecular tensegrity triangles

Posted by Jim Lewis on May 2nd, 2016

Schematic design, sequence, and crystal pictures. Credit: Zheng et al. and Nature.

In writing this blog I occasionally find that I missed work that is an important part of a developing story. Over the years, DNA nanotechnology has been one of the most promising paths from current nanoscience and nanotechnology to the ultimate goal of general-purpose high-throughput atomically precise manufacturing. Most of the recent progress we have reported on DNA nanotechnology has been based upon the scaffolded DNA origami technique or, to a lesser extent, the DNA bricks technique. The original introduction to DNA nanotechnology came in a 1987 paper by DNA nanotechnology pioneer Nadrian Seeman and his chemist collaborator Bruce Robinson “The design of a biochip: a self-assembling molecular-scale memory device” (full text behind a pay wall), which proposed a self-assembling DNA scaffold that could serve as a framework for a molecular wire and switch. This proposal was based on Seeman’s earlier (1985) suggestion that ligation of DNA branched junction building blocks could lead to a periodic array, analogous to the crystallization of molecular systems.

Three papers by Seeman and his collaborators published the last several years (2009, 2014, 2015) highlight progress toward Seeman’s original vision of a practical macroscopic DNA crystal array with cavities that are large on the molecular scale and could be used to precisely order molecular components in three dimensions. This post considers the earliest of these. The first step from concept to reality is explained by the title of the article “From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal“. The full text is behind a pay wall, but a free PubMed Central version is available.

The authors note that producing a macroscopic 3D periodic array of precisely arranged molecular components should be possible with appropriate branched DNA motifs with ‘sticky’ tails. “It is essential that the directions of propagation associated with the sticky ends do not share the same plane, but extend to form a 3D arrangement of matter.” Based on a ‘DNA tensegrity triangle’ motif that they had reported in 2004, they report here the construction of ~250-µm-sized DNA crystals, five orders of magnitude larger than the nanometer scale of molecular components.

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Five ionized atoms provide scalable implementation of quantum computation algorithm

Posted by Jim Lewis on April 3rd, 2016

Researchers have designed and built a quantum computer from five atoms in an ion trap. The computer uses laser pulses to carry out Shor’s algorithm on each atom, to correctly factor the number 15. Image: Jose-Luis Olivares/MIT

Last November we cited work done at the University of New South Wales in Australia that established an architecture for a scalable atomically precise quantum computer, implemented in silicon. A collaboration from MIT and the University of Innsbruck in Austria has now put forth a similar claim, but using a very different physical implementation. A hat tip to Nanotechnology Now for reprinting this MIT news release written by Jennifer Chu “The beginning of the end for encryption schemes?“:

New quantum computer, based on five atoms, factors numbers in a scalable way.

What are the prime factors, or multipliers, for the number 15? Most grade school students know the answer — 3 and 5 — by memory. A larger number, such as 91, may take some pen and paper. An even larger number, say with 232 digits, can (and has) taken scientists two years to factor, using hundreds of classical computers operating in parallel.

Because factoring large numbers is so devilishly hard, this “factoring problem” is the basis for many encryption schemes for protecting credit cards, state secrets, and other confidential data. It’s thought that a single quantum computer may easily crack this problem, by using hundreds of atoms, essentially in parallel, to quickly factor huge numbers.

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DNA nanotechnology defeats drug resistance in cancer cells

Posted by Jim Lewis on April 2nd, 2016

Researchers at The Ohio State University are working to develop DNA nanostructures that deliver medicine to drug-resistant cancer cells. These electron microscope images show the structures empty (left) and loaded with the cancer drug daunorubicin (right). The researchers have demonstrated for the first time that such “DNA origami” structures can be used to treat drug-resistant leukemia cells. Images by Randy Patton, courtesy of The Ohio State University.

Scaffolded DNA origami, added to the structural DNA nanotechnology toolkit 10 years ago, is a very powerful technique for folding DNA into complex nanostructures. We’ve cited its use to make make dynamic nanomachines (for example, here), and to make simple nanorobots for potential medical application (here). A recent news release from Ohio State University, written by Pam Frost Gorder, makes clear that even simple atomically precise DNA nanostructures hold great potential for solving a major problem, perhaps the major problem encountered during cancer chemotherapy: the evolution of drug resistance by the cancer. “DNA ‘Trojan horse’ smuggles drugs into resistant cancer cells

Cells mistake DNA casing for food, consume drugs and die

Researchers at The Ohio State University are working on a new way to treat drug-resistant cancer that the ancient Greeks would approve of—only it’s not a Trojan horse, but DNA that hides the invading force.

In this case, the invading force is a common cancer drug.

In laboratory tests, leukemia cells that had become resistant to the drug absorbed it and died when the drug was hidden in a capsule made of folded up DNA.

Previously, other research groups have used the same packaging technique, known as “DNA origami,” to foil drug resistance in solid tumors. This is the first time researchers have shown that the same technique works on drug-resistant leukemia cells.

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Foresight Institute appoints Julia Bossmann as new president

Posted by Jim Lewis on March 30th, 2016

Menlo Park, California – Foresight Institute, a leading think-tank for transformative future technologies, announced that Julia Bossmann has joined the organization as president.

“Julia’s breadth of vision for atomically-precise construction, artificial intelligence, and other transformative technologies will bring new energy to Foresight,” says Foresight co-founder Christine Peterson.

Bossmann holds a Masters degree with highest honors in psychology and neuroscience from the University of Dusseldorf and USC. Her professional experience includes scientific research in labs in Germany and in the USA, management consulting at McKinsey & Company, R&D at Bosch Research and Technology, and entrepreneurship at Anticip8 and Synthetic. Bossmann is a GSP alumna at Singularity University and a Global Shaper at the World Economic Forum.

Foresight Institute’s leadership change coincides with the organization’s 30-year anniversary. While keeping its esteemed cross-domain technical workshops going, Bossmann plans to expand engagement with the public and the scientific community. Interim president Steven Burgess continues to serve as COO.

“Foresight Institute has been leading thought on the technologies that transform our world,” says Ms. Bossmann. “With the current rise of world-changing technologies such as nanotechnology, synthetic biology, and artificial intelligence, never before has its mission been as critical and relevant as it is today. The key to our future is to make sure that the necessary beneficial innovations happen soon, and that they happen in a way that benefits society at large.”

About Foresight Institute

Foresight Institute is a leading think tank and public interest organization focused on transformative future technologies. Founded in 1986, its mission is to discover and promote the upsides, and help avoid the downsides, of nanotechnology, AI, biotech, and similar life-changing developments.

For further information, please contact

Nanotechnologies to advance solar energy utilization

Posted by Jim Lewis on March 25th, 2016

This cell consists of nanostructured arrays of anodes and cathodes, oxidation and reduction catalysts, and a central conductive membrane that allows for ion exchange. Credit: Lewis Research Group, Caltech

A few weeks ago Science published a review written by California Institute of Technology Chemistry Professor Nate Lewis titled “Research opportunities to advance solar energy utilization”. The link to the paper from Lewis’s publication page leads to the full text article on the journal’s web site. Prof. Lewis’s one-page summary of his own review concludes that “Considerable opportunities for cost reduction that can achieve both evolutionary and revolutionary performance improvements are present for all types of solar energy–conversion technologies.” The review enumerates those technologies, focusing on production of solar electricity through photovoltaics, solar thermal, and artificial photosynthesis to produce fuels from sunlight. Two fundamental constraints on solar energy systems are made explicit: (1) the low energy density of sunlight at Earth’s surface, necessitating large areas needed to capture and convert solar power; (2) the intermittent nature of sunlight, requiring affordable technologies for large-scale energy storage.

The first indication of the variety of opportunities available is the table listing a dozen types of photovoltaic materials available to absorb light and produce electricity, characterized according to the nature of the material, the maturity of the technology, production, and efficiency. The materials listed vary greatly in terms of chemical nature, physical form, and how they are currently manufactured. Increasing control over the structure of matter, ultimately approaching atomic precision, will give greater control over ease of manufacture, cost, durability, and efficiency of energy conversion. In addition to the efficiency of energy capture and conversion, factors like single crystal or thin film, or how well the photovoltaic material is encapsulated can affect, weight, ease and cost of installation, keeping toxic materials out of the environment, etc. Opportunities to improve current and near-term systems through research and innovation are accordingly more varied than immediately apparent. Another opportunity is cost reduction through replacement of expensive materials with earth-abundant materials.

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Caltech celebrates ten years of Scaffolded DNA Origami

Posted by Jim Lewis on March 14th, 2016

DNA origami smiley faces, each 1/1000 the width of a human hair, demonstrate that virtually any shape can be folded from DNA. (Scale bar: 100 nanometers) Credit: Paul W.K. Rothemund/Caltech

Since we frequently report progress in structural DNA nanotechnology made possible by the scaffolded DNA origami technique (most recently here), I cannot resist passing on these two news items that I stumbled upon at the Caltech web site, even though it is a day late for the first one, written by Lori Dajose: “Ten Years of DNA Origami“:

On March 16, 2006, Research Professor of Bioengineering, Computing and Mathematical Sciences, and Computation and Neural Systems Paul Rothemund (BS ’94) published a paper in Nature detailing his new method for folding DNA into shapes and patterns on the scale of a few nanometers. This marked a turning point in DNA nanotechnology, enabling precise control over designed molecular structures. Ten years later, the field has grown considerably. On March 14–16, 2016, the Division of Engineering and Applied Science will hold a symposium titled “Ten Years of DNA Origami” to honor Rothemund’s contribution to the field, to survey the spectrum of research it has inspired, and to take a look at what is to come.

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Crowd-sourced RNA structure design uncovers new insights

Posted by Jim Lewis on March 12th, 2016

An Eterna interface used to enable players to select nucleotides when assessing the difficulty of RNA secondary structure design puzzles. Credit: Andersen-Lee et al., J. Mol. Biol. 2016.

Two years ago we commented on the success of “citizen scientists” playing an online game in outperforming the best available computerized design algorithms in designing RNA molecules to fold into predetermined structures. A news article appearing last month in Science, written by John Bohannon and discussing an Open Access paper (“Principles for Predicting RNA Secondary Structure Design Difficulty“) just published in the Journal of Molecular Biology, makes clear that the progress has continued “For RNA paper based on a computer game, authorship creates an identity crisis“:

… Today’s paper shows how far the effort has come. Among the game’s thousands of RNA design “puzzles,” there seem to be a small set that are particularly difficult. Among the most challenging structural features to figure out is symmetry, where an RNA strand folds into two or more identically shaped loops. The Eterna game includes an interface for players to propose hypotheses about how particular RNA structures will or will not fold into particular shapes. Those were distilled into a set of “designability” rules. The question was: Do only human designers struggle with thorny design problems, or do computer simulations tussle too?

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Will medical 3D printing advance nanotechnology?

Posted by Jim Lewis on March 12th, 2016

The world's first 3D-printed vertebrae was implanted in a Chordoma cancer patient. Credit: Ralph Mobbs

About four years ago we speculated that the advent of personal 3D printing for computers might accelerate progress toward atomically precise manufacturing. A few months later we noted the extension of 3D printing from microscale into nanoscale resolution (about 100 nm—still three orders of magnitude from atomic precision, and still using only one material). Since then progress in the technology, often referred to as “additive manufacturing”, has been impressive, especially in medical applications, even to the point of progressing toward 3D printing of tissues and organs. One especially striking example of this progress is described by Steve Smith at Medical Daily “World’s First 3D-Printed Vertebrae Saves Man With Chordoma Cancer From Becoming A Quadriplegic“:

What a time it is for 3D printing in health care. Over the past year alone, doctors have successfully separated conjoined twins, given a cancer patient a titanium rib cage, and created muscle, bone, and ears from 3D-printing materials. This list continues to grow; in December 2015, a man in his 60s received the first 3D-printed vertebrae. Without it, he would have become fully paralyzed. …

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Tightly-fitted DNA parts form dynamic nanomachine

Posted by Jim Lewis on March 10th, 2016

Three multilayer DNA components make up this rotary mechanism. The parts join together with a tight fit and leave just 2 nanometers of play around the axle, allowing the arm to swing but not wobble. Credit: Dietz Lab/TUM

Since its invention in 2006 by Paul Rothemund, scaffolded DNA origami has been used to build increasingly complex 2D and 3D structures, including organizing nanoscale functional objects in 3D space. The past few years have seen increasing progress in extending the usefulness of this very versatile method of constructing nanostructures from DNA. Three years ago we noted the report from Hendrik Dietz’s group of improvements in technique that resulted in faster folding, gave higher yields, and provided structures assembled with sub-nanometer positional precision. Higher yields of more precisely assembled DNA nanostructures opened the way to using DNA origami to build more dynamic structures evincing mechanical movements. A year ago we cited the accomplishments of a former postdoctoral fellow in Dietz’s group, Carlos Castro, in achieving well-defined programmed motions with DNA nanostructures, thus beginning to fabricate parts for machine designs based upon the way that macroscopic machines work. We reported additional progress from Castro and his colleagues here and here. A few months later we cited a report from Dietz’s lab on DNA components with complementary shapes that self assemble into nanoscale machinery. Finally, last December we noted the accomplishment of the Dietz group in using DNA nanotechnology to position molecules with atomic precision. A new result from the Dietz group recently published in the open access journal Science Advances and also available from Dietz’s publications page demonstrates (quoting from the abstract) “a nanoscale rotary mechanism that reproduces some of the dynamic properties of biological rotary motors in the absence of an energy source, such as random walks on a circle with dwells at docking sites.” Both this and the previous advance of positioning molecules with atomic precision are described in a press release from the Technical University of Munich “Nanoscale rotor and gripper push DNA origami to new limits“:

Dietz lab’s latest DNA nanomachines demonstrate dynamics and precision

Scientists at the Technical University of Munich (TUM) have built two new nanoscale machines with moving parts, using DNA as a programmable, self-assembling construction material. In the journal Science Advances, they describe a rotor mechanism formed from interlocking 3-D DNA components. Another recent paper, in Nature Nanotechnology, reported a hinged molecular manipulator, also made from DNA. These are just the latest steps in a campaign to transform so-called “DNA origami” into an industrially useful, commercially viable technology.

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DNA nanotechnology provides new ways to arrange nanoparticles into crystal lattices

Posted by Jim Lewis on February 19th, 2016

Several years ago we pointed to work from the collaboration of two Foresight Feynman Prize winners (Chad A. Mirkin, 2002, Experimental and George C. Schatz, 2008, Theoretical) that advanced the concept of using DNA to link together nanoparticles in specific 3D configurations: “Using DNA as bonds to build new materials from nanoparticles“. A news article written by Robert F. Service in a recent issue of ScienceDNA makes lifeless materials shapeshift” describes another major advance from Mirkin’s group, taking their 2011 advance to the next level:

Researchers have engineered tiny gold particles that can assemble into a variety of crystalline structures simply by adding a bit of DNA to the solution that surrounds them. Down the road, such reprogrammable particles could be used to make materials that reshape themselves in response to light, or to create novel catalysts that reshape themselves as reactions proceed.

“This paper is very exciting,” says Sharon Glotzer, a chemical engineer at the University of Michigan, Ann Arbor, who calls it “a step towards pluripotent matter.” David Ginger, a chemist at the University of Washington, Seattle, agrees: “This is a proof of concept of something that has been a nanoparticle dream.” Neither Glotzer nor Ginger has ties to the current research. …

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Improving crystallographic resolution through using less perfect crystals

Posted by Jim Lewis on February 18th, 2016

The analysis of the Bragg peaks alone (top) reveals far less detail than the analysis of the continuous diffraction pattern (bottom). Magnifying glasses show real data. Credit: DESY, Eberhard Reimann

Sometimes atomic resolution imaging can be a big help in understanding how molecular machinery works. A news release from the Biodesign Institute of Arizona State University suggests that this may become easier to do “New method opens crystal clear views of biomolecules – Fundamental discovery triggers paradigm shift in crystallography“:

A scientific breakthrough gives researchers access to the blueprint of thousands of molecules of great relevance to medicine, energy and biology. In a new study, researchers from Arizona State University (ASU), Deutsches Elektronen-Synchrotron (DESY) and Stanford Linear Accelerator Laboratory (SLAC) describe a simple way to determine the 3-dimensional structures of proteins and other molecules, many of which are inaccessible by existing methods.

The research findings appear in the current issue of the journal Nature [abstract].

Imaging the molecular building blocks of living things at the atomic scale is tricky. Often, the most difficult step is getting such molecules to form high-quality crystals needed for X-ray imaging. This international team describes a new method that can produce sharp images relying on crystals with very small imperfections, using the world’s brightest X-ray source at the Department of Energy’s SLAC National Accelerator Laboratory.

“Once the full potential of the new method is understood, it could turn out to be one of the biggest advances since the birth of crystallography,” said Mike Dunne, director of the Linac Coherent Light Source (LCLS) X-ray laser, a DOE Office of Science User Facility.

The structures of biomolecules reveal their modes of action and provide insights into the workings of the machinery of life. Unlocking the molecular structure of particular proteins, for example, can provide the basis for developing tailor-made drugs against numerous diseases or advancing clean energy technologies with the efficiency of nature and the stability of engineered systems.

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DNA nanotechnology cages localize and optimize enzymatic reactions

Posted by Jim Lewis on February 16th, 2016

Individual enzymes (orange and green) are first attached to half-cage structures. Half cages are then assembled into full cages, where reactants are brought into close proximity. Credit: Jason Drees for the Biodesign Institute, Arizona State University

About 7 years ago we pointed to two research reports as “evidence of the growing capability of DNA scaffolds to support complex and interactive functions” (Advancing nanotechnology by organizing functional components on addressable DNA scaffolds). One of the research groups featured in that post has just published another paper using DNA cages to hold enzymes and their substrates in the proper position to make reactions more efficient. A hat tip to nanowerk for reprinting this Arizona State University news release “Chemical Cages: new technique advances synthetic biology“:

Living systems rely on a dizzying variety of chemical reactions essential to development and survival. Most of these involve a specialized class of protein molecules—the enzymes.

In a new study, Hao Yan, director of the Center for Molecular Design and Biomimetics at Arizona State University’s Biodesign Institute presents a clever means of localizing and confining enzymes and the substrate molecules they bind with, speeding up reactions essential for life processes.

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Roles of materials research and polymer chemistry in developing nanotechnology

Posted by Jim Lewis on February 16th, 2016

Nanoarchitectonics: a new materials horizon for nanotechnology. Credit Materials Horizons, Ariga et al. DOI: 10.1039/C5MH00012B

A review written by a group at the National Institute for Materials Science, Ibaraki, Japan, and published in’s Polymer Journal introduces the concept of “nanoarchitectonics” and explores why nanotechnology is not just an extension of microtechnology “What are the emerging concepts and challenges in NANO? Nanoarchitectonics, hand-operating nanotechnology and mechanobiology” [abstract]:

Most of us may mistakenly believe that sciences within the nano regime are a simple extension of what is observed in micrometer regions. We may be misled to think that nanotechnology is merely a far advanced version of microtechnology. These thoughts are basically wrong. For true developments in nanosciences and related engineering outputs, a simple transformation of technology concepts from micro to nano may not be perfect. A novel concept, nanoarchitectonics, has emerged in conjunction with well-known nanotechnology. In the first part of this review, the concept and examples of nanoarchitectonics will be introduced. In the concept of nanoarchitectonics, materials are architected through controlled harmonized interactions to create unexpected functions. The second emerging concept is to control nano-functions by easy macroscopic mechanical actions. To utilize sophisticated forefront science in daily life, high-tech-driven strategies must be replaced by low-tech-driven strategies. As a required novel concept, hand-operation nanotechnology can control nano and molecular systems through incredibly easy action. Hand-motion-like macroscopic mechanical motions will be described in this review as the second emerging concept. These concepts are related bio-processes that create the third emerging concept, mechanobiology and related mechano-control of bio-functions. According to this story flow, we provide some incredible recent examples such as atom-level switches, operation of molecular machines by hand-like easy motions, and mechanical control of cell fate. To promote and activate science and technology based on these emerging concepts in nanotechnology, the contribution and participation of polymer scientists are crucial. We hope that some readers would have interests within what we describe.

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Multiple advances in de novo protein design and prediction

Posted by Jim Lewis on February 14th, 2016

David Baker, UW professor of biochemistry, in his lab at the Institute for Protein Design. Credit: UW Institute for Protein Design

Concluding our brief update on Eric Drexler’s 1981 proposal that de novo protein design provides a path from biotechnology to general capabilities for molecular manipulation, we return to this University of Washington news release “Big moves in protein structure prediction and design”:

In addition to [their recent reports] on modular construction of proteins with repeating motifs [de novo protein design and rational design of protein architectures not found in nature], here are some other recent developments [from the research group of David Baker at the University of Washington Institute for Protein Design]:

Evolution offers clues to shaping proteins: The function of many proteins tends to stay the same across species, even after their amino acid sequences have changed over billions of years of evolution. Locating co-evolved pairs of amino acids helps calculate their proximity when the molecule folds. UW graduate student Sergey Ovchinnikov applied this co-evolution DNA sequence analysis in an E-Life paper published Sept. 3, 2015, “Large-scale determination of previously unsolved protein structures using evolutionary information.” [Open Access] The effort illuminated for the first time the structures of 58 families of proteins that have hundreds of thousands of additional, structurally related family members.

“This achievement was a grand slam home run in the history of protein structure prediction,” said Baker.

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Rational design of protein architectures not found in nature

Posted by Jim Lewis on February 11th, 2016

Designed monomeric repeat architectures. Credit: L. Doyle et al. Nature.

Continuing our coverage of several major advances in de novo protein design recently reported by the research group of David A. Baker with a consideration of the second of the two research papers they published two months ago in Nature: “Rational design of alpha-helical tandem repeat proteins with closed architecture.” [abstract, full text PDF courtesy of the Baker lab], which concerns the rational design of a class of proteins that play important roles in binding macromolecules, as scaffolds, and as building blocks for assembling more complex materials. The University of Washington news release we cited last time continues to explain the significance of understanding and designing protein structures “Big moves in protein structure prediction and design“:

… The protein structure problem is figuring out how a protein’s chemical makeup predetermines its molecular structure, and in turn, its biological role. UW researchers have developed powerful algorithms to make unprecedented, accurate, blind predictions about the structure of large proteins of more than 200 amino acids in length. This has opened the door to predicting the structures for hundreds of thousands of recently discovered proteins in the ocean, soil, and gut microbiome.

Equally difficult is designing amino acid sequences that will fold into new protein structures.

Researchers have now shown the possibility of doing this with precision for protein folds inspired by naturally occurring proteins. More important, researchers can now devise amino acid sequences to fashion novel, previously unknown folds, far surpassing what is predicted to occur in the natural world.

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De novo protein design space extends far beyond biology

Posted by Jim Lewis on February 3rd, 2016

Foldit is a protein molecule modeling program used by citizen scientists worldwide to contribute to protein design research. Credit: University of Washington Institute for Protein Design

In his first (1981) publication on what he later (1986) termed nanotechnology Eric Drexler pointed to molecular engineering as a pathway from current biotechnology toward “general capabilities for molecular manipulation”, more recently described as “high-throughput atomically precise manufacturing“. Specifically, he pointed to de novo protein design as a path leading eventually to complex non-biological machinery, suggesting that designing proteins to fold as needed will be easier than predicting how natural proteins will fold. Accordingly de novo protein design has been one of our favorite topics on Nanodot—for example, these milestones from the past five years: “Designing protein-protein interactions for advanced nanotechnology“, “Gamers, citizen science, and protein structures“, “Crowd-sourced protein design a promising path to advanced nanotechnology“, “Nanotechnology milestone: general method for designing stable proteins“, “Computational design of protein-small molecule interactions“.

This past year, several major advances in de novo protein design have been reported by the research group of David A. Baker, who shared the 2004 Feynman Prize in Nanotechnology in the Theory category, at the University of Washington, and their collaborators at the Fred Hutchinson Cancer Research Institute. A hat tip to ScienceDaily for reprinting this University of Washington news release “Big moves in protein structure prediction and design“:

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Foresight advisor MIT Prof. Marvin Minsky (1927-2016)

Posted by Jim Lewis on January 26th, 2016

Marvin Minsky at One Laptop per Child office, Cambridge Mass. 2008 (credit: Bcjordan/Wikimedia Commons)

“We are greatly saddened to hear of the death of Marvin Minsky, age 88. A pioneer in artificial intelligence, Marvin served as an Advisor to Foresight Institute from its earliest days, extending back to our predecessor organization, the MIT Nanotechnology Study Group. He wrote the Foreword to the first nanotechnology book, Engines of Creation, and was the dissertation advisor for the first-ever PhD in Molecular Nanotechnology, granted by MIT to K. Eric Drexler. Marvin’s genius and humor are well-known, and his insights will be immensely missed.”
—Christine Peterson, co-founder Foresight Institute

Conference video: Nanoscale Materials, Devices, and Processing Predicted from First Principles

Posted by Jim Lewis on January 15th, 2016

Credit: William Goddard

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 seventh speaker at the Computation and Molecular Nanotechnolgies session, William Goddard, presented “Nanoscale Materials, Devices, and Processing Predicted from First Principals”. – video length 34:22. Prof. Goddard addressed some of the method developments to allow modeling of large-scale systems, followed by some examples. He noted that the grand vision over the past 25 years has been that theory can be used to predict something useful. To predict new systems where there is no empirical data it is necessary to start with first principles.

Prof Goddard reviewed the advances that enabled going from first principles to nanoscopic systems of interest. Starting from quantum mechanics to describe a few hundred—perhaps a thousand—atoms, it was necessary to describe realistic temperatures, pressures, and concentrations in systems with millions or billions of atoms.

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Conference video: Mythbusting Knowledge Transfer Mechanisms through Science Gateways

Posted by Jim Lewis on January 14th, 2016

Credit: Gerhard Klimeck

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 fifth speaker at the Computation and Molecular Nanotechnolgies session, Gerhard Klimeck, presented “Mythbusting Knowledge Transfer Mechanisms through Science Gateways” . – video length 40:28. Prof. Klimeck addressed novel ways to disseminate nanotechnology simulations to broader audiences using as an example a user facility, the web site nanoHUB. About 12,000 users sign up for accounts and run half a million simulations throughout the year. Even more people view lectures, seminars, tutorials, for which no account is needed. Looking at a display of the use of the facility from day to day, Prof. Klimeck asked whether the bursts of activity that appear show signs of knowledge transfer happening. Some of this data illustrates the mythbusting over the past ten years—all the things we were told we could not do. For example, the facility used to have about a thousand users per year, and then the tools were made interactive and suddenly that grew to about 12,000 today. Lectures and seminars were introduced and led to dramatic growth. Citing recent interest in MOOCs (massive open online course), Prof. Klimeck noted that they had been a MOOC for a number of years.

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