Automating DNA origami opens many new uses

Automating DNA origami opens door to many new uses. Like 3-D printing did for larger objects, method makes it easy to build nanoparticles out of DNA.

Scientia — Researchers can build complex, nanometer-scale structures of almost any shape and form, using strands of DNA. But these particles must be designed by hand, in a complex and laborious process.

3D surface- versus DNA-based renderings of diverse DNA nanoparticles designed autonomously by the algorithm DAEDALUS.
image by Digizyme

This has limited the technique, known as DNA origami, to just a small group of experts in the field.

Now a team of researchers at MIT and elsewhere has developed an algorithm that can build these DNA nanoparticles automatically.

In this way the algorithm, which is reported together with a novel synthesis approach in the journal Science this week, could allow the technique to be used to develop nanoparticles for a much broader range of applications, including scaffolds for vaccines, carriers for gene editing tools, and in archival memory storage.

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Unlike traditional DNA origami, in which the structure is built up manually by hand, the algorithm starts with a simple, 3-D geometric representation of the final shape of the object, and then decides how it should be assembled from DNA, according to Mark Bathe, an associate professor of biological engineering at MIT, who led the research.

“The paper turns the problem around from one in which an expert designs the DNA needed to synthesize the object, to one in which the object itself is the starting point, with the DNA sequences that are needed automatically defined by the algorithm,” Bathe says. “Our hope is that this automation significantly broadens participation of others in the use of this powerful molecular design paradigm.”

The algorithm first represents the object as a perfectly smooth, continuous outline of its surface. It then breaks the surface up into a series of polygonal shapes.

Next, it routes a long, single strand of DNA, called the scaffold, which acts like a piece of thread, throughout the entire structure to hold it together.

A new algorithm for DNA origami starts with a simple, 3-D geometric representation of the final shape of the object, and then decides how it should be assembled from DNA.
Image courtesy of the researchers.

The algorithm weaves the scaffold in one fast and efficient step, which can be used for any shape of 3-D object, Bathe says.

“That [step] is a powerful part of the algorithm, because it does not require any manual or human interface, and it is guaranteed to work for any 3-D object very efficiently,” he says.

The algorithm, which is known as DAEDALUS (DNA Origami Sequence Design Algorithm for User-defined Structures) after the Greek craftsman and artist who designed labyrinths that resemble origami’s complex scaffold structures, can build any type of 3-D shape, provided it has a closed surface. This can include shapes with one or more holes, such as a torus.

In contrast, a previous algorithm, published last year in the journal Nature, is only capable of designing and building the surfaces of spherical objects, and even then still requires manual intervention.

Most previous work on DNA origami has explored 2-D and 3-D structures whose design required some steps to be done by hand, says Paul Rothemund, a research professor at Caltech, who was not involved in the paper.

“The current work provides a complete pipeline, starting from a 3-D form, and arriving at a DNA design and a corresponding predicted atomic model which can be compared quantitatively with experiments,” he says.

The team’s strategy in designing and synthesizing the DNA nanoparticles was also validated using 3-D cryo-electron microscopy reconstructions by Bathe’s collaborator, Wah Chiu at Baylor College of Medicine.

The researchers are now investigating a number of applications for the DNA nanoparticles built by the DAEDALUS algorithm. One such application is a scaffold for viral peptides and proteins for use as vaccines.

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The surface of the nanoparticles could be designed with any combination of peptides and proteins, located at any desired location on the structure, in order to mimic the way in which a virus appears to the body’s immune system.

The researchers demonstrated that the DNA nanoparticles are stable for more than six hours in serum, and are now attempting to increase their stability further.

The nanoparticles could also be used to encapsulate the CRISPR-Cas9 gene editing tool. The CRISPR-Cas9 tool has enormous potential in therapeutics, thanks to its ability to edit targeted genes. However, there is a significant need to develop techniques to package the tool and deliver it to specific cells within the body, Bathe says.

This is currently done using viruses, but these are limited in the size of package they can carry, restricting their use. The DNA nanoparticles, in contrast, are capable of carrying much larger gene packages and can easily be equipped with molecules that help target the right cells or tissue.

The team is also investigating the use of the nanoparticles as DNA memory blocks. Previous research has shown that information can be stored in DNA, in a similar way to the 0s and 1s used to store data digitally. The information to be stored is “written” using DNA synthesis and can then be read back using DNA sequencing technology.

“The current work provides a complete pipeline, starting from a 3-D form, and arriving at a DNA design and a corresponding predicted atomic model which can be compared quantitatively with experiments,” says MIT’s Mark Bathe.
Image courtesy of the researchers.

Using the DNA nanoparticles would allow this information to be stored in a structured and protected way, with each particle akin to a page or chapter of a book. Recalling a particular chapter or book would then be as simple as reading that nanoparticle’s identity, somewhat like using library index cards, Bathe says.

The most exciting aspect of the work, however, is that it should significantly broaden participation in the application of this technology, Bathe says, much like 3-D printing has done for complex 3-D geometric models at the macroscopic scale.

Bathe’s co-authors on the paper are Rémi Veneziano, a postdoc in the Department of Biological Engineering; Sakul Ratanalert, a graduate student in the departments of Biological Engineering and Chemical Engineering; and others from Baylor College of Medicine and Arizona State University.

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– Credit and Resource –

MIT | Helen Knight

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Automating DNA origami opens many new uses

Microsystems Nanodevice at one-hundredth the cost

New techniques for building microelectromechanical microsystems show promise.

External row of seven emitters that are part of a 49-emitter array. The scalloping on the exterior of the emitters, due to the layer-by-layer manufacturing, is visible.
Image: Anthony Taylor and Luis F Velásquez-García (edited by MIT News)

Scientia — Microelectromechanical systems — or MEMS — were a $12 billion business in 2014. But that market is dominated by just a handful of microsystems devices, such as the accelerometers that reorient the screens of most smartphones.

That’s because manufacturing MEMS has traditionally required sophisticated semiconductor fabrication facilities, which cost tens of millions of dollars to build. Potentially useful MEMS have languished in development because they don’t have markets large enough to justify the initial capital investment in production.

Two recent papers from researchers at MIT’s Microsystems Technologies Laboratories offer hope that that might change. In one, the researchers show that a MEMS-based gas sensor manufactured with a desktop device performs at least as well as commercial sensors built at conventional production facilities.

In the other paper, they show that the central component of the desktop fabrication device can itself be built with a 3-D printer. Together, the papers suggest that a widely used type of MEMS gas sensor could be produced at one-hundredth the cost with no loss of quality.

A completed chip with a wired graphene oxide gas sensor. The graphene oxide film is the greenish dot covering the electrode structure.
Image: Anthony Taylor and Luis F Velásquez-García

The researchers’ fabrication device sidesteps many of the requirements that make conventional MEMS manufacture expensive. “The additive manufacturing we’re doing is based on low temperature and no vacuum,” says Luis Fernando Velásquez-García, a principal research scientist in MIT’s Microsystems Technology Laboratories and senior author on both papers. “The highest temperature we’ve used is probably 60 degrees Celsius. In a chip, you probably need to grow oxide, which grows at around 1,000 degrees Celsius. And in many cases the reactors require these high vacuums to prevent contamination. We also make the devices very quickly. The devices we reported are made in a matter of hours from beginning to end.”

Welcome resistance

For years, Velásquez-García has been researching manufacturing techniques that involve dense arrays of emitters that eject microscopic streams of fluid when subjected to strong electric fields. For the gas sensors, Velásquez-García and Anthony Taylor, a visiting researcher from the British company Edwards Vacuum, use so-called “internally fed emitters.” These are emitters with cylindrical bores that allow fluid to pass through them.

In this case, the fluid contained tiny flakes of graphene oxide. Discovered in 2004, graphene is an atom-thick form of carbon with remarkable electrical properties. Velásquez-García and Taylor used their emitters to spray the fluid in a prescribed pattern on a silicon substrate. The fluid quickly evaporated, leaving a coating of graphene oxide flakes only a few tens of nanometers thick.

The flakes are so thin that interaction with gas molecules changes their resistance in a measurable way, making them useful for sensing. “We ran the gas sensors head to head with a commercial product that cost hundreds of dollars,” Velásquez-García says. “What we showed is that they are as precise, and they are faster. We make at a very low cost — probably cents — something that works as well as or better than the commercial counterparts.”

To produce those sensors, Velásquez-García and Taylor used electrospray emitters that had been built using conventional processes. However, in the December issue of the Journal of Microelectromechanical Systems, Velásquez-García reports using an affordable, high-quality 3-D printer to produce plastic electrospray emitters whose size and performance match those of the emitters that yielded the gas sensors.

Made to order

In addition to making electrospray devices more cost-effective, Velásquez-García says, 3-D printing also makes it easier to customize them for particular applications. “When we started designing them, we didn’t know anything,” Velásquez-García says. “But at the end of the week, we had maybe 15 generations of devices, where each design worked better than the previous versions.”

Indeed, Velásquez-García says, the advantages of electrospray are not so much in enabling existing MEMS devices to be made more cheaply as in enabling wholly new devices. Besides making small-market MEMS products cost-effective, electrospray could enable products incompatible with existing manufacturing techniques.

Optical micrograph of a fabricated conductometric graphene oxide gas sensor. The inset (top left corner) shows a close-up view of the active area of the sensor.
Image: Anthony Taylor and Luis F Velásquez-García

“In some cases, MEMS manufacturers have to compromise between what they intended to make, based on the models, and what you can make based on the microfabrication techniques,” Velásquez-García says. “Only a few devices that fit into the description of having large markets and not having subpar performance are the ones that have made it.”

Electrospray could also lead to novel biological sensors, Velásquez-García says. “It allows us to deposit materials that would not be compatible with high-temperature semiconductor manufacturing, like biological molecules,” he says.

“For sure, the paper opens new technical paths to making gas microsensors,” says Jan Dziuban, head of the Division of Microengineering at Wroclaw University of Technology in Poland. “From a technical point of view, the process may be easily adapted to mass fabrication.”

“But promising results must be proved statistically,” he cautions. “Personal experience tells me that plenty of very promising materials for new sensors, utilizing nanostructured materials, which have been published in high-level scientific papers, haven’t resulted in reliable products.”

– Credit and Resource –

Larry Hardesty | MIT News Office

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Microsystems Nanodevice at one-hundredth the cost

Printing transparent glass in 3-D

New system in 3-D printing is the first to create strong, solid glass structures from computerized designs.

The glass 3-D printing process.
Photo: Steven Keating

Scientia — The technology behind 3-D printing — which initially grew out of work at MIT — has exploded in recent years to encompass a wide variety of materials, including plastics and metals. Simultaneously, the cost of 3-D printers has fallen sufficiently to make them household consumer items.

Now a team of MIT researchers has opened up a new frontier in 3-D printing: the ability to print optically transparent glass objects.

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The new system, described in the Journal of 3D Printing and Additive Manufacturing, was developed by Neri Oxman, an associate professor at the MIT Media Lab; Peter Houk, director of the MIT Glass Lab; MIT researchers John Klein and Michael Stern; and six others.

Other groups have attempted to 3-D print glass objects, but a major obstacle has been the extremely high temperature needed to melt the material. Some have used tiny particles of glass, melded together at a lower temperature in a technique called sintering. But such objects are structurally weak and optically cloudy, eliminating two of glass’s most desirable attributes: strength and transparency.

The high-temperature system developed by the MIT team retains those properties, producing printed glass objects that are both strong and fully transparent to light. Like other 3-D printers now on the market, the device can print designs created in a computer-assisted design program, producing a finished product with little human intervention.

In the present version, molten glass is loaded into a hopper in the top of the device after being gathered from a conventional glassblowing kiln. When completed, the finished piece must be cut away from the moving platform on which it is assembled.

In operation, the device’s hopper, and a nozzle through which the glass is extruded to form an object, are maintained at temperatures of about 1,900 degrees Fahrenheit, far higher than the temperatures used for other 3-D printing. The stream of glowing molten glass from the nozzle resembles honey as it coils onto a platform, cooling and hardening as it goes.

One challenge the researchers faced was keeping the filament of glass hot enough so the next layer of the structure would adhere to it, but not so hot that the structure would collapse into a shapeless lump. They ended up producing three separate components that can independently be heated to the required temperatures: the upper reservoir for the stock of molten glass, the nozzle at the bottom of that chamber, and a lower chamber where the printed object is built up.

Scanning electron microscope image of a sample from a printed glass prism.
Image: James Weaver

The concept began as a project in a course on additive manufacturing, Klein says; he and others decided to refine the concept when initial work showed the idea had promise. But it was still a long and laborious process, with a lot of trial-and-error.

“Glass is inherently a very difficult material to work with,” Klein says: Its viscosity changes with temperature, requiring precise control of temperature at all stages of the process.

The new process could allow unprecedented control over the glass shapes that can be produced, Oxman says.

“We can design and print components with variable thicknesses and complex inner features — unlike glassblowing, where the inner features reflect the outer shape,” Oxman explains. For example, she adds, “We can control solar transmittance. … Unlike a pressed or blown-glass part, which necessarily has a smooth internal surface, a printed part can have complex surface features on the inside as well as the outside, and such features could act as optical lenses.”

Oxman adds that she foresees the process being adapted to create much larger structures.

Photo: Andy Ryan

“Could we surpass the modern architectural tradition of discrete formal and functional partitions, and generate an all-in-one building skin that is at once structural and transparent?” she asks. “Because glass is at once structural and transparent, it is relatively easy to consider the integration of structural and environmental building performance within a single integrated skin.”

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Houk cites several additional directions for pushing the research further. One is adding pressure to the system — either through a mechanical plunger or compressed gas — to produce a more uniform flow, and thus a more uniform width to the extruded filament of glass. Additional work will focus on the use of colors in the glass, which the team has already demonstrated in limited testing.

Klein says the printing system is an example of multidisciplinary work facilitated by MIT’s flexible departmental boundaries — in this case, involving team members from the Media Lab, the Department of Mechanical Engineering, and the MIT Glass Lab, which is part of the Department of Materials Science and Engineering.

Photo: Chikara Inamura

– Credit and Resource –

David L. Chandler | MIT News Office

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Printing transparent glass in 3-D