DNA Nanotechnology Tools: From Design to Applications: Current Opportunities and Collaborations – Wyss Institute – Harvard University

Suite of DNA nanotechnology devices engineered to overcome specific bottlenecks in the development of new therapies, diagnostics, and understanding of molecular structures

Lead Inventors

William Shih Wesley Wong

Advantages

• DNA as building blocks
• Broad applications
• Low cost with big potential

DNA nanostructures with their potential for cell and tissue permeability, biocompatibility, and high programmability at the nanoscale level are promising candidates as new types of drug delivery vehicles, highly specific diagnostic devices, and tools to decipher how biomolecules dynamically change their shapes, and interact with each other and with candidate drugs. Wyss Institute researchers are providing a suite of diverse, multifunctional DNA nanotechnological tools with unique capabilities and potential for a broad range of clinical and biomedical research areas.

DNA nanotechnological devices for therapeutic drug delivery

DNA nanostructures have future potential to be widely used to transport and present a variety of biologically active molecules such as drugs and immune-enhancing antigens and adjuvants to target cells and tissues in the human body.

DNA origami as high-precision delivery components of cancer vaccines

The Wyss Institute has developed cancer vaccines to improve immunotherapies. These approaches use implantable or injectable biomaterial-based scaffolds that present tumor-specific antigens, and biomolecules that attract dendritic immune cells (DCs) into the scaffold, and activate them so that after their release they can orchestrate anti-tumor T cell responses against tumors carrying the same antigens. To be activated most effectively, DCs likely need to experience tumor antigens and immune-boosting CpG adjuvant molecules at particular ratios (stoichiometries) and configurations that register with the density and distribution of receptor molecules on their cell surface.

Specifically developed DNA origami, programmed to assemble into rigid square-lattice blocks that co-present tumor antigens and adjuvants to DCs within biomaterial scaffolds with nanoscale precision have the potential to boost the efficacy of therapeutic cancer vaccines, and can be further functionalized with anti-cancer drugs.

Chemical modification strategy to protect drug-delivering DNA nanostructures

DNA nanostructures such as self-assembling DNA origami are promising vehicles for the delivery of drugs and diagnostics. They can be flexibly functionalized with small molecule and protein drugs, as well as features that facilitate their delivery to specific target cells and tissues. However, their potential is hampered by their limited stability in the body’s tissues and blood. To help fulfill the extraordinary promise of DNA nanostructures, Wyss researchers developed an easy, effective and scalable chemical cross-linking approach that can provide DNA nanostructures with the stability they need as effective vehicles for drugs and diagnostics.

In two simple cost-effective steps, the Wyss’ approach first uses a small-molecule, unobtrusive neutralizing agent, PEG-oligolysine, that carries multiple positive charges, to cover DNA origami structures. In contrast to commonly used Mg²⁺ions that each neutralize only two negative changes in DNA structures, PEG-oligolysine covers multiple negative charges at one, thus forming a stable “electrostatic net,” which increases the stability of DNA nanostructures about 400-fold. Then, by applying a chemical cross-linking reagent known as glutaraldehyde, additional stabilizing bonds are introduced into the electrostatic net, which increases the stability of DNA nanostructures by another 250-fold, extending their half-life into a range that is compatible with a broad range of clinical applications.

DNA nanotechnological devices as ultrasensitive diagnostic and analytical tools

The generation of detectable DNA nanostructures in response to a disease or pathogen-specific nucleic acids, in principle, offers a means for highly effective biomarker detection in diverse samples. A single molecule binding event of a synthetic oligonucleotide to a target nucleic acid can nucleate the creation of much larger structures by the cooperative assembly of smaller synthetic DNA units like DNA tiles or bricks into larger structures that then can be visualized in simple laboratory assays. However, a central obstacle to these approaches is the occurrence of (1) non-specific binding and (2) non-specific nucleation events in the absence of a specific target nucleic acid which can lead to false-positive results. Wyss DNA nanotechnologists have developed two separately applicable but combinable solutions for these problems.

Digital counting of biomarker molecules with DNA nanoswitch catenanes

To enable the initial detection (binding) of biomarkers with ultra-high sensitivity and specificity, Wyss researchers have developed a type of DNA nanoswitch that, designed as a larger catenane (Latin catenameaning chain), is assembled from mechanically interlocked ring-shaped substructures with specific functionalities that together enable the detection and counting of single biomarker molecules. In the “DNA Nanoswitch Catenane” structure, both ends of a longer synthetic DNA strand are linked to two antibody fragments that each specifically bind different parts of the same biomarker molecule of interest, thus allowing for high target specificity and sensitivity.

This bridging-event causes the strand to close into a “host ring,” which it is interlocked at different regions with different “guest rings.” Closing of the host ring switches the guest rings into a configuration that allows the synthesis of a new DNA strand. The newly synthesized diagnostic strand then can be unambiguously detected as a single digital molecule count, while disrupting the antibody fragment/biomarker complex starts a new biomarker counting cycle. Both, the target binding specificity and the synthesis of a target-specific DNA strand also enable the combination of multiple DNA nanoswitch catenanes to simultaneously count different biomarker molecules in a single multiplexed reaction.

For ultrasensitive diagnostics, it is desirable to have the fastest amplification and the lowest rate of spurious nucleation. DNA nanotechnology approaches have the potential to deliver this in an enzyme-free, low-cost manner.

WILLIAM SHIH

A rapid amplification platform for diverse biomarkers

A rapid, low-cost and enzyme-free detection and amplification platform avoids non-specific nucleation and amplification and allows the self-assembly of much larger micron-scale structures from a single seed in just minutes. The method, called “Crisscross Nanoseed Detection” enables the ultra-cooperative assembly of ribbons starting from a single biomarker binding event. The micron-scale structures are densely woven from single-stranded “DNA slats,” whereby an inbound slat snakes over and under six or more previously captured slats on a growing ribbon end in a “crisscross” manner, forming weak but highly-specific interactions with its interacting DNA slats. The nucleation of the assembly process is strictly target-seed specific and the assembly can be carried out in a one-step reaction in about 15 minutes without the addition of further reagents, and over a broad range of temperatures. Using standard laboratory equipment, the assembled structures then can be rapidly visualized or otherwise detected, for example, using high-throughput fluorescence plate reader assays.

CURRENT OPPORTUNITY – STARTUP

Crisscross Nanoseed Detection: Nanotechnology-Powered Infectious Disease Diagnostics

Enzyme-free DNA nanotechnology for rapid, ultrasensitive, and low-cost detection of infectious disease biomarkers with broad accessibility in point-of-care settings.

The DNA assembly process in the Crisscross Nanoseed Detection method can also be linked to the action of DNA nanoswitch catenanes that highly specifically detect a biomarker molecule leading to preservation of a molecular record. Each surviving record can nucleate the assembly of a crisscross nanostructure, combining high-specificity binding with amplification for biomarker detection.

Wyss researchers are currently developing the approach as a multiplexable low-cost diagnostic for the COVID-19 causing SARS-CoV-2 virus and other pathogens that could give accurate results faster and at lower costs than currently used techniques.

Nanoscale devices for determining the structure and identity of proteins at the single-molecule level

The ability to identify and quantify proteins from trace biological samples would have a profound impact on both basic research and clinical practice, from monitoring changes in protein expression within individual cells, to enabling the discovery of new biomarkers of disease. Furthermore, the ability to also determine their structures and interactions would open up new avenues for drug discovery and characterization. Over the past decades, developments in DNA analysis and sequencing have unquestionably revolutionized medicine – yet equivalent developments for protein analysis have remained a challenge. While methods such as mass spectrometry for protein identification, and cryoEM for structure determination have rapidly advanced, challenges remain regarding resolution and the ability to work with trace heterogeneous samples.

To help meet this challenge, researchers at the Wyss Institute have developed a new approach that combines DNA nanotechnology with single-molecule manipulation to enable the structural identification and analysis of proteins and other macromolecules. “DNA Nanoswitch Calipers” (DNCs) offer a high-resolution approach to “fingerprint proteins” by measuring distances and determining geometries within single proteins in solution. DNCs are nanodevices designed to measure distances between DNA handles that have been attached to target molecules of interest. DNC states can be actuated and read out using single-molecule force spectroscopy, enabling multiple absolute distance measurements to be made on each single-molecule.

DNCs could be widely adapted to advance research in different areas, including structural biology, proteomics, diagnostics and drug discovery.

All technologies are in development and available for industry collaborations.

University of Waterloo developing DNA-based COVID-19 vaccine

Researchers at the University of Waterloo are developing a DNA-based vaccine that can be delivered through a nasal spray.

Researchers at the University of Waterloo are developing a DNA-based vaccine that can be delivered through a nasal spray.

The vaccine will work by using bacteriophage, a process that will allow the vaccine to replicate within bacteria already in the body and is being designed to target tissues in the nasal cavity and lower respiratory tract.

“When complete, our DNA-based vaccine will be administered non-invasively as a nasal spray that delivers nanomedicine engineered to immunize and decrease COVID-19 infections,” explains Roderick Slavcev, a professor in the School of Pharmacy who specializes in designing vaccines, pharmaceuticals and gene-therapy treatments. “This research combines the expertise of many and leverages existing technology developed by my team, which we’re reconfiguring for a COVID-19 application.”

When completed, the researchers aim to have the DNA-based vaccine enter cells in targeted tissues and cause them to produce a virus-like particle (VLP) that will stimulate an immune response in people.

The VLP will look similar to the structure of SARS-CoV-2 (the virus which causes COVID-19), but is harmless. This similarity will activate the body’s natural immune response to protect against viral infections comparable to the VLP, including SARS-CoV-2. It will also bind to receptors that SARS-CoV-2 would bind to, limiting the possible sites for transmission. By causing these changes in the body, the vaccine will build immunity against COVID-19 and decrease the severity of infections in progress – serving as both a therapeutic and a vaccine.

Every detail of the vaccine, from ensuring the bacteriophage target specific cells in the respiratory tract to creating a minimal VLP to impersonate SARS-CoV-2, is specifically engineered by the researchers and requires testing.

To achieve the design of such a complex project, Slavcev is teaming up with Emmanuel Ho, another professor at the School of Pharmacy, and Marc Aucoin, professor of chemical engineering. Ho’s team is designing the nanomedication that will be delivered by the nasal spray, which is currently being tested. Aucoin’s lab is constructing and purifying the VLP and boosting immunity following the initial administration of the therapeutic vaccine.

“It is the collaborative effort of our talented teams that makes this multidisciplinary project so feasible and necessarily efficient as a potential universal vaccine solution against SARS-CoV infections,” says Slavcev. “To practice science with such urgency alongside such talented colleagues and their students is not only immensely educational, it is extremely rewarding.”

Slavcev’s team has completed design of the bacteriophage delivery system and is currently modifying this system to apply to COVID-19.  Additional design of components and further testing will take place later this year. Components of the research are supported by a grant from the Natural Sciences and Engineering Research Council of Canada.

Note: This research has not yet been peer-reviewed and is being released as part of UWaterloo’s commitment to help inform Canada’s COVID-19 response.

Covid-19 Diagnostic Based on MIT Technology to be Tested on Patients Soon

This scanning electron microscope image shows SARS-CoV-2 (yellow)—also known as 2019-nCoV, the virus that causes COVID-19—isolated from a patient, emerging from the surface of cells (blue/pink) cultured in the lab. Image: NIAID-RML

A variety of MIT research projects could aid efforts to detect and prevent the spread of coronavirus.

As more Covid-19 cases appear in the United States and around the world, the need for fast, easy-to-use diagnostic tests is becoming ever more pressing. A startup company spun out from MIT is now working on a paper-based test that can deliver results in under half an hour, based on technology developed at MIT’s Institute for Medical Engineering and Science (IMES).

Cambridge-based E25Bio, which developed the test, is now preparing to submit it to the FDA for “emergency use authorization,” which would grant temporary approval for using the device on patient samples during public health emergencies.

Elsewhere around MIT, several other research groups are working on projects that may help further scientists’ understanding of how coronaviruses are transmitted and how infection may be prevented. Their work touches on fields ranging from diagnostics and vaccine development to more traditional disease prevention measures such as social distancing and handwashing.

Faster diagnosis

The technology behind the new E25Bio diagnostic was developed by Lee Gehrke, the Hermann L.F. von Helmholtz Professor at IMES, and other members of his lab, including Irene Bosch, a former IMES research scientist who is now the CTO of E25Bio.

For the past several years, Gehrke, Bosch, and others in the lab have been working on diagnostic devices that work similar to a pregnancy test but can identify viral proteins from patient samples. The researchers have used this technology, known as lateral flow technology, to create tests for Ebola, dengue fever, and Zika virus, among other infectious diseases.

The tests consist of strips of paper that are coated with antibodies that bind to a specific viral protein. A second antibody is attached to specialized nanoparticles, and the patient’s sample is added to a solution of those particles. The test strip is then dipped in this solution. If the viral protein is present, it attaches to the antibodies on the paper strip as well as the nanoparticle-bound antibodies, and a colored spot appears on the strip within 20 minutes.

Currently, there are two primary types of Covid-19 diagnostics available. One such test screens patient blood samples for antibodies against the virus. However, antibodies are often not detectable until a few days after symptoms begin. Another type of test looks for viral DNA in a sputum sample. These tests can detect the virus earlier in the infection, but they require polymerase chain reaction (PCR), a technology that amplifies the amount of DNA to detectable levels and takes several hours to perform.

“Our hope is that, similar to other tests that we’ve developed, this will be usable on the day that symptoms develop,” Gehrke says. “We don’t have to wait for antibodies to the virus to come up.”

If the U.S. Food and Drug Administration grants the emergency authorization, E25Bio could start testing the diagnostic with patient samples, which they haven’t been able to do yet. “If those are successful, then the next step would be to talk about using it for actual clinical diagnosis,” Gehrke says.

Another advantage of this approach is that the paper tests can be easily and inexpensively manufactured in large quantities, he adds.

RNA vaccines

On Feb. 24, only about a month after the first U.S. case of coronavirus was reported, the Cambridge-based biotech company Moderna announced it had an experimental vaccine ready to test. That speedy turnaround is due to the unique advantages of RNA vaccines, says Daniel Anderson, an MIT professor of chemical engineering, who also works on such vaccines, though not specifically for coronavirus.

“A key advantage of messenger RNA is the speed with which you can identify a new sequence and use it to come up with a new vaccine,” Anderson says.

Traditional vaccines consist of an inactivated form of a viral protein that induces an immune response. However, these vaccines usually take a long time to manufacture, and for some diseases, they are too risky. Vaccines that consist of messenger RNA are an appealing alternative because they induce host cells to produce many copies of the proteins they encode, provoking a stronger immune response than proteins delivered on their own.

RNA vaccines can also be quickly reprogrammed to target different viral proteins, as long as the sequence encoding the protein is known. The main obstacle to developing such vaccines so far has been finding effective and safe ways to deliver them. Anderson’s lab has been working on such strategies for several years, and in a recent study he showed that packing such vaccines into a special type of lipid nanoparticles can enhance the immune response that they produce.

“Messenger RNA can encode the viral antigens, but in order to work, we need to find a way to deliver these antigens to the correct part of the body so that they get expressed and generate an immune response. We also need to make sure that the vaccine causes appropriate immune stimulation to get a strong response,” Anderson says.

Anthony Fauci, director of the National Institute of Allergy and Infectious Diseases (NIAID), has estimated that it will take at least 12 to 18 months to fully test any potential Covid-19 vaccine for safety and effectiveness.

Keep your distance

Over the last decade, Lydia Bourouiba, an associate professor directing the Fluid Dynamics of Disease Transmission Laboratory at MIT, has focused on characterizing and modeling infectious disease dynamics and transmission at various scales. Through experiments in the lab and clinical environment, she has reported that when a person coughs or sneezes, they do not emit a spray of individual droplets that quickly fall to the ground and evaporate, as scientists had once thought. Instead, they produce a complex cloud of hot and moist air that traps droplets of all sizes together, propelling them much further through the air than any individual droplet would travel on its own.

On average, her experiments have revealed that a cough can transmit droplets up to 13 to 16 feet, while a sneeze can eject them up to 26 feet away. Surrounding air conditions can act to further disperse the residual droplets in upper levels of rooms.

Bourouiba notes that the presence of the high-speed gas cloud is independent of the type of organism or pathogen that the cloud may contain. The droplets within it depend on pathogenesis coupled with a patient’s physiology — a combination which her laboratory has focused on deciphering in the context of influenza. She is now expanding her studies and modeling to translate the work to Covid-19, and says now is a critical time to invest in research.

“This virus is going to stay with us for a while — and certainly data suggest that it is not going to suddenly disappear when the weather changes,” she says. “There’s a fine and important balance between safety, precautions and action that is important to strike to enable and dramatically accelerate research to be done now so we can be better prepared and informed for actions in the weeks and months to come when the worst of the pandemic will unfold.”

She is also working with others to evaluate ways to limit a cloud’s dispersal and slow Covid-19 transmission to health care workers and others in shared spaces. “A surgical mask is not protective against inhalation of a pathogen from the cloud,” she says. “For an infected patient wearing it, it can contain some of the forward ejecta from coughs or sneezes, but these are very violent ejections and masks are completely open on all sides, and fluid flows through the path of least resistance.”

Based on the data, she recommends that health care workers consider wearing a respirator, whenever possible. And, for the general public, Bourouiba emphasizes that the risk of contracting COVID-19 remains relatively low locally, and that risk should be thought of in the context of the community.

Wash those hands

Another good way to protect yourself against all of those tiny infectious droplets is to wash your hands. (Again, and again, and again.)

Ruben Juanes, an MIT professor of civil and environmental engineering, and of earth, atmospheric and planetary sciences, published a study in December showing the importance of improving rates of handwashing at key airports in order to curtail the spread of an epidemic. Now, he says, following the Covid-19 outbreak, governments around the world have imposed unprecedented restrictions on mobility, including the closure of airports and suspension of flight routes.

At the same time, the World Health Organization, U.S. Centers for Disease Control, and many other health agencies all recommend hand-hygiene as the number one precaution measure against disease spread. “Following our recent paper on the impact of hand-hygiene on global disease spreading,” Juanes says, “we are now investigating the combined effect of restrictions on human mobility and enhanced engagement with hand-hygiene on the global spread of COVID-19 through the world air-transportation network.”

Juanes says he and Christos Nicolaides PhD ’14, a professor at the University of Cyprus who was the lead author of the previous study, are working “with fine-grained, worldwide air-traffic data that accounts for all flights for the period between Jan. 15, 2020 until today (accounting for closures/cancellations) and the corresponding period of 2019 (base level) to elucidate the role of travel restrictions on the global spread of Covid-19 through detailed epidemiological modeling.”

“Furthermore,” he adds, “we simulate different hand-hygiene strategies at airports on top of travel restrictions with the goal of proposing an optimal strategy that combines travel restrictions and enhanced hand hygiene, to mitigate the advance of Covid-19 both in the short term (weeks) and the long term (the next flu season).”

Juanes says they will make the results immediately available via medarXiv, while the work follows peer-review in a journal. This would also allow the information to reach other academic and government institutions in a more timely way, he says.

DNA Nanomachines Are Opening Medicine to the World of Physics

When I imagine the inner workings of a robot, I think hard, cold mechanics running on physics: shafts, wheels, gears. Human bodies, in contrast, are more of a contained molecular soup operating on the principles of biochemistry.

Yet similar to robots, our cells are also attuned to mechanical forces—just at a much smaller scale. Tiny pushes and pulls, for example, can urge stem cells to continue dividing, or nudge them into maturity to replace broken tissues. Chemistry isn’t king when it comes to governing our bodies; physical forces are similarly powerful. The problem is how to tap into them.

In a new perspectives article in Science, Dr. Khalid Salaita and graduate student Aaron Blanchard from Emory University in Atlanta point to DNA as the solution. The team painted a futuristic picture of DNA mechanotechnology, in which we use DNA machines to control our biology. Rather than a toxic chemotherapy drip, for example, a cancer patient may one day be injected with DNA nanodevices that help their immune cells better grab onto—and snuff out—cancerous ones.

“For a long time,” said Salaita, “scientists have been good at making micro devices, hundreds of times smaller than the width of a human hair. It’s been more challenging to make functional nano devices, thousands of times smaller than that. But using DNA as the component parts is making it possible to build extremely elaborate nano devices because the DNA parts self-assemble.”

Just as the steam engine propelled civilization through the first industrial revolution, DNA devices may fundamentally change medicine, biological research, and the development of biomaterials, further merging man and machine.

Why DNA?

When picturing a tiny, whirling machine surveying the body, DNA probably isn’t the first candidate that comes to mind. Made up of long chains of four letters—A, T, C, and G—DNA is normally secluded inside a tiny porous “cage” in every cell, in the shape of long chains wrapped around a protein “core.”

Yet several properties make DNA a fascinating substrate for making mechano-machines, the authors said. One is its predictability: like soulmates, A always binds to T, and C with G. This chemical linking in turn forms the famous double helix structure. By giving the letters little chemical additions, or swapping them out altogether with unnatural synthetic letters, scientists have been able to form entirely new DNA assemblies, folded into various 3D structures.

Read More: Detecting HIV diagnostic antibodies with DNA nanomachines

Rather than an unbreakable, immutable chain, DNA components are more like Japanese origami paper, or Lego blocks. While they can’t make every single shape—try building a completely spherical Death Star out of Lego—the chemistry is flexible enough that scientists can tweak its structure, stiffness, and coiling by shifting around the letters or replacing them with entirely new ones.

 

The Rise of DNA Machines

In the late fall of 1980, Dr. Nadrian Seeman was relaxing at the campus pub at New York University when he noticed a mind-bending woodcut, Depth, by MC Escher. With a spark of insight, he realized that he could form similar lattice shapes using DNA, which would make it a lot easier for him to study the molecule’s shape. More than a decade later, his lab engineered the first artificial 3D nanostructure—a cube made out of DNA molecules. The field of DNA nanotechnology was born.

Originally considered a novelty, technologists rushed to make increasingly complex shapes, such as smiley faces, snowflakes, a tiny world map, and more recently, the world’s smallest playable tic-tac-toe set. It wasn’t just fun. Along the way, scientists uncovered sophisticated principles and engineering techniques to shape DNA strands into their desired structures, forming a blueprint of DNA engineering.

Then came the DNA revolution. Reading and writing the molecule from scratch became increasingly cheaper, making it easier to experiment with brand-new designs. Additional chemical or fluorescent tags or other modifications gave scientists a direct view of their creations. Rather than a fringe academic pursuit, DNA origami became accessible to most labs, and the number of devices rapidly exploded—devices that can sense, transmit, and generate mechanical forces inside cells.

“If you put together these three main components of mechanical devices, you begin to get hammers and cogs and wheels and you can start building nano machines,” said Salaita.

The Next Generation

Salaita is among several dozen labs demoing the practical uses of DNA devices.

For example, our cells are full of long-haul driver proteins that carry nutrients and other cargo throughout their interior by following specific highways (it eerily looks like a person walking down a tightrope). Just as too much traffic damages our roadways, changes in our cells’ logistical players can also harm the cell’s skeleton. Here, scientists have used DNA “handles” to measure force-induced changes like stretching, unfolding, and rupture of molecules involved in our cells’ distribution system to look for signs of trouble.

Then there are DNA tension sensors, which act like scales and other force gauges in our macroscopic world. Made up of a stretchable DNA “spring” to extend with force, and a fluorescent “ruler” that measures the extension, each sensor is anchored at one end (generally, the glass bottom of a Petri dish) and binds to a cell at the other. If the pulling force exceeds a certain threshold, the “spring” unfolds and quenches the fluorescent light in the ruler, giving scientists a warning that the cellular tugging is too strong.

The work may sound abstruse, but its implications are plenty. One is for CAR-T, the revolutionary cancer treatment that uses gene therapy to amp up immune cells with better “graspers” to target tumor cells. The “kiss of death” between graspers and tumors are extremely difficult to measure because it’s light and fleeting. Using a DNA tension sensor, the team was able to track the force during the interaction, which could help scientists engineer better CAR-T therapies. A similar construct, the DNA tension gauge tether, irreversibly ruptures under too much force. The gauge is used to track how stem cells develop into brain cells under mechanical forces, and how immune cells track down and recognize foreign invasion.

“[Immune] T cells are constantly sampling cells throughout your body using these mechanical tugs. They bind and pull on proteins on a cell’s surface and, if the bond is strong, that’s a signal that the T cell has found a foreign agent,” explained Salaita. DNA devices provide an unprecedented look at these forces in the immune system, which in turn could predict how strongly the body will mount an immune response.

To the authors, however, the most promising emerging DNA devices don’t just observe—they can also generate forces. DNA walkers, for example, uses DNA feet to transport (and sort) molecular cargo while walking down a track also made of DNA strands. When the feet “bind” to the “track” (A to T, C to G), it releases energy that propel the walker forward.

Even more exciting are self-assembling DNA machines. The field has DNA-based devices that “transmit, sense and generate mechanical forces,” the authors said. But eventually, their integration will produce nanomachines that “exert mechanical control over living systems.”

The Fourth Industrial Revolution

As costs keep dropping, the authors believe we’ll witness even more creative and sophisticated DNA nanomachines.

Several hiccups do stand in the way. Like other biomolecules, foreign DNA can be chopped up by the body’s immune system as an “invader.” However, the team believes that the limitation won’t be a problem in the next few years as biochemistry develops chemically-modified artificial DNA letters that resist the body’s scissors.

Another problem is that the DNA devices can generate very little force—less than a billionth the weight of a paperclip, which is a little too low to efficiently control forces in our cells. The authors have a solution here too: coupling many force-generating DNA units together, or engineer “translators” that can turn electrical energy into mechanical force—similar to the way our muscles work.

Fundamentally, any advancements in DNA mechanotechnology won’t just benefit medicine; they will also feed back into the design of nanomaterials. The “techniques, tools and design principles…are not specific” to DNA, the authors said. Add in computer-aided design templates, similar to those used in 3D printing, and “potentially anyone can dream up a nano-machine design and make it a reality,” said Salaita.

 

DNA ‘Origami’ takes Flight in Emerging Field of Nano Machines – “(a) … tool may eventually be used to fine tune immunotherapies for individual cancer patients”

DNA mechanotechnology expands the opportunities for research involving biomedicine and materials sciences, says Khalid Salaita, right, professor of chemistry at Emory University and co-author of the article, along with Aaron Blanchard, left, a graduate student in the Salaita Lab. Credit: Emory University

Just as the steam engine set the stage for the Industrial Revolution, and micro transistors sparked the digital age, nanoscale devices made from DNA are opening up a new era in bio-medical research and materials science.

The journal Science describes the emerging uses of DNA mechanical devices in a “Perspective” article by Khalid Salaita, a professor of chemistry at Emory University, and Aaron Blanchard, a graduate student in the Wallace H. Coulter Department of Biomedical Engineering, a joint program of Georgia Institute of Technology and Emory.

The article heralds a new field, which Blanchard dubbed “DNA mechanotechnology,” to engineer DNA machines that generate, transmit and sense mechanical forces at the nanoscale.

“For a long time,” Salaita says, “scientists have been good at making micro devices, hundreds of times smaller than the width of a human hair. It’s been more challenging to make functional nano devices, thousands of times smaller than that. But using DNA as the component parts is making it possible to build extremely elaborate nano devices because the DNA parts self-assemble.”

DNA, or deoxyribonucleic acid, stores and transmits genetic information as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C) and thymine (T). The DNA bases have a natural affinity to pair up with each other—A with T and C with G. Synthetic strands of DNA can be combined with natural DNA strands from bacteriophages. By moving around the sequence of letters on the strands, researchers can get the DNA strands to bind together in ways that create different shapes. The stiffness of DNA strands can also easily be adjusted, so they remain straight as a piece of dry spaghetti or bend and coil like boiled spaghetti.

The idea of using DNA as a construction material goes back to the 1980s, when biochemist Nadrian Seeman pioneered DNA nanotechnology. This field uses strands DNA to make functional devices at the nanoscale. The ability to make these precise, three-dimensional structures began as a novelty, nicknamed DNA origami, resulting in objects such as a microscopic map of the world and, more recently, the tiniest-ever game of tic-tac-toe, played on a DNA board.

Work on novelty objects continues to provide new insights into the mechanical properties of DNA. These insights are driving the ability to make DNA machines that generate, transmit and sense mechanical forces.

“If you put together these three main components of mechanical devices, you begin to get hammers and cogs and wheels and you can start building nano machines,” Salaita says. “DNA mechanotechnology expands the opportunities for research involving biomedicine and materials science. It’s like discovering a new continent and opening up fresh territory to explore.”

Potential uses for such devices include drug delivery devices in the form of nano capsules that open up when they reach a target site, nano computers and nano robots working on nanoscale assembly lines.

The use of DNA self-assembly by the genomics industry, for biomedical research and diagnostics, is further propelling DNA mechanotechnology, making DNA synthesis inexpensive and readily available. “Potentially anyone can dream up a nano-machine design and make it a reality,” Salaita says.

He gives the example of creating a pair of nano scissors. “You know that you need two rigid rods and that they need to be linked by a pivot mechanism,” he says. “By tinkering with some open-source software, you can create this design and then go onto a computer and place an order to custom synthesize your design. You’ll receive your order in a tube. You simply put the tube contents into a solution, let your device self-assemble, and then use a microscope to see if it works the way you thought that it would.”

Salaita’s lab is one of only about 100 around the world working at the forefront of DNA mechanotechnology. He and Blanchard developed the world’s strongest synthetic DNA-based motor, which was recently reported in Nano Letters.

A key focus of Salaita’s research is mapping and measuring how cells push and pull to learn more about the mechanical forces involved in the human immune system.

Salaita developed the first DNA force gauges for cells, providing the first detailed view of the mechanical forces that one molecule applies to another molecule across the entire surface of a living cell. Mapping such forces may help to diagnose and treat diseases related to cellular mechanics. Cancer cells, for instance, move differently from normal cells, and it is unclear whether that difference is a cause or an effect of the disease.

In 2016, Salaita used these DNA force gauges to provide the first direct evidence for the mechanical forces of T cells, the security guards of the immune system. His lab showed how T cells use a kind of mechanical “handshake” or tug to test whether a cell they encounter is a friend or foe. These mechanical tugs are central to a T cell’s decision for whether to mount an immune response.

“Your blood contains millions of different types of T cells, and each T cell is evolved to detect a certain pathogen or foreign agent,” Salaita explains. “T cells are constantly sampling cells throughout your body using these mechanical tugs. They bind and pull on proteins on a cell’s surface and, if the bond is strong, that’s a signal that the T cell has found a foreign agent.”

Salaita’s lab built on this discovery in a paper recently published in the Proceedings of the National Academy of Sciences (PNAS). Work led by Emory chemistry graduate student Rong Ma refined the sensitivity of the DNA force gauges. Not only can they detect these mechanical tugs at a force so slight that it is nearly one-billionth the weight of a paperclip, they can also capture evidence of tugs as brief as the blink of an eye.

The research provides an unprecedented look at the mechanical forces involved in the immune system. “We showed that, in addition to being evolved to detect certain foreign agents, T cells will also apply very brief mechanical tugs to foreign agents that are a near match,” Salaita says. “The frequency and duration of the tug depends on how closely the foreign agent is matched to the T cell receptor.”

The result provides a tool to predict how strong of an immune response a T cell will mount. “We hope this tool may eventually be used to fine tune immunotherapies for individual cancer patients,” Salaita says. “It could potentially help engineer T cells to go after particular cancer cells.”

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Explore further T cells use ‘handshakes’ to sort friends from foes

Computer scientists create reprogrammable molecular computing system – “Nano DNA Apps”

 

“Biology is proof that chemistry is inherently information-based and can store information that can direct algorithmic behavior at the molecular level,” he says.

Computer scientists at Caltech have designed DNA molecules that can carry out reprogrammable computations, for the first time creating so-called algorithmic self-assembly in which the same “hardware” can be configured to run different “software.”

In a paper published in Nature on March 21, a team headed by Caltech’s Erik Winfree (PhD ’98), professor of computer science, computation and neural systems, and bioengineering, showed how the DNA computations could execute six-bit algorithms that perform simple tasks. The system is analogous to a computer, but instead of using transistors and diodes, it uses molecules to represent a six-bit binary number (for example, 011001) as input, during computation, and as output. One such algorithm determines whether the number of 1-bits in the input is odd or even, (the example above would be odd, since it has three 1-bits); while another determines whether the input is a palindrome; and yet another generates random numbers.

 

“Think of them as nano apps,” says Damien Woods, professor of computer science at Maynooth University near Dublin, Ireland, and one of two lead authors of the study. “The ability to run any type of software program without having to change the hardware is what allowed computers to become so useful. We are implementing that idea in molecules, essentially embedding an algorithm within chemistry to control chemical processes.”

The system works by self-assembly: small, specially designed DNA strands stick together to build a logic circuit while simultaneously executing the circuit algorithm. Starting with the original six bits that represent the input, the system adds row after row of molecules–progressively running the algorithm.

 

Modern digital electronic computers use electricity flowing through circuits to manipulate information; here, the rows of DNA strands sticking together perform the computation. The end result is a test tube filled with billions of completed algorithms, each one resembling a knitted scarf of DNA, representing a readout of the computation. The pattern on each “scarf” gives you the solution to the algorithm that you were running. The system can be reprogrammed to run a different algorithm by simply selecting a different subset of strands from the roughly 700 that constitute the system.

 

“We were surprised by the versatility of programs we were able to design, despite being limited to six-bit inputs,” says David Doty, fellow lead author and assistant professor of computer science at the University of California, Davis.

“When we began experiments, we had only designed three programs. But once we started using the system, we realized just how much potential it has. It was the same excitement we felt the first time we programmed a computer, and we became intensely curious about what else these strands could do. By the end, we had designed and run a total of 21 circuits.”

 

The researchers were able to experimentally demonstrate six-bit molecular algorithms for a diverse set of tasks. In mathematics, their circuits tested inputs to assess if they were multiples of three, performed equality checks, and counted to 63. Other circuits drew “pictures” on the DNA “scarves,” such as a zigzag, a double helix, and irregularly spaced diamonds.

Probabilistic behaviors were also demonstrated, including random walks, as well as a clever algorithm (originally developed by computer pioneer John von Neumann) for obtaining a fair 50/50 random choice from a biased coin.

 

Both Woods and Doty were theoretical computer scientists when beginning this research, so they had to learn a new set of “wet lab” skills that are typically more in the wheelhouse of bioengineers and biophysicists.

“When engineering requires crossing disciplines, there is a significant barrier to entry,” says Winfree. “Computer engineering overcame this barrier by designing machines that are reprogrammable at a high level–so today’s programmers don’t need to know transistor physics. Our goal in this work was to show that molecular systems similarly can be programmed at a high level, so that in the future, tomorrow’s molecular programmers can unleash their creativity without having to master multiple disciplines.”

“Unlike previous experiments on molecules specially designed to execute a single computation, reprogramming our system to solve these different problems was as simple as choosing different test tubes to mix together,” Woods says. “We were programming at the lab bench.”

Although DNA computers have the potential to perform more complex computations than the ones featured in the Nature paper, Winfree cautions that one should not expect them to start replacing the standard silicon microchip computers. That is not the point of this research.

“These are rudimentary computations, but they have the power to teach us more about how simple molecular processes like self-assembly can encode information and carry out algorithms. Biology is proof that chemistry is inherently information-based and can store information that can direct algorithmic behavior at the molecular level,” he says.

 

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly

Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin & Erik Winfree
Naturevolume 567, pages366–372 (2019)

 

NEW NANOTECH DRIVES HEALING BY “TALKING” TO WOUNDS

A Time To Heal

Researchers from Imperial College London have created a new molecule that can “talk” to the cells in the area near injured tissues to encourage wound healing.

“This intelligent healing is useful during every phase of the healing process, has the potential to increase the body’s chance to recover, and has far-reaching uses on many different types of wounds,” lead researcher Ben Almquist said in a news release.

Setting A TrAP

The Imperial team describes the wound-healing molecules, which it calls traction force-activated payloads (TrAPs), in a study published Monday in the journal Advanced Materials.

The first step to creating TrAPs was folding segments of DNA into aptamers, which are three-dimensional shapes that latch tightly to proteins. The researchers then added a “handle” to one end of the aptamer.

As cells navigated the area near a wound during lab testing, they would pull on this handle, causing the aptamer to open and release proteins that encouraged wound healing. By changing the handle, the researchers found they could control which cells activated the TrAPs.

According to Almquist, “TrAPs provide a flexible method of actively communicating with wounds, as well as key instructions when and where they are needed.”

To The Clinic

It can take a long time for research to move from the laboratory to the clinical trial stage, but the TrAPs team might be able to speed along the path. That’s because aptamers are already used for drug delivery, meaning they’re already considered safe for human use.

TrAPs are also fairly straightforward to create, meaning it wouldn’t be difficult to scale the technology to industrial levels. According to the researchers’ paper, doctors could then deliver the TrAPs via anything from collagen sponges to polyacrylamide gels. So if future testing goes well, the molecules could soon change how we heal a variety of wounds.

READ MORE: New Material Could ‘Drive Wound Healing’ Using the Body’s Inbuilt Healing System [Imperial College London]

More on aptamers: New Nanobots Kill Cancerous Tumors by Cutting off Their Blood Supply

Story Source:

Materials provided by Imperial College London. Original written by Caroline Brogan. Note: Content may be edited for style and length.

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Journal Reference:

1. Anna Stejskalová, Nuria Oliva, Frances J. England, Benjamin D. Almquist. Biologically Inspired, Cell‐Selective Release of Aptamer‐Trapped Growth Factors by Traction Forces. Advanced Materials, 2018 DOI: 10.1002/adma.201806380

Synthetic organisms are about to challenge what ’being’ and ‘alive’ really means

We need to begin a serious debate about whether artificially evolved humans are our future, and if we should put an end to these experiments before it is too late.

In 2016, Craig Venter and his team at Synthetic Genomics announced that they had created a lifeform called JCVI-syn3.0, whose genome consisted of only 473 genes.

This stripped-down organism was a significant breakthrough in the development of artificial life as it enabled us to understand more fully what individual genes do. (In the case of JCVI-syn3.0, most of them were used to create RNA and proteins, preserve genetic fidelity during reproduction and create the cell membrane.

The functions of about a third remain a mystery.)

Venter’s achievement followed an earlier breakthrough in 2014, when Floyd Romesberg at Romesberg Lab in California succeeded in creating xeno nucleic acid (XNA), a synthetic alternative to DNA, using amino acids not found among the naturally occurring four nucleotides: adenine, cytosine, guanine and thymine. 

And, most recently we have seen huge advances in the use of CRISPR, a gene-editing tool that allows substitution or injection of DNA sequences at chosen locations in a genome.

Read More: Why Bill Gates is Betting on this Synthetic Biology Start-Up

Together, these developments mean that in 2019 we will have to take seriously the possibility of our developing multicellular artificial life, and we will need to start thinking about the ethical and philosophical challenges such a possibility brings up.

In the near future we can reasonably anticipate that a large number of unnatural single-cell life forms will be created using artificially edited genomes to correct for genetic defects or to add new features to an organism’s phenotype.

It is already possible to design bacterial forms, for example, that can metabolise pollutants or produce particular substances.

We can also anticipate that new life forms may be created that have never existed in nature through the use of conventional and perhaps artificially arranged codons (nucleotide sequences that manage protein synthesis).

These are likely to make use of the conventional machinery of mitotic cell reproduction and of conventional ribosomes, creating proteins through RNA or XNA interpretation.

And there will be increasing pressures to continue this research. We may need to accelerate the evolution of terrestrial life forms, for example, including homo sapiens, so that they carry traits and capabilities needed for life in space or even on our own changing planet. 

All of this will bring up serious issues as to how we see ourselves – and behave – as a species.

While the creation of multicellular organisms that are capable of sexual reproduction is still a long way off, in 2019 we will need to begin a serious debate about whether artificially evolved humans are our future, and if we should put an end to these experiments before it is too late.

By Vint Cerf of ‘Wired’

MIT Team invents method to shrink objects to the nanoscale – “Implosion Manufacturing” – Applications from Optics to Medicine to Robotics – Materials from Quantum Dots, Metals and DNA

According to professor Ed Boyden, many research labs are already stocked with the equipment required for this kind of fabrication. Credit: The researchers

” … These tiny structures could have applications in many fields, from optics to medicine to robotics, the researchers say.”

MIT researchers have invented a way to fabricate nanoscale 3-D objects of nearly any shape. They can also pattern the objects with a variety of useful materials, including metals, quantum dots, and DNA.

“It’s a way of putting nearly any kind of material into a 3-D pattern with nanoscale precision,” says Edward Boyden, an associate professor of biological engineering and of brain and cognitive sciences at MIT.

Using the new technique, the researchers can create any shape and structure they want by patterning a polymer scaffold with a laser. After attaching other useful materials to the scaffold, they shrink it, generating structures one thousandth the volume of the original.

These tiny structures could have applications in many fields, from optics to medicine to robotics, the researchers say. The technique uses equipment that many biology and materials science labs already have, making it widely accessible for researchers who want to try it.

Boyden, who is also a member of MIT’s Media Lab, McGovern Institute for Brain Research, and Koch Institute for Integrative Cancer Research, is one of the senior authors of the paper, which appears in the Dec. 13 issue of Science. The other senior author is Adam Marblestone, a Media Lab research affiliate, and the paper’s lead authors are graduate students Daniel Oran and Samuel Rodriques.

Implosion fabrication

Existing techniques for creating nanostructures are limited in what they can accomplish. Etching patterns onto a surface with light can produce 2-D nanostructures but doesn’t work for 3-D structures. It is possible to make 3-D nanostructures by gradually adding layers on top of each other, but this process is slow and challenging. And, while methods exist that can directly 3-D print nanoscale objects, they are restricted to specialized materials like polymers and plastics, which lack the functional properties necessary for many applications. Furthermore, they can only generate self-supporting structures. (The technique can yield a solid pyramid, for example, but not a linked chain or a hollow sphere.)

To overcome these limitations, Boyden and his students decided to adapt a technique that his lab developed a few years ago for high-resolution imaging of brain tissue. This technique, known as expansion microscopy, involves embedding tissue into a hydrogel and then expanding it, allowing for high resolution imaging with a regular microscope. Hundreds of research groups in biology and medicine are now using expansion microscopy, since it enables 3-D visualization of cells and tissues with ordinary hardware.

By reversing this process, the researchers found that they could create large-scale objects embedded in expanded hydrogels and then shrink them to the nanoscale, an approach that they call “implosion fabrication.”

As they did for expansion microscopy, the researchers used a very absorbent material made of polyacrylate, commonly found in diapers, as the scaffold for their nanofabrication process. The scaffold is bathed in a solution that contains molecules of fluorescein, which attach to the scaffold when they are activated by laser light.

Using two-photon microscopy, which allows for precise targeting of points deep within a structure, the researchers attach fluorescein molecules to specific locations within the gel. The fluorescein molecules act as anchors that can bind to other types of molecules that the researchers add.

“You attach the anchors where you want with light, and later you can attach whatever you want to the anchors,” Boyden says. “It could be a quantum dot, it could be a piece of DNA, it could be a gold nanoparticle.”

“It’s a bit like film photography—a latent image is formed by exposing a sensitive material in a gel to light. Then, you can develop that latent image into a real image by attaching another material, silver, afterwards. In this way implosion fabrication can create all sorts of structures, including gradients, unconnected structures, and multi-material patterns,” Oran says.

Once the desired molecules are attached in the right locations, the researchers shrink the entire structure by adding an acid. The acid blocks the negative charges in the polyacrylate gel so that they no longer repel each other, causing the gel to contract. Using this technique, the researchers can shrink the objects 10-fold in each dimension (for an overall 1,000-fold reduction in volume). This ability to shrink not only allows for increased resolution, but also makes it possible to assemble materials in a low-density scaffold. This enables easy access for modification, and later the material becomes a dense solid when it is shrunk.

“People have been trying to invent better equipment to make smaller nanomaterials for years, but we realized that if you just use existing systems and embed your materials in this gel, you can shrink them down to the nanoscale, without distorting the patterns,” Rodriques says.

Currently, the researchers can create objects that are around 1 cubic millimeter, patterned with a resolution of 50 nanometers. There is a tradeoff between size and resolution: If the researchers want to make larger objects, about 1 cubic centimeter, they can achieve a resolution of about 500 nanometers. However, that resolution could be improved with further refinement of the process, the researchers say.

Better optics

The MIT team is now exploring potential applications for this technology, and they anticipate that some of the earliest applications might be in optics—for example, making specialized lenses that could be used to study the fundamental properties of light. This technique might also allow for the fabrication of smaller, better lenses for applications such as cell phone cameras, microscopes, or endoscopes, the researchers say. Farther in the future, the researchers say that this approach could be used to build nanoscale electronics or robots.

“There are all kinds of things you can do with this,” Boyden says. “Democratizing nanofabrication could open up frontiers we can’t yet imagine.”

Many research labs are already stocked with the equipment required for this kind of fabrication. “With a laser you can already find in many biology labs, you can scan a pattern, then deposit metals, semiconductors, or DNA, and then shrink it down,” Boyden says.

 Explore further: High-resolution imaging with conventional microscopes

More information: D. Oran el al., “3D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds,” Science (2018). science.sciencemag.org/cgi/doi … 1126/science.aau5119

T.E. Long el al., “Printing nanomaterials in shrinking gels,” Science (2018). science.sciencemag.org/cgi/doi … 1126/science.aav5712

Journal reference: Science  

Provided by: Massachusetts Institute of Technology

 

‘Swiss army knife’ Nanovaccine carries multiple weapons to battle tumors – cancer

Source: National Institute of Biomedical Imaging and Bioengineering

Summary: Researchers have developed a synergistic cancer nanovaccine packing DNA and RNA sequences that modulate the immune response, along with anti-tumor antigens, into one small nanoparticle.

(Above) Large particles (left) containing the DNA and RNA components are coated with electronically charged molecules that shrink the particle. The tumor-specific neoantigen is then complexed with the surface to complete construction of the nanovaccine. Upper left: electron micrograph of large particle. Credit: Zhu, et al. Nat Comm.

 

 

Scientists are using their increasing knowledge of the complex interaction between cancer and the immune system to engineer increasingly potent anti-cancer vaccines. The nanovaccine produced an immune response that specifically killed tumor tissue, while simultaneously inhibiting tumor-induced immune suppression to block lung tumor growth in a mouse model of metastatic colon cancer.

Now researchers at the National Institute of Biomedical Imaging and Bioengineering (NIBIB) have developed a synergistic nanovaccine packing DNA and RNA sequences that modulate the immune response, along with anti-tumor antigens, into one small nanoparticle. The nanovaccine produced an immune response that specifically killed tumor tissue, while simultaneously inhibiting tumor-induced immune suppression. Together this blocked lung tumor growth in a mouse model of metastatic colon cancer.

The molecular dance between cancer and the immune system is a complex one and scientists continue to identify the specific molecular pathways that rev up or tamp down the immune system. Biomedical engineers are using this knowledge to create nanoparticles that can carry different molecular agents that target these pathways. The goal is to simultaneously stimulate the immune system to specifically attack the tumor while also inhibiting the suppression of the immune system, which often occurs in cancer patients. The aim is to press on the gas pedal of the immune system while also releasing the emergency brake.

A key hurdle is to design a system to reproducibly and efficiently create a nanoparticle loaded with multiple agents that synergize to mount an enhanced immune attack on the tumor. Engineers at the NIBIB report the development and testing of such a nanovaccine in the November issue of Nature Communications.

Making all the parts fit

Guizhi Zhu, Ph.D., a post-doctoral fellow in the NIBIB Laboratory of Molecular Imaging and Nanomedicine (LOMIN) and lead author on the study, explains the challenge. “We are very excited about putting multiple cooperating molecules that have anti-cancer activity into one nanovaccine to increase effectiveness. However, the bioengineering challenge is fitting everything in to a small particle and designing a way to maintain its structural integrity and biological activity.”

Zhu and his colleagues have created what they call a “self-assembling, intertwining DNA-RNA nanocapsule loaded with tumor neoantigens.” They describe it as a synergistic vaccine because the components work together to stimulate and enhance an immune attack against a tumor.

The DNA component of the vaccine is known to stimulate immune cells to work with partner immune cells for antitumor activation. The tumor neoantigens are pieces of proteins that are only present in the tumor; so, when the DNA attracts the immune cells, the immune cells interact with the tumor neoantigens and mount an expanded and specific immune response against the tumor. The RNA is the component that inhibits suppression of the immune system. The engineered RNA binds to and degrades the tumor’s mRNA that makes a protein called STAT3. Thus, the bound mRNA is blocked from making STAT3, which may suppress the immune system. The result is an enhanced immune response that is specific to the tumor and does not harm healthy tissues.

In addition to engineering a system where the DNA, RNA and tumor neoantigens self-assemble into a stable nanoparticle, an important final step in the process is shrinking the particle. Zhu explains: “Shrinking the particle is a critical step for activating an immune response. This is because a very small nanoparticle can more readily move through the lymphatic vessels to reach the parts of the immune system such as lymph nodes. A process that is essential for immune activation.”

The method for shrinking also had to be engineered. This was achieved by coating the particle with a positively charged polypeptide that interacts with the negatively charged DNA and RNA components to condense it to one-tenth of its original size.

Testing the nanovaccine

To create a model of metastatic colon cancer, the researchers injected human colon cancer cells into the circulation of mice. The cells infiltrate different organs and grow as metastatic colon cancer. One of the prime sites of metastasis is the lung.

The nanovaccine was injected under the skin of the mice 10, 16, and 22 days after the colon cancer cells were injected. To compare to the nanovaccine, two control groups of mice were analyzed; one group was injected with just the DNA and the neoantigen in solution but not formed into a nanovaccine particle, and the second control group was injected with an inert buffer solution.

At 40 days into the experiment, lung tumors from the nanovaccine-treated and the control groups were assessed by PET-CT imaging, and then removed and weighed. In mice treated with the nanovaccine, tumors were consistently one tenth the size of the tumors that were found in mice in both control groups.

Further testing revealed that mice receiving the nanovaccine had a significant increase in circulating cytotoxic T lymphocytes (CTLs) that specifically targeted the neoantigen on the colon cancer cells. CTLs are cells that attack and kill virus-infected cells and those damaged in other ways, such as cancerous cells.

An important aspect of the nanovaccine approach is that it mounts an anti-tumor immune response that circulates through the system, and therefore is particularly valuable for finding and inhibiting metastatic tumors growing throughout the body.

The researchers view their nanovaccine as an important part of eventual therapies combining immunotherapy with other cancer killing approaches.

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Story Source:

Materials provided by National Institute of Biomedical Imaging and Bioengineering. Note: Content may be edited for style and length.

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Journal Reference:

1. Guizhi Zhu, Lei Mei, Harshad D. Vishwasrao, Orit Jacobson, Zhantong Wang, Yijing Liu, Bryant C. Yung, Xiao Fu, Albert Jin, Gang Niu, Qin Wang, Fuwu Zhang, Hari Shroff, Xiaoyuan Chen. Intertwining DNA-RNA nanocapsules loaded with tumor neoantigens as synergistic nanovaccines for cancer immunotherapy. Nature Communications, 2017; 8 (1) DOI: 10.1038/s41467-017-01386-7