DNA

Subterms

    Latest story

    150 Shares169 Views

    Engineers find a new way to convert carbon dioxide into useful products

    by

    MIT chemical engineers have devised an efficient way to convert carbon dioxide to carbon monoxide, a chemical precursor that can be used to generate useful compounds such as ethanol and other fuels.

    If scaled up for industrial use, this process could help to remove carbon dioxide from power plants and other sources, reducing the amount of greenhouse gases that are released into the atmosphere.

    “This would allow you to take carbon dioxide from emissions or dissolved in the ocean, and convert it into profitable chemicals. It’s really a path forward for decarbonization because we can take CO2, which is a greenhouse gas, and turn it into things that are useful for chemical manufacture,” says Ariel Furst, the Paul M. Cook Career Development Assistant Professor of Chemical Engineering and the senior author of the study.

    The new approach uses electricity to perform the chemical conversion, with help from a catalyst that is tethered to the electrode surface by strands of DNA. This DNA acts like Velcro to keep all the reaction components in close proximity, making the reaction much more efficient than if all the components were floating in solution.

    Furst has started a company called Helix Carbon to further develop the technology. Former MIT postdoc Gang Fan is the lead author of the paper, which appears in the Journal of the American Chemical Society Au. Other authors include Nathan Corbin PhD ’21, Minju Chung PhD ’23, former MIT postdocs Thomas Gill and Amruta Karbelkar, and Evan Moore ’23.

    Breaking down CO2

    Converting carbon dioxide into useful products requires first turning it into carbon monoxide. One way to do this is with electricity, but the amount of energy required for that type of electrocatalysis is prohibitively expensive.

    To try to bring down those costs, researchers have tried using electrocatalysts, which can speed up the reaction and reduce the amount of energy that needs to be added to the system. One type of catalyst used for this reaction is a class of molecules known as porphyrins, which contain metals such as iron or cobalt and are similar in structure to the heme molecules that carry oxygen in blood. 

    During this type of electrochemical reaction, carbon dioxide is dissolved in water within an electrochemical device, which contains an electrode that drives the reaction. The catalysts are also suspended in the solution. However, this setup isn’t very efficient because the carbon dioxide and the catalysts need to encounter each other at the electrode surface, which doesn’t happen very often.

    To make the reaction occur more frequently, which would boost the efficiency of the electrochemical conversion, Furst began working on ways to attach the catalysts to the surface of the electrode. DNA seemed to be the ideal choice for this application.

    “DNA is relatively inexpensive, you can modify it chemically, and you can control the interaction between two strands by changing the sequences,” she says. “It’s like a sequence-specific Velcro that has very strong but reversible interactions that you can control.”

    To attach single strands of DNA to a carbon electrode, the researchers used two “chemical handles,” one on the DNA and one on the electrode. These handles can be snapped together, forming a permanent bond. A complementary DNA sequence is then attached to the porphyrin catalyst, so that when the catalyst is added to the solution, it will bind reversibly to the DNA that’s already attached to the electrode — just like Velcro.

    Once this system is set up, the researchers apply a potential (or bias) to the electrode, and the catalyst uses this energy to convert carbon dioxide in the solution into carbon monoxide. The reaction also generates a small amount of hydrogen gas, from the water. After the catalysts wear out, they can be released from the surface by heating the system to break the reversible bonds between the two DNA strands, and replaced with new ones.

    An efficient reaction

    Using this approach, the researchers were able to boost the Faradaic efficiency of the reaction to 100 percent, meaning that all of the electrical energy that goes into the system goes directly into the chemical reactions, with no energy wasted. When the catalysts are not tethered by DNA, the Faradaic efficiency is only about 40 percent.

    This technology could be scaled up for industrial use fairly easily, Furst says, because the carbon electrodes the researchers used are much less expensive than conventional metal electrodes. The catalysts are also inexpensive, as they don’t contain any precious metals, and only a small concentration of the catalyst is needed on the electrode surface.

    By swapping in different catalysts, the researchers plan to try making other products such as methanol and ethanol using this approach. Helix Carbon, the company started by Furst, is also working on further developing the technology for potential commercial use.

    The research was funded by the U.S. Army Research Office, the CIFAR Azrieli Global Scholars Program, the MIT Energy Initiative, and the MIT Deshpande Center. More

    More stories

    • 75 Shares169 Views

      in Energy

      Turning carbon dioxide into valuable products

      by

      Carbon dioxide (CO2) is a major contributor to climate change and a significant product of many human activities, notably industrial manufacturing. A major goal in the energy field has been to chemically convert emitted CO2 into valuable chemicals or fuels. But while CO2 is available in abundance, it has not yet been widely used to generate value-added products. Why not?

      The reason is that CO2 molecules are highly stable and therefore not prone to being chemically converted to a different form. Researchers have sought materials and device designs that could help spur that conversion, but nothing has worked well enough to yield an efficient, cost-effective system.

      Two years ago, Ariel Furst, the Raymond (1921) and Helen St. Laurent Career Development Professor of Chemical Engineering at MIT, decided to try using something different — a material that gets more attention in discussions of biology than of chemical engineering. Already, results from work in her lab suggest that her unusual approach is paying off.

      The stumbling block

      The challenge begins with the first step in the CO2 conversion process. Before being transformed into a useful product, CO2 must be chemically converted into carbon monoxide (CO). That conversion can be encouraged using electrochemistry, a process in which input voltage provides the extra energy needed to make the stable CO2 molecules react. The problem is that achieving the CO2-to-CO conversion requires large energy inputs — and even then, CO makes up only a small fraction of the products that are formed.

      To explore opportunities for improving this process, Furst and her research group focused on the electrocatalyst, a material that enhances the rate of a chemical reaction without being consumed in the process. The catalyst is key to successful operation. Inside an electrochemical device, the catalyst is often suspended in an aqueous (water-based) solution. When an electric potential (essentially a voltage) is applied to a submerged electrode, dissolved CO2 will — helped by the catalyst — be converted to CO.

      But there’s one stumbling block: The catalyst and the CO2 must meet on the surface of the electrode for the reaction to occur. In some studies, the catalyst is dispersed in the solution, but that approach requires more catalyst and isn’t very efficient, according to Furst. “You have to both wait for the diffusion of CO2 to the catalyst and for the catalyst to reach the electrode before the reaction can occur,” she explains. As a result, researchers worldwide have been exploring different methods of “immobilizing” the catalyst on the electrode.

      Connecting the catalyst and the electrode

      Before Furst could delve into that challenge, she needed to decide which of the two types of CO2 conversion catalysts to work with: the traditional solid-state catalyst or a catalyst made up of small molecules. In examining the literature, she concluded that small-molecule catalysts held the most promise. While their conversion efficiency tends to be lower than that of solid-state versions, molecular catalysts offer one important advantage: They can be tuned to emphasize reactions and products of interest.

      Two approaches are commonly used to immobilize small-molecule catalysts on an electrode. One involves linking the catalyst to the electrode by strong covalent bonds — a type of bond in which atoms share electrons; the result is a strong, essentially permanent connection. The other sets up a non-covalent attachment between the catalyst and the electrode; unlike a covalent bond, this connection can easily be broken.

      Neither approach is ideal. In the former case, the catalyst and electrode are firmly attached, ensuring efficient reactions; but when the activity of the catalyst degrades over time (which it will), the electrode can no longer be accessed. In the latter case, a degraded catalyst can be removed; but the exact placement of the small molecules of the catalyst on the electrode can’t be controlled, leading to an inconsistent, often decreasing, catalytic efficiency — and simply increasing the amount of catalyst on the electrode surface without concern for where the molecules are placed doesn’t solve the problem.

      What was needed was a way to position the small-molecule catalyst firmly and accurately on the electrode and then release it when it degrades. For that task, Furst turned to what she and her team regard as a kind of “programmable molecular Velcro”: deoxyribonucleic acid, or DNA.

      Adding DNA to the mix

      Mention DNA to most people, and they think of biological functions in living things. But the members of Furst’s lab view DNA as more than just genetic code. “DNA has these really cool physical properties as a biomaterial that people don’t often think about,” she says. “DNA can be used as a molecular Velcro that can stick things together with very high precision.”

      Furst knew that DNA sequences had previously been used to immobilize molecules on surfaces for other purposes. So she devised a plan to use DNA to direct the immobilization of catalysts for CO2 conversion.

      Her approach depends on a well-understood behavior of DNA called hybridization. The familiar DNA structure is a double helix that forms when two complementary strands connect. When the sequence of bases (the four building blocks of DNA) in the individual strands match up, hydrogen bonds form between complementary bases, firmly linking the strands together.

      Using that behavior for catalyst immobilization involves two steps. First, the researchers attach a single strand of DNA to the electrode. Then they attach a complementary strand to the catalyst that is floating in the aqueous solution. When the latter strand gets near the former, the two strands hybridize; they become linked by multiple hydrogen bonds between properly paired bases. As a result, the catalyst is firmly affixed to the electrode by means of two interlocked, self-assembled DNA strands, one connected to the electrode and the other to the catalyst.

      Better still, the two strands can be detached from one another. “The connection is stable, but if we heat it up, we can remove the secondary strand that has the catalyst on it,” says Furst. “So we can de-hybridize it. That allows us to recycle our electrode surfaces — without having to disassemble the device or do any harsh chemical steps.”

      Experimental investigation

      To explore that idea, Furst and her team — postdocs Gang Fan and Thomas Gill, former graduate student Nathan Corbin PhD ’21, and former postdoc Amruta Karbelkar — performed a series of experiments using three small-molecule catalysts based on porphyrins, a group of compounds that are biologically important for processes ranging from enzyme activity to oxygen transport. Two of the catalysts involve a synthetic porphyrin plus a metal center of either cobalt or iron. The third catalyst is hemin, a natural porphyrin compound used to treat porphyria, a set of disorders that can affect the nervous system. “So even the small-molecule catalysts we chose are kind of inspired by nature,” comments Furst.

      In their experiments, the researchers first needed to modify single strands of DNA and deposit them on one of the electrodes submerged in the solution inside their electrochemical cell. Though this sounds straightforward, it did require some new chemistry. Led by Karbelkar and third-year undergraduate researcher Rachel Ahlmark, the team developed a fast, easy way to attach DNA to electrodes. For this work, the researchers’ focus was on attaching DNA, but the “tethering” chemistry they developed can also be used to attach enzymes (protein catalysts), and Furst believes it will be highly useful as a general strategy for modifying carbon electrodes.

      Once the single strands of DNA were deposited on the electrode, the researchers synthesized complementary strands and attached to them one of the three catalysts. When the DNA strands with the catalyst were added to the solution in the electrochemical cell, they readily hybridized with the DNA strands on the electrode. After half-an-hour, the researchers applied a voltage to the electrode to chemically convert CO2 dissolved in the solution and used a gas chromatograph to analyze the makeup of the gases produced by the conversion.

      The team found that when the DNA-linked catalysts were freely dispersed in the solution, they were highly soluble — even when they included small-molecule catalysts that don’t dissolve in water on their own. Indeed, while porphyrin-based catalysts in solution often stick together, once the DNA strands were attached, that counterproductive behavior was no longer evident.

      The DNA-linked catalysts in solution were also more stable than their unmodified counterparts. They didn’t degrade at voltages that caused the unmodified catalysts to degrade. “So just attaching that single strand of DNA to the catalyst in solution makes those catalysts more stable,” says Furst. “We don’t even have to put them on the electrode surface to see improved stability.” When converting CO2 in this way, a stable catalyst will give a steady current over time. Experimental results showed that adding the DNA prevented the catalyst from degrading at voltages of interest for practical devices. Moreover, with all three catalysts in solution, the DNA modification significantly increased the production of CO per minute.

      Allowing the DNA-linked catalyst to hybridize with the DNA connected to the electrode brought further improvements, even compared to the same DNA-linked catalyst in solution. For example, as a result of the DNA-directed assembly, the catalyst ended up firmly attached to the electrode, and the catalyst stability was further enhanced. Despite being highly soluble in aqueous solutions, the DNA-linked catalyst molecules remained hybridized at the surface of the electrode, even under harsh experimental conditions.

      Immobilizing the DNA-linked catalyst on the electrode also significantly increased the rate of CO production. In a series of experiments, the researchers monitored the CO production rate with each of their catalysts in solution without attached DNA strands — the conventional setup — and then with them immobilized by DNA on the electrode. With all three catalysts, the amount of CO generated per minute was far higher when the DNA-linked catalyst was immobilized on the electrode.

      In addition, immobilizing the DNA-linked catalyst on the electrode greatly increased the “selectivity” in terms of the products. One persistent challenge in using CO2 to generate CO in aqueous solutions is that there is an inevitable competition between the formation of CO and the formation of hydrogen. That tendency was eased by adding DNA to the catalyst in solution — and even more so when the catalyst was immobilized on the electrode using DNA. For both the cobalt-porphyrin catalyst and the hemin-based catalyst, the formation of CO relative to hydrogen was significantly higher with the DNA-linked catalyst on the electrode than in solution. With the iron-porphyrin catalyst they were about the same. “With the iron, it doesn’t matter whether it’s in solution or on the electrode,” Furst explains. “Both of them have selectivity for CO, so that’s good, too.”

      Progress and plans

      Furst and her team have now demonstrated that their DNA-based approach combines the advantages of the traditional solid-state catalysts and the newer small-molecule ones. In their experiments, they achieved the highly efficient chemical conversion of CO2 to CO and also were able to control the mix of products formed. And they believe that their technique should prove scalable: DNA is inexpensive and widely available, and the amount of catalyst required is several orders of magnitude lower when it’s immobilized using DNA.

      Based on her work thus far, Furst hypothesizes that the structure and spacing of the small molecules on the electrode may directly impact both catalytic efficiency and product selectivity. Using DNA to control the precise positioning of her small-molecule catalysts, she plans to evaluate those impacts and then extrapolate design parameters that can be applied to other classes of energy-conversion catalysts. Ultimately, she hopes to develop a predictive algorithm that researchers can use as they design electrocatalytic systems for a wide variety of applications.

      This research was supported by a grant from the MIT Energy Initiative Seed Fund.

      This article appears in the Spring 2022 issue of Energy Futures, the magazine of the MIT Energy Initiative. More

    • 100 Shares99 Views

      in Environment

      From bridges to DNA: civil engineering across disciplines

      by

      How is DNA like a bridge? This question is not a riddle or logic game, it is a concern of Johannes Kalliauer’s doctoral thesis.

      As a student at TU Wien in Austria, Kalliauer was faced with a monumental task: combining approaches from civil engineering and theoretical physics to better understand the forces that act on DNA.

      Kalliauer, now a postdoc at the MIT Concrete Sustainability Hub, says he modeled DNA as though it were a beam, using molecular dynamics principles to understand its structural properties.

      “The mechanics of very small objects, like DNA helices, and large ones, like bridges, are quite similar. Each may be understood in terms of Newtonian mechanics. Forces and moments act on each system, subjecting each to deformations like twisting, stretching, and warping,” says Kalliauer.

      As a 2020 article from TU Wien noted, Kalliauer observed a counterintuitive behavior when examining DNA at an atomic level. Unlike a typical spring which becomes less coiled as it is stretched, DNA was observed to become more wound as its length was increased. 

      In situations like these where conventional logic appears to break down, Kalliauer relies on the intuition he has gained as an engineer.

      “To understand this strange behavior in DNA, I turned to a fundamental approach: I examined what was the same about DNA and macroscopic structures and what was different. Civil engineers use methods and calculations which have been developed over centuries and which are very similar to the ones I employed for my thesis,” Kalliauer explains. 

      As Kalliauer continues, “Structural engineering is an incredibly versatile discipline. If you understand it, you can understand atomistic objects like DNA strands and very large ones like galaxies. As a researcher, I rely on it to help me bring new viewpoints to fields like biology. Other civil engineers can and should do the same.”

      Kalliauer, who grew up in a small town in Austria, has spent his life applying unconventional approaches like this across disciplines. “I grew up in a math family. While none of us were engineers, my parents instilled an appreciation for the discipline in me and my two older sisters.”

      After middle school, Kalliauer attended a technical school for civil engineering, where he discovered a fascination for mechanics. He also worked on a construction site to gain practical experience and see engineering applied in a real-world context.

      Kalliauer studied out of interest intensely, working upwards of 100 hours per week to better understand coursework in university. “I asked teachers and professors many questions, often challenging their ideas. Above everything else, I needed to understand things for myself. Doing well on exams was a secondary concern.”

      In university, he studied topics ranging from car crash testing to concrete hinges to biology. As a new member of the CSHub, he is studying how floods may be modeled with the statistical physics-based model provided by lattice density functional theory.

      In doing this, he builds on the work of past and present CSHub researchers like Elli Vartziotis and Katerina Boukin. 

      “It’s important to me that this research has a real impact in the world. I hope my approach to engineering can help researchers and stakeholders understand how floods propagate in urban contexts, so that we may make cities more resilient,” he says. More

    • 113 Shares99 Views

      in Security

      Structures considered key to gene expression are surprisingly fleeting

      by

      In human chromosomes, DNA is coated by proteins to form an exceedingly long beaded string. This “string” is folded into numerous loops, which are believed to help cells control gene expression and facilitate DNA repair, among other functions. A new study from MIT suggests that these loops are very dynamic and shorter-lived than previously thought.

      In the new study, the researchers were able to monitor the movement of one stretch of the genome in a living cell for about two hours. They saw that this stretch was fully looped for only 3 to 6 percent of the time, with the loop lasting for only about 10 to 30 minutes. The findings suggest that scientists’ current understanding of how loops influence gene expression may need to be revised, the researchers say.

      “Many models in the field have been these pictures of static loops regulating these processes. What our new paper shows is that this picture is not really correct,” says Anders Sejr Hansen, the Underwood-Prescott Career Development Assistant Professor of Biological Engineering at MIT. “We suggest that the functional state of these domains is much more dynamic.”

      Hansen is one of the senior authors of the new study, along with Leonid Mirny, a professor in MIT’s Institute for Medical Engineering and Science and the Department of Physics, and Christoph Zechner, a group leader at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, and the Center for Systems Biology Dresden. MIT postdoc Michele Gabriele, recent Harvard University PhD recipient Hugo Brandão, and MIT graduate student Simon Grosse-Holz are the lead authors of the paper, which appears today in Science.

      Out of the loop

      Using computer simulations and experimental data, scientists including Mirny’s group at MIT have shown that loops in the genome are formed by a process called extrusion, in which a molecular motor promotes the growth of progressively larger loops. The motor stops each time it encounters a “stop sign” on DNA. The motor that extrudes such loops is a protein complex called cohesin, while the DNA-bound protein CTCF serves as the stop sign. These cohesin-mediated loops between CTCF sites were seen in previous experiments.

      However, those experiments only offered a snapshot of a moment in time, with no information on how the loops change over time. In their new study, the researchers developed techniques that allowed them to fluorescently label CTCF DNA sites so they could image the DNA loops over several hours. They also created a new computational method that can infer the looping events from the imaging data.

      “This method was crucial for us to distinguish signal from noise in our experimental data and quantify looping,” Zechner says. “We believe that such approaches will become increasingly important for biology as we continue to push the limits of detection with experiments.”

      The researchers used their method to image a stretch of the genome in mouse embryonic stem cells. “If we put our data in the context of one cell division cycle, which lasts about 12 hours, the fully formed loop only actually exists for about 20 to 45 minutes, or about 3 to 6 percent of the time,” Grosse-Holz says.

      “If the loop is only present for such a tiny period of the cell cycle and very short-lived, we shouldn’t think of this fully looped state as being the primary regulator of gene expression,” Hansen says. “We think we need new models for how the 3D structure of the genome regulates gene expression, DNA repair, and other functional downstream processes.”

      While fully formed loops were rare, the researchers found that partially extruded loops were present about 92 percent of the time. These smaller loops have been difficult to observe with the previous methods of detecting loops in the genome.

      “In this study, by integrating our experimental data with polymer simulations, we have now been able to quantify the relative extents of the unlooped, partially extruded, and fully looped states,” Brandão says.

      “Since these interactions are very short, but very frequent, the previous methodologies were not able to fully capture their dynamics,” Gabriele adds. “With our new technique, we can start to resolve transitions between fully looped and unlooped states.”

      Play video

      The researchers hypothesize that these partial loops may play more important roles in gene regulation than fully formed loops. Strands of DNA run along each other as loops begin to form and then fall apart, and these interactions may help regulatory elements such as enhancers and gene promoters find each other.

      “More than 90 percent of the time, there are some transient loops, and presumably what’s important is having those loops that are being perpetually extruded,” Mirny says. “The process of extrusion itself may be more important than the fully looped state that only occurs for a short period of time.”

      More loops to study

      Since most of the other loops in the genome are weaker than the one the researchers studied in this paper, they suspect that many other loops will also prove to be highly transient. They now plan to use their new technique study some of those other loops, in a variety of cell types.

      “There are about 10,000 of these loops, and we’ve looked at one,” Hansen says. “We have a lot of indirect evidence to suggest that the results would be generalizable, but we haven’t demonstrated that. Using the technology platform we’ve set up, which combines new experimental and computational methods, we can begin to approach other loops in the genome.”

      The researchers also plan to investigate the role of specific loops in disease. Many diseases, including a neurodevelopmental disorder called FOXG1 syndrome, could be linked to faulty loop dynamics. The researchers are now studying how both the normal and mutated form of the FOXG1 gene, as well as the cancer-causing gene MYC, are affected by genome loop formation.

      The research was funded by the National Institutes of Health, the National Science Foundation, the Mathers Foundation, a Pew-Stewart Cancer Research Scholar grant, the Chaires d’excellence Internationale Blaise Pascal, an American-Italian Cancer Foundation research scholarship, and the Max Planck Institute for Molecular Cell Biology and Genetics. More