Biomedical engineers have built simple machines out of DNA, consisting of arrays whose units switch reversibly between two different shapes.
The arrays’ inventors say they could be harnessed to make nanotech sensors or amplifiers. Potentially, they could be combined to form logic gates, the parts of a molecular computer.
The arrays’ properties are described in Science.
The DNA machines can relay discrete bits of information through space or amplify a signal, says senior author Yonggang Ke, PhD, an assistant professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory.
“In the field of DNA-based computing, the DNA contains the information, but the molecules are floating around in solution,” Ke says. “What’s new here is that we are linking the parts together in a physical machine.”
Similarly, several laboratories have already made nanotech machines such as tweezers and walkers out of DNA. Ke says his team’s work with DNA arrays sheds light on how to build structures with more complex, dynamic behaviors.
The arrays’ structures look like accordion-style retractable security gates. Extending or contracting one unit pushes nearby units to change shape as well, working like a domino cascade whose tiles are connected.
The arrays’ units get their stability from the energy gained when DNA double helices stack up. To be stable, the units’ four segments can align as pairs side by side in two different orientations. By leaving out one strand of the DNA at the edge of an array, the engineers create an external trigger. When that strand is added, it squeezes the edge unit into changing shape (see illustration).
To visualize the DNA arrays, the engineers used atomic force microscopy. They built rectangular 11×4 and 11×7 arrays, added trigger strands and could observe the cascade propagate from the corner unit to the rest of the array. The arrays’ cascades can be stopped or resumed at selected locations by designing break points into the arrays. The units’ shape conversions are modulated by temperature or chemical denaturants.
For reference, the rectangular arrays are around 50 nanometers wide and a few hundred nanometers long – slightly smaller than a HIV or influenza virion.
To build the DNA array structures, the engineers used both origami (folding one long “scaffold” strand with hundreds of “staple” strands) and modular brick approaches. Both types of arrays self-assemble through DNA strands finding their complimentary strands in solution. The origami approach led to more stable structures in conditions of elevated temperature or denaturant.
In the Science paper, the engineers showed that they could build rectangles and tubes of array units. They also include a cuboid that has three basic conformations, more than the two-dimensional array units with two conformations. Ke says his team is working on larger, more complex machines with three-dimensional shapes, which can be made using the same basic design principles.
Learn more: Switchable DNA mini-machines relay information
The Latest on: Molecular computer
One step closer to understanding explosive sensitivity with molecule design
on April 18, 2018 at 10:25 am
"Or rather, partly right!" added Cawkwell. Using a molecular dynamics computer code written at Los Alamos called "LATTE" Cawkwell is able to model the making and breaking of chemical bonds in explosives very accurately. "The chemistry comes from the ... […]
Brain networks: Keeping the excitement under control
on April 18, 2018 at 8:58 am
Crucial steps in this processing take place in the neocortex, which has a layered structure like six computer servers stacked on top of ... Max Delbrück Center for Molecular Medicine in the Helmholtz Association. "Brain networks: Keeping the excitement ... […]
Keeping the excitement under control
on April 18, 2018 at 7:30 am
Crucial steps in this processing take place in the neocortex, which has a layered structure like six computer servers stacked on top of ... 10.1038/s41467-018-03995-2 About the Max Delbrück Center for Molecular Medicine The Max Delbrück Center for ... […]
Simulation of the AsqJ enzyme opens up new options for pharmaceutical chemistry
on April 17, 2018 at 11:26 am
But how does this happen on a molecular level? "Understanding the exact function ... An aim of future research will be to design enzymes in a computer to, for example, produce new drugs. Technical University of Munich (TUM). (2018, April 17). […]
The enzyme designers
on April 17, 2018 at 9:06 am
But how does this happen on a molecular level? "Understanding the exact function ... An aim of future research will be to design enzymes in a computer to, for example, produce new drugs. The research was funded by the European Research Council (ERC ... […]
Synthetic Biology Market: Global Market Estimation, Dynamics, Regional Share, Trends, Competitor Analysis 2012-2016 and Forecast 2017-2023
on April 16, 2018 at 4:16 pm
In addition, increase in funding from government in life science research and development and advancements in molecular biology expected to boost the synthetic biology market during the forecast period. Furthermore, private institutional contribution to ... […]
‘Molecular Chaperones,’ Scuff Protection Among 2018 Showcase Award Winners
on April 16, 2018 at 9:52 am
Biological Sciences: “Investigating the housekeepers of the cell: Molecular chaperones at fertilization ... Justin Foley, Felix Sibert. Computer Science: “A Robot: Can You Get My Paper from the Printer?” Isabella DeMeo, Ran Bi, Zachariah Watkins ... […]
I Want to Preserve My Brain So My Mind Can Be Uploaded to a Computer in the Future
on April 10, 2018 at 10:27 pm
Giulio Prisco is a futurist, theoretical physicist, and computer scientist. He writes about science ... being toxic to the biological machinery of life by wreaking havoc on a molecular scale,” reads an Alcor position statement. Vitrification without ... […]
Are We Quantum Computers?
on March 27, 2018 at 12:11 pm
molecular biology, biochemistry, colloid science and behavioral neuroscience, the project will seek explicit experimental evidence to answer whether we might in fact be quantum computers. “We are extremely grateful to the Heising-Simons Foundation for ... […]
Cargo-sorting molecular robots, humans as the ultimate fire starters, and molecular modeling with quantum computers
on September 14, 2017 at 11:20 am
This week we hear stories on the gut microbiome’s involvement in multiple sclerosis, how wildfires start—hint: It’s almost always people—and a new record in quantum computing with Online News Editor David Grimm. Andrew Wagner talks to Lulu Qian ... […]
via Google News and Bing News