Generation of DNA origami nanostructures by shape annealing

To tackle nanostructure design, researchers at Carnegie Mellon University are developing automated design tools for a new approach to DNA origami.Credit: Faculty of Engineering

When it comes to creating nanotechnology, it’s not easy to build by hand. Instead, researchers need nano-sized ones that can be self-organizing. DNA origami is a method of folding DNA strands into nano-sized shapes. It can be used to manufacture nanomachines, sensors, and nanorobots for use in areas ranging from biophysics to physical computing.

However, the design process behind these structures requires the designer to think ahead of time what the final product will look like and design complex structures one by one from a single strand of DNA. This process is very time consuming and limits the design space that can be explored.

In recent years, semi-automated tools have been released to assist in the design process, and these tools have greatly expanded user functionality. However, there was no fully automated design tool for creating the multi-layered DNA origami structures that make up most of the DNA origami designs used today.

“There are more efficient and powerful ways to design these structures,” says Rebecca Taylor, an assistant professor of mechanical engineering. “The lack of automated functionality to generate multi-layer DNA origami was a major kind of need in the field.”

A new approach to DNA origami design came from CMU’s interdisciplinary research team. Tito Babatunde, Ph.D. student in Mechanical Engineering, has proposed a new method for generating and optimizing the design of DNA origami nanostructures. With the advice of Rebecca Taylor and Jonathan Cagan, she combined their expertise to work on nanostructure design.

“There is a truly interdisciplinary approach here,” says Cagan, a professor of mechanical engineering. “We took two separate fields and found that they overlap to provide something that is truly unique and can be enhanced.”

Cagan pioneered a generative computational approach called shape annealing. Shape annealing is used to design complex structures by exploring a wide range of designs before deciding what is best for them. This approach eliminates the need for researchers to waste time and materials on defective designs. In this project, Babatunde fuses shape annealing with the basic methods of binding and forming DNA.

DNA follows a set of simple rules that dictate which compounds can be paired. With a well-understood rule, researchers can take advantage of their predictability. Researchers start with a single strand of DNA and “staple” it into the desired 2D or 3D shape. When this process is complete, the DNA nanostructures serve as a scaffold for the final part of nanotechnology.

In their treatise, Babatunde and her team show that this design generation process works in a variety of shapes. In addition to using the classic design shape, the team has shown that the program works for Stanford bunny. Stanford bunny is a complex shape used to show the flexibility of work.

Second, Babatunde makes the algorithm more generalized. Future projects may include integrating more constraints, such as outer coatings and meshes. In addition, the team can use the algorithm in other situations and explore different types of DNA origami algorithms. But Babatande is most excited to create the physical parts of nanotechnology from DNA structures.

“I’m looking forward to not only using our approach to designing nanostructures, but also building them in the lab,” said Babatande. “By building these innovative structures, this technology demonstrates the impact of responsive nanomachines for drug delivery to nanomechanical sensors and nanolithography.”

The paper was published in Applied science In Mechanical design in DNA nanotechnology A special problem.

Origami-based tires can change shape while the vehicle is moving

For more information:
Bolutito Babatunde et al. Generation of DNA origami nanostructures by shape annealing, Applied science (2021). DOI: 10.3390 / app11072950

Carnegie Mellon University Mechanical Engineering Courtesy

Quote: Use of DNA for small techniques: https: // Shape Annealing (2021) obtained on May 10, 2021 , May 10) Generation of DNA origami nanostructures

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Generation of DNA origami nanostructures by shape annealing

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