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Innovative Twists to Nanotechnology Create DNA-Building Toolkit

By BiotechDaily International staff writers
Posted on 03 Apr 2013
 Image: An S-shaped DNA structure (A) a sphere (B) and a screw (C), along with microscopy images of the actual nanostructures. Each scale bar is 200 nm, and the images on the right zoom-in on the images in a 200-nm by 200-nm square. (Photo courtesy of Biodesign Institute).
Image: An S-shaped DNA structure (A) a sphere (B) and a screw (C), along with microscopy images of the actual nanostructures. Each scale bar is 200 nm, and the images on the right zoom-in on the images in a 200-nm by 200-nm square. (Photo courtesy of Biodesign Institute).
In a new discovery that signifies a key step in resolving a critical design hurdle, investigators have generated a wide range of two-dimensional (2D) and 3D structures that advance the boundaries of the nascent field of DNA nanotechnology.

The field of DNA nanotechnology utilizes nature’s design guidelines and the chemical characteristics of DNA to self-assemble into an increasingly complicated group of molecules for biomedical and electronic applications. Arizona State University (ASU; Phoenix, USA) Prof. Hao Yan led the research team, and some of his lab’s achievements include constructing Trojan horse-like structures to optimize drug delivery to cancerous cells, single molecule sensors, electrically conductive gold nanowires, and programmable molecular robots.

With their bio-inspired architectural machinery, the group continues to study the physical and geometric limits of building at the molecular level. “People in this field are very interested in making wire frame or mesh structures,” said Prof. Yan. “We needed to come up with new design principles that allow us to build with more complexity in three dimensions.”

In their latest twist to the technology, Prof. Yan’s team made new 2D and 3D objects that look like wire-frame art of spheres as well as scissors, molecular tweezers, a screw, hand fan, and even a spider web. The investigators published their findings in the March 22, 2013, issue of Science.

The scientists’ ‘bottom up,’ twist, molecular Lego design approach focuses on a DNA structure called a Holliday junction. In nature, this cross-shaped, double-stacked DNA structure is similar to the four-way traffic stop of genetics—where two distinct DNA helices temporality assemble to exchange genetic data. The Holliday junction is the crossroads responsible for the diversity of life on Earth, and ensures that children are given a unique rearranging of features from the parent’s DNA.

In nature, the Holliday junction twists the double-stacked strands of DNA at an angle of about 60°, which is perfect for swapping genes but sometimes frustrating for DNA nanotechnology scientists, because it limits the design rules of their structures. “In principal, you can use the scaffold to connect multiple layers horizontally,” [which many research teams have utilized since the development of DNA origami by Cal Tech’s Paul Rothemund in 2006]. However, when you go in the vertical direction, the polarity of DNA prevents you from making multiple layers,” said Prof. Yan. “What we needed to do is rotate the angle and force it to connect.”

Making the new structures that Prof. Yan envisaged required re-modifying the Holliday junction by rotating and flipping around the junction point approximately half a clock face (150°). Such an exploit has not been considered in existing designs. “The initial idea was the hardest part,” said Prof. Yan. “Your mind doesn’t always see the possibilities so you forget about it. We had to break the conceptual barrier that this could happen.”

In the new study, by varying the length of the DNA between each Holliday junction, they could force the geometry at the Holliday junctions into an unconventional rearrangement, making the junctions more flexible to construct for the first time in the vertical dimension. Prof. Yan calls the barbeque grill-shaped structure a DNA gridiron. “We were amazed that it worked,” said Prof. Yan. “Once we saw that it actually worked, it was relatively easy to implement new designs. Now it seems easy in hindsight. If your mindset is limited by the conventional rules, it’s really hard to take the next step. Once you take that step, it becomes so obvious.”

The DNA gridiron designs are programmed into a viral DNA, where a string-shaped single strand of DNA is pushed out and folded together with the help of small, staple strands of DNA that help shape the final DNA structure. In a test tube, the mixture is heated, and then quickly cooled, and everything self-assembles and molds into the final shape once cooled. Next, using sophisticated atomic force microscopy (AFM) and transmission electron microscopy (TEM) imaging technology, the researchers were able to study the shapes and sizes of the final products and determine that they had formed accurately.

This application has allowed them to assemble multilayered, 3D structures and curved objects for new applications. “Most of our research team is now devoted toward finding new applications for this basic toolkit we are making,” concluded Dr. Yan. “There is still a long way to go and a lot of new ideas to explore. We just need to keep talking to biologists, physicists, and engineers to understand and meet their needs.”

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