The twist in their ‘bottom up,’ molecular Lego design strategy focuses on a DNA structure called a Holliday junction.
In nature, this cross-shaped, double-stacked DNA structure is like the 4-way traffic stop of genetics – where 2 separate DNA helices temporality meet to exchange genetic information. The Holliday junction is the crossroads responsible for the diversity of life on Earth, and ensures that children are given a unique shuffling of traits from a mother and father’s DNA.
In nature, the Holliday junction twists the double-stacked strands of DNA at an angle of about 60-degrees, 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 Yan. “What we needed to do is rotate the angle and force it to connect.”
The fundamental unit in Hao Yan’s new nanostructures rely on modifying a 4-arm DNA junction. The relaxed DNA geometry found in a 4-arm junction (B) can be rotated 150 degrees clockwise or 30 degrees counterclockwise (C) to form the right angles needed to make a DNA Gridiron (D and E).
Photo by: Biodesign Institute
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 build for the first time in the vertical dimension. Yan calls the backyard barbeque grill-shaped structure a DNA Gridiron.
“We were amazed that it worked!” said 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 spaghetti-shaped single strand of DNA is spit out and folded together with the help of small ‘staple’ strands of DNA that help mold the final DNA structure. In a test tube, the mixture is heated, then rapidly cooled, and everything self-assembles and molds into the final shape once cooled. Next, using sophisticated AFM and TEM imaging technology, they are able to examine the shapes and sizes of the final products and determine that they had formed correctly.
This approach has allowed them to build multilayered, 3-D 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,” said 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.”
ABSTRACT – Engineering wireframe architectures and scaffolds of increasing complexity is one of the important challenges in nanotechnology. We present a design strategy to create gridiron-like DNA structures. A series of four-arm junctions are used as vertices within a network of double-helical DNA fragments. Deliberate distortion of the junctions from their most relaxed conformations ensures that a scaffold strand can traverse through individual vertices in multiple directions. DNA gridirons were assembled, ranging from two-dimensional arrays with reconfigurability to multilayer and three-dimensional structures and curved objects.
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