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Ahead of the curve: New techniques advance DNA nanotech

An automated computer tool allows researchers to custom design structures, which self-assemble from DNA. A few of the nanoarchitectures — measuring just a few billionths of a meter is size — are seen in this graphic, along with accompanying magnified images of the completed structures. Illustration courtesy of Duke University

December 27, 2022

DNA nanotechnology is a rapidly evolving field, thriving in the borderlands between biology and chemistry. Pioneering design principles allow researchers to construct an extraordinary array of two- and three-dimensional forms at the scale of just billionths of a meter, using the molecule of life as a building material.

In a new study, Professor Hao Yan from Arizona State University, Professor John Reif from Duke University and their colleagues describe a technique for considerably expanding the versatility and range of DNA nano-objects.

The method allows researchers to produce tiny structures displaying curvatures and asymmetries that are difficult or impossible to create using conventional approaches. The study describes a first-of-its-kind computer-aided design tool that can automate the complex and cumbersome design process, ensuring that the nanoarchitectures properly assemble into the desired forms.

“The collaboration between computer scientists and chemists made designing DNA nanostructures with complex curvatures much easier, assisted by the newly developed automated design software,” Yan said.

In addition to directing the Biodesign Center for Molecular Design and Biomimetics at Arizona State University, Yan is the Milton D. Glick Distinguished Professor in Chemistry and Biochemistry with ASU’s School of Molecular Sciences. He has just been elected to the rank of NAI Fellow by the National Academy of Inventors.

The study appears in the current issue of the journal Science Advances.

The new technique is a variant of a process known as DNA origami, in which pieces of DNA are assembled like nanoscale tinker toys, using the base-pairing properties of DNA’s four nucleotides. These nucleotides stick together in a regular and predictable manner, enabling nanoarchitects like Yan, Reif and colleagues to design elaborate structures that self-assemble in a test tube. The delicate nanoarchitectures are so small, some 50,000 of them could comfortably rest on the head of a pin.

DNA origami has been used to create forms of aesthetic beauty as well as those of importance for biomedical, computer and electronic device applications. A few of these innovative designs include a DNA spider-like walker, stars, quasicrystals, flowers, birds and other diverse shapes, cartwheeling nanomachines and cancer-fighting nanobots programmed to seek and destroy tumors. These and many other infinitesimal architectures can be visualized using sophisticated techniques like transmission electron microscopy.

Despite the impressive and growing assortment of nanoforms built with DNA, researchers still struggle to design and build asymmetric DNA forms and those of irregular shape, involving changes in curvature.

In conventional DNA origami, a single strand of DNA is twisted into a scaffold of the desired nanoform through base-pairing properties, then fixed in place with shorter staple strands. Although the technique has proven highly versatile, some nanoforms are exceptionally difficult to design and fabricate, involving time-consuming and tedious trial and error, as many variables can adversely affect proper self-assembly.

Among these are fully enclosed, capsule-like DNA structures, useful for many applications, including sequestering molecules to be moved from place to place and shielding therapeutic drugs from degradation in the body, before they can reach their intended targets.

Composing such forms using traditional DNA origami methods is taxing and unreliable, often resulting in inaccurate or failed structures. The new technique introduces curved DNA helices into the design process, offering much more fine-grained control over resulting geometries. 

Using bundles of DNA helices in the design process, the researchers were able to exert fine-grained control over both concave and convex curvatures, compared with conventional block-based designs. A probabilistic algorithm sorts through myriad design possibilities for a given form, optimizing strand routing for each design, without the need for painstaking and inaccurate human trial and error. The computer-guided, curved DNA helices enable researchers to more accurately approximate nature’s astonishing variety and geometric ingenuity. 

The new open-source software program was developed by PhD student Dan Fu in Reif’s group at Duke University. The curved DNA nanostructures were assembled and imaged by students Raghu Pradeep Narayanan and Abhay Prasad in Yan’s lab at ASU.

The software relies on new techniques of DNA design first described in 2011 by Yan, who was a postdoc with Reif at Duke 20 years ago before joining the faculty at ASU. The method involves coiling a long DNA double helix into concentric rings that stack on each other to form the contours of the desired object, like using coils of clay to make a pot.

The study describes the construction of bowls, spheres and vases, as well as an ellipse and a clover pattern, which combined concave and convex curvatures. Multilayer designs combined with targeted reinforcement of these structures prevent structural disintegration or collapse, even under conditions of high strain and curvature.

The design advances will enable researchers to broadly expand an already diverse menagerie of DNA forms.

This research was supported by the National Science Foundation (1909848, 2113941, 2004250, 1931487).

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