DNA art: Scientists use genetic sequencing to create a variety of shapes

The resulting creations can be turned into tiny containers to deliver drugs or find other applications.
Loukia Papadopoulos
Designing with DNA.
Designing with DNA.

Arizona State University 

Researchers at Duke University have engineered a new open-source program that can convert drawings or digital models into nanoscale sculptures made of DNA, according to a press release by the institution published last month.

The researchers explained in their statement that the resulting structures are more than mere nano-sculptures. They are creations that can be turned into tiny containers to deliver drugs, or molds for casting metal nanoparticles with specific shapes for solar cells, medical imaging, and other applications.

The intricate work saw the collaboration of Duke Ph.D. student Dan Fu with his adviser John Reif and co-authors Raghu Pradeep Narayanan and Abhay Prasad in professor Hao Yan’s lab at Arizona State. 

The blueprint of life

“To most people, DNA is the blueprint of life; the genetic instructions for all living things, from penguins to poplar trees. But to teams like Reif’s and Yan’s, DNA is more than a carrier of genetic information -- it’s source code and construction material,” stated the press release.

“There are four “letters,” or bases, in the genetic code of DNA, which pair up in a predictable way in our cells to form the rungs of the DNA ladder. It’s these strict base-pairing properties of DNA -- A with T, and C with G -- that the researchers have co-opted. By designing DNA strands with specific sequences, they can “program” the strands to piece themselves together into different shapes.”

DNA art: Scientists use genetic sequencing to create a variety of shapes
A DNA molecule.

The novel software is called DNAxiS and it works by coiling a long DNA double helix into concentric rings that stack on each other to form the contours of the object. The process has been described as similar to using coils of clay to make a pot. 

Need stronger structures? No problem! The sculptures can be reinforced with additional layers for increased stability.

A wide variety of forms

The result is a program that can create a wide variety of forms: cones, gourds, and clover leaf shapes. Most notably, DNAxiS is the first such software tool that lets users design these types of shapes automatically, using algorithms to determine where to place the short DNA “staples” to join the longer DNA rings together and hold the shapes in place.

“If there are too few, or if they're in the wrong position, the structure won't form correctly,” Fu explained. “Before our software, the curvature of the shapes made this an especially difficult problem.”

Although practical applications of the novel software in the lab or clinic may still be years away, Reif said “it's a big step forward in terms of automated design of novel three-dimensional structures.”

The paper has been published in the journal Science Advances.

Study abstract:

Improving the precision and function of encapsulating three-dimensional (3D) DNA nanostructures via curved geometries could have transformative impacts on areas such as molecular transport, drug delivery, and nanofabrication. However, the addition of non-rasterized curvature escalates design complexity without algorithmic regularity, and these challenges have limited the ad hoc development and usage of previously unknown shapes. In this work, we develop and automate the application of a set of previously unknown design principles that now includes a multilayer design for closed and curved DNA nanostructures to resolve past obstacles in shape selection, yield, mechanical rigidity, and accessibility. We design, analyze, and experimentally demonstrate a set of diverse 3D curved nanoarchitectures, showing planar asymmetry and examining partial multilayer designs. Our automated design tool implements a combined algorithmic and numerical approximation strategy for scaffold routing and crossover placement, which may enable wider applications of general DNA nanostructure design for nonregular or oblique shapes.

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