MIT, Arizona State University, and Baylor University
Hard Science

Scientists Find a Better Way to Make Structures to Create DNA Based Tech

The new program makes folding DNA into required shapes as easy as the push of a button.

Todd JaquithMay 27th 2016
News
MIT, Arizona State University, and Baylor University

The Littlest Origami

When it comes to building at the nanoscale, DNA is the construction material of choice. That may seem a little strange. After all, DNA is nature’s hard drive, encoding the software of life.

But the macromolecule turns out to be a very hardy and versatile building material, perfectly suited to building complex structures with dimensions measured in nanometers—what is known as “DNA origami.”

Biology has settled on the DNA double helix as the default configuration, but there are many more possibilities. Rearrange the base pairs or insert other molecules, and DNA can twist into just about any shape you could wish for.

Digital rendering of the diverse DNA structures autonomously designed by the DAEDALUS algorithm. Credit: Digizyme
Digital rendering of the diverse DNA structures autonomously designed by the DAEDALUS algorithm. Credit: Digizyme

And the uses for such fine-scale DNA manipulation are virtually endless. Imagine DNA-based drug delivery mechanisms, or—more in keeping with the nucleic acid’s traditional role—a dense information storage system capable of recording terabytes of data in something less than the size of a pinhead.

The problem is, synthesizing and manipulating DNA is prohibitively difficult; the laborious business of assembling DNA by hand, one base pair at a time, and determining how to obtain the desired shape, requires multiple PhDs and more time than anyone is likely to want to waste.

DAEDALUS

But now a team of researchers from MIT, Arizona State University, and Baylor University have devised a new computer algorithm that does all the hard work for you. The results of their research have been published in the journal Science.

“The paper turns the problem around from one in which an expert designs the DNA needed to synthesize the object, to one in which the object itself is the starting point, with the DNA sequences that are needed automatically defined by the algorithm,” says Mark Bathe, associate professor of biological engineering at MIT, and lead researcher for the study.

Some of the DNA shapes actually created with the DAEDALUS algorithm, with cryo-electron microscopy images at far right. Credit: Bathe et al.
Some of the DNA shapes actually created with the DAEDALUS algorithm, with cryo-electron microscopy images at far right. Credit: Bathe et al.

The new algorithm, which the team has called DAEDALUS, automates the entire business of sculpting DNA shapes; essentially, you begin with the desired shape (which must have a closed surface) and feed it into the algorithm, which then maps out the order of bases (adenine, guanine, cytosine and thymine) needed to produce the DNA “scaffold.”

DAEDALUS means “open source” DNA origami, enabling anyone with the inclination and access to the algorithm to design and create their own DNA-based, nanoscale objects. What Henry Ford’s assembly line concept did for manufacturing, DAEDALUS promises to do for nanoscale structures.

The team is already investigating the wealth of potential applications for these nanoparticles, including creating delivery vehicles for the CRISPR-Cas9 gene editing tool, or designing binary DNA memory blocks.

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