CAMBRIDGE, Mass. — While the primary job of DNA in cells is to carry genetic information from one generation to the next, some scientists also see the highly stable and programmable molecule as an ideal building material for nanoscale structures that could be used to deliver drugs, act as biosensors, perform artificial photosynthesis and more.
Trying to build DNA structures on a large scale was once considered unthinkable. But about five years ago, Caltech computational bioengineer Paul Rothemund laid out a new design strategy called DNA origami: the construction of two-dimensional shapes from a DNA strand folded over on itself and secured by short “staple” strands. Several years later, William Shih’s lab at Harvard Medical School translated this concept to three dimensions, allowing design of complex curved and bent structures that opened new avenues for synthetic biological design at the nanoscale.
A major hurdle to these increasingly complex designs has been automation of the design process. Now a team at MIT, led by biological engineer Mark Bathe, has developed software that makes it easier to predict the three-dimensional shape that will result from a given DNA template. While the software doesn’t fully automate the design process, it makes it considerably easier for designers to create complex 3-D structures, controlling their flexibility and potentially their folding stability.
“We ultimately seek a design tool where you can start with a picture of the complex three-dimensional shape of interest, and the algorithm searches for optimal sequence combinations,” says Bathe, the Samuel A. Goldblith Assistant Professor of Applied Biology. “In order to make this technology for nanoassembly available to the broader community — including biologists, chemists, and materials scientists without expertise in the DNA origami technique — the computational tool needs to be fully automated, with a minimum of human input or intervention.”
Bathe and his colleagues described their new software in the Feb. 25 issue of Nature Methods. In that paper, they also provide a primer on creating DNA origami with collaborator Hendrik Dietz at the Technische Universitaet Muenchen. “One bottleneck for making the technology more broadly useful is that only a small group of specialized researchers are trained in scaffolded DNA origami design,” Bathe says.
DNA consists of a string of four nucleotide bases known as A, T, G and C, which make the molecule easy to program. According to nature’s rules, A binds only with T, and G only with C. “With DNA, at the small scale, you can program these sequences to self-assemble and fold into a very specific final structure, with separate strands brought together to make larger-scale objects,” Bathe says.
Rothemund’s origami design strategy is based on the idea of getting a long strand of DNA to fold in two dimensions, as if laid on a flat surface. In his first paper outlining the method, he used a viral genome consisting of approximately 8,000 nucleotides to create 2-D stars, triangles and smiley faces.
That single strand of DNA serves as a “scaffold” for the rest of the structure. Hundreds of shorter strands, each about 20 to 40 bases in length, combine with the scaffold to hold it in its final, folded shape.
“DNA is in many ways better suited to self-assembly than proteins, whose physical properties are both difficult to control and sensitive to their environment,” Bathe says.
Bathe’s new software program interfaces with a software program from Shih’s lab called caDNAno, which allows users to manually create scaffolded DNA origami from a two-dimensional layout. The new program, dubbed CanDo, takes caDNAno’s 2-D blueprint and predicts the ultimate 3-D shape of the design. This resulting shape is often unintuitive, Bathe says, because DNA is a flexible object that twists, bends and stretches as it folds to form a complex 3-D shape.
Written by Anne Trafton, MIT News Office