Scientists Create Custom 3-dimensional Structures With 'DNA Origami'

While creation of structures from single layers of DNA has been reported previously, William Shih, PhD, senior author of the study appearing in the May 21 issue of Nature, said the multi-layer process he and his colleagues developed should enable scientists to make customized DNA objects approximating almost any three-dimensional shape. Multilayered objects are more rigid and stable, thus better able to withstand the intracellular environment, which "is chaotic and violent, like being in a hurricane," Shih said. "We think this is a big advance."

Shih is a researcher in Dana-Farber's Cancer Biology program. He is also an assistant professor in the Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School, and a Core Faculty member of the Wyss Institute for Biologically Inspired Engineering at Harvard.

Masters of the ancient Japanese art of origami make a series of folds in a single piece of paper to form stunningly intricate models of animals and other shapes. "We focus on doing this with DNA," explained Shih. While DNA is best known as the stuff of which genes are made, here the scientists use long DNA molecules strictly as a building component, not a blueprint for making proteins. Shih and his colleagues reported in the Nature paper that they were able to construct a number of DNA objects, including a genie bottle, two kinds of crosses, a square nut, and a railed bridge.

DNA origami is an outgrowth of research in nanotechnology - using atoms and molecules as building blocks for new devices that can be deployed in medicine, electronics, and other fields. Scientists envision using the minuscule structures -- which are about the size of small viruses -- to mimic some of the "machines" within cells that carry out essential functions, like forming containers for molecular cargos and transporting them from one place to another.

"This is something that nature is very good at -- making many complex machines with great control. Nature optimizes cellular technology through millions of years of evolution; we don't have that much time, so we need to come up with other design approaches," Shih said.

DNA origami are built as a sheet of parallel double-helices, each consisting of two intertwined strands made up of units called nucleotides. Long strands of DNA serving as a "scaffold" are folded back and forth by short strands of DNA serving as "staples" that knit together segments of the scaffold. The DNA sheet, which Shih likens to the thin bamboo mat that sushi chefs use to prepare maki rolls with filling, is then programmed to curl on itself into a series of layers that are locked in place by staples that traverse multiple layers.

With the design in hand, the scientists then order the DNA staple strands from a company, which take about three days to be synthesized and shipped. Fabricating the desired structure involves mixing the DNA scaffold and staple strands, quickly heating the mixture, and then slowly cooling the sample. This process coaxes the DNA to "self-assemble" and make billions of copies of the desired object. The process takes about a week, though the researchers intend to improve this rate. Finally, the researchers can check the finished product using an electron microscope.

The tiny machines the researchers are aiming for could, for example, act as navigation aids to guide bubble-like sacs filled with medicines. "These machines could be placed on the outside of the drug-delivery vehicles to help them cross biological barriers, or help them outwit mechanisms that are trying to remove things from the bloodstream, so they can reach their target," suggested Shih.

The technology could also be useful in diagnostics of the future. While current lab tests can measure the concentration of different substances in the body, it may be possible with DNA "to measure the concentration of something within a single cell," said Shih.

In addition to Shih and Douglas, the authors of the Nature paper include Hendrik Dietz, PhD, Tim Liedl, PhD, Björn Högberg, PhD, and Franziska Graf, of Dana-Farber and Harvard Medical School.

The research was supported by grants from the National Institutes of Health, the Claudia Adams Barr Program, the Wyss Institute for Biologically Inspired Engineering at Harvard, and several fellowships.