Scientists create custom 3-dimensional structures with ‘DNA origami’

EUREKALERT

Contact: Bill Schaller
william_schaller@dfci.harvard.edu
617-632-5357
Dana-Farber Cancer Institute

BOSTON–By combining the art of origami with nanotechnology, Dana-Farber Cancer Institute researchers have folded sheets of DNA into multilayered objects with dimensions thousands of times smaller than the thickness of a human hair. These tiny structures could be forerunners of custom-made biomedical nanodevices such as “smart” delivery vehicles that would sneak drugs into patients’ cells, where they would dump their cargo on a specific molecular target.

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, Bjrn Hgberg, 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.

Dana-Farber Cancer Institute (www.dana-farber.org) is a principal teaching affiliate of the Harvard Medical School and is among the leading cancer research and care centers in the United States. It is a founding member of the Dana-Farber/Harvard Cancer Center (DF/HCC), designated a comprehensive cancer center by the National Cancer Institute.

Excessive hair syndrome

New research provides exciting genetic insight into a rare syndrome that first appeared in the medical literature in the mid 1800s with the case of Julia Pastrana, the world’s most notorious bearded lady. The study, published by Cell Press in the May 21st issue of the American Journal of Human Genetics, reveals intriguing molecular clues about the pathogenesis of this mysterious condition that has captured the attention of the public since the Middle Ages.

Congenital generalized hypertrichosis (CGH) represents a group of conditions characterized by excessive hair growth over the entire body, well beyond the average limits for a particular age, sex or race. Congenital generalized hypertrichosis terminalis (CGHT) with gingival hypertrophy is a distinct subgroup of CGH that is associated with universal overgrowth of darkly pigmented hairs, enlarged gums and a distortion of facial features, the phenotype famously exhibited by Julia Pastrana.

“Although it has long been believed that most people with CGH have some kind of genetic defect, the specific genetic mutations that underlie CGHT, with or without gingival hyperplasia, had not been discovered until now,” explains senior study author Dr. Xue Zhang from the Chinese Academy of Medical Sciences and Peking Union Medical College in Beijing. The condition has been very difficult to study because it is so rare.

Dr. Zhang and colleagues performed a sophisticated, high resolution genetic analysis of several members of three Chinese families with CGHT and an individual with a sporadic case of CGHT with gingival hyperplasia. The researchers mapped the genetic locus for this syndrome and discovered that genetic defects on chromosome 17q24.2-q24.3 were responsible for CGHT with or without gingival hyperplasia.

The three families exhibited different DNA deletions whereas the sporadic case was associated with a DNA duplication within the identified chromosome region. These different copy number mutations affected 4 to 8 genes. “Our work clearly establishes CGHT as a genomic disorder. However, further studies are needed to elucidate the exact molecular mechanisms by which copy number mutations on 17q24.2-q24.3 lead to the defining characteristics of this rare disorder,” concludes Dr. Zhang.