Weaving Barrels from DNA

Good things really do come in small packages, according to a group of students at Harvard University. They constructed a tiny container–about 30 nanometers in diameter–made entirely of DNA, which could one day be used to deliver drugs or gene or protein-based therapies to specific tissues in the body.

“We know DNA is a very stable building material,” says Valerie Hoi-Ting Lau, one of the students involved in the project. “Now we’re trying to take advantage of the fact that it’s programmable.” Lau and others presented their barrel at the International Genetically Engineered Machines competition at MIT earlier this month (see “Bizarre Bacterial Creations”).

The world of DNA architecture has exploded in recent years, with scientists building two-dimensional smiley faces and complex maps, as well as three-dimensional octagons. The chemicals that make up long, winding DNA molecules bind together according to a predictable set of rules, so it’s possible to design DNA sequences that will form into various shapes.

While DNA architecture previously took years to design and construct, a method developed earlier this year provides a relatively easy way to program DNA into specific shapes (see “Do-It-Yourself Nanotech”). A single long strand of DNA is studded with shorter snippets of specially designed DNA sequences that act as the chemical equivalent of staples. Each snippet will only bind to a specific spot on the DNA molecule. Strategically placing these staples along the DNA strand allows the molecule to self-assemble into different shapes.

By adapting this method to build three-dimensional structures, the students and their advisor William Shih, a Harvard scientist who has been a leader in DNA architecture, designed a DNA sequence that would fold into a tiny, hollow container. The final structure, which is shaped like an open barrel, consists of a single DNA molecule that zigzags back and forth to create a pleated sheet. The sheet is programmed to curve around on itself, creating a double-walled cylinder. (Click here to see pictures of the barrel.)

“It was really a breakthrough result,” says Shih. Previous DNA containers, such as octagons, have had large holes in their walls, but researchers think the walls of this structure are quite solid, theoretically allowing the barrel to safely encase nanosize treasures.

In addition, some DNA-based structures have an inherent floppiness that makes three-dimensional shapes collapse. But the building method used to create the barrel–lining up a series of DNA helices into a pleated-sheet structure–seems to provide new strength. “I suspect that Shih’s style of making 3-D structures will prove to be particularly rigid,” says Paul Rothemund, a scientist at the California Institute of Technology in Pasadena, CA who developed the method on which the project is based.

Rothemund adds that one of the most complicated aspects of DNA architecture is confirming that the finished structure takes the shape of the original design. The Harvard students have taken pictures of their DNA barrel using an electron microscope, which shows that it is the right size and shape. They also ran preliminary tests to determine if the barrel can really protect its cargo from the outside environment. Sure enough, they found that a chemical placed inside the barrel is effectively shielded from another chemical that usually binds to it.

If the students can get their creation to work, they’ll overcome one of the lingering problems with DNA-based designs: finding a practical application for the tiny structures. “If … they can make containers for the delivery of drugs, it will demonstrate that using DNA as a technological material really is a useful enterprise!” says Rothemund.

Ultimately, the students hope to create a container that could carry any type of drug and be molecularly targeted to specific types of cells. Newer therapies, such as those that are gene or protein-based, are often difficult to deliver and need to be directed to certain tissues. Some must be delivered via injection or, in a few experimental cases, infused directly into the brain. The students are already working on ways to decorate the barrels with different molecules that bind only to certain cells or proteins.

While the work is still in the very early phase, Shih dreams big about what could happen in the future. “It’s interesting in the long term because we do have so much control over the shapes of these objects,” he says. “People have generated DNA molecules that act as computers, so you could have a drug-delivery device that has an onboard computer that does primitive computations, making decisions about when and where to release the drug.” Of course, Shih says, “there’s still quite a bit of work to be done.”