Photograph: Mike Pick. Origami pattern by Thoki Yenn.
A smiley face glowed on the March 16, 2006, cover of Nature. “DNA Origami,” read the headline. “Nanoscale Shapes the Easy Way.” Inside, a relatively brief, single-author paper outlined a method for designing shapes made from DNA that would fold up on their own. The smiling prototype and the playful cover line may have been cute. But the changes the paper brought to a number of far-flung fields were nothing short of profound: Tiny, self-assembling structures, with applications in everything from biology to chip design, were now within our grasp.
Three years later, the research sparked by this breakthrough has just begun to bear fruit, as evidenced by a flurry of papers this summer. Caltech’s Paul Rothemund, the author of the Nature paper, and his collaborators at IBM published a way to fasten DNA origami to microchip materials. William Shih at Harvard led a team that developed three-dimensional shapes and curving structures, among many refinements to the technique. And Jørgen Kjems of Denmark’s Aarhus University published a method to build miniature boxes, equipped with multiple locks and molecules that glow red and green. As it turned out, everyone from cell biologists to drug delivery experts to materials scientists had been looking for just such a way to build.
Building Blocks from Life
In biology, DNA carries information, but it is also in many ways an ideal building material. DNA’s sequence dictates the shape it folds into, and it is cheap and easy to manufacture strands with a custom sequence. And while the precise rules of protein folding are one of the great unsolved mysteries of biology, the folding of single- and double-stranded DNA is chemically well-understood.
DNA had thus been an attractive structural material for nanoengineers for decades, ever since NYU’s Ned Seemans founded the field of DNA nanotechnology in the 1970s. With tiny components that assemble themselves, it was hoped that miniature motors and microchips could be manufactured in beakers for almost no cost. But there was a major barrier to the realization of self-assembling machines. For while nanoengineers could manufacture custom DNA and predict how it would fold, there was no good way to program it into anything but the most basic of shapes.
Paul Rothemund had learned of Seemans’ work in the early 1990s while trying to build a DNA computer—a series of molecules that can perform computations, like a mechanical calculator. But he grew entranced by the idea of DNA shapes that could self-assemble. With this “bottom-up” assembly, a revolution in chip design—and computing speed—could be achieved. Three months of programming brought him to a process that landed him on the cover of Nature—and which has opened the floodgates of nanotech innovation.
DNA origami is actually something of a misnomer; as William Shih notes, the process is more like DNA knitting. Think of a strand of DNA as a straight line—it has no area of its own. But by folding the line back and forth on itself, you can produce a flat plane.
In Rothemund’s method, a length of single-stranded DNA folds back and forth to fill in a flat shape, be it a star, a square, or a smiley face. Then, shorter strands stick parallel and perpendicular to it, turning the single-stranded DNA into a double helix that links back to itself, stabilizing the shape. Finally, a computer tests the shape for structural stability. The finished product, to use the knitting metaphor, is a star, square, or smiley face-shaped blanket.
At the end of his Nature paper, Rothemund pondered the wide-open possibilities of this kind of DNA self-assembly. “I believe that scaffolded DNA origami can be adapted to create more complex or larger structures,” he wrote. “[It] could find use in fields as diverse as molecular biology and device physics.”
The World’s Smallest Doctor
Of the many possible applications of DNA origami, drug delivery is one of the most enticing. One of the major struggles in targeted pharmacology has been getting molecules through cell membranes, says Harvard’s William Shih, a process that bacteria and viruses have mastered, but humans have not. A DNA structure, equipped with the right tools, could help penetrate that barrier. Shih envisions a DNA origami cage with a drug inside, all encased in a lipid envelope that can fuse with a cell’s membrane. Using proteins attached to its surface, the structure would detect whether a cell is infected. When infection is identified, the lipid envelope would merge with the cell membrane, spitting the DNA cage into the cell. Traveling around the circulatory system, these cellular doctors would eventually biodegrade harmlessly.
This dream is still far from becoming a reality. But Shih’s lab has refined point after point of the DNA origami process, laying a foundation for the folding permutations future scientists will need to build functional structures out of DNA.
Shih and his colleagues published the first method for building 3-D DNA origami in May. Rothemund’s method created flat planes, but by folding a plane up accordion-style one can eventually create an object with volume. Shih’s lab produced nanoscale sculptures based on this idea. And in August they published the first method for building curved shapes in Science.
While many of his team’s advances are incremental, they are adding up to a versatile set of new tools. Shih has good taste in choosing what problems to solve, says Rothemund. And Shih says “it’s very exhilarating” to be building the field from scratch.
Unlocking Drug Delivery
As Shih builds the foundation for a revolution in drug delivery, Kjems and his colleagues at Aarhus University in Denmark are working on making a prototype. In May, they published a construction that could also be used to deliver pharmaceuticals: a DNA box that unlocks when it senses infection.
One of the handy characteristics of DNA origami is that its customizable shape makes it highly modular. Designers can assemble several flat planes into a box, keep other molecules inside, and fuse chemicals, dyes, fluorescent proteins, and other kinds of markers to the exterior. If DNA structures could encapsulate drug molecules, then release them when they sense specific markers on the outside of a cell, tremendous specificity in drug application could be achieved.
Using Rothemund’s method, Kjems and his team built a six-sided container, made of flat DNA squares stitched together with short strands. These boxes can open to up to potentially eight different “keys,” which can be anything from microRNAs to cellular markers. To let them see whether the boxes are ajar, they added fluorescent proteins to the locks so that the box glows green when open and red when closed.
The first application of these boxes would likely be as sensors, Kjems says. One could mix them into a sample taken from a patient and see if the sample glows green, indicating that the box has unlocked for a specific disease signature. Eventually, they could be used to deliver drugs in vivo.
But Kjems thinks they could form parts of what is essentially a biological computer. “The box is already a very simple computer. It’s a gate that has two states, like a transistor in a computer,” he says. The transistors could talk to each other, unlocking boxes that contain keys for boxes further down the chain. This could allow researchers to trigger cascades of biochemical reactions; they would essentially be programming a biological system.
Programming with DNA
DNA origami is many times smaller than the features etched on microchips. And just as proteins and other molecules can be fused to DNA origami in hundreds of places, gold nanoparticles and silicon nanowires can be attached as well. Rothemund has been working to construct miniature circuits based on just that principle.
The major problem with using DNA origami to build circuits is that they are made in solution and will pile up randomly on any flat surface. Instead of a finely textured, exquisitely organized platform, early attempts showed the would-be chip components accreted in ugly clumps. But by etching small triangular patches that stick to the DNA, Rothemund and his collaborators at IBM managed to get the miniscule structures to line up in neat rows. Next they will be working to get the protocol to work for non-equilateral structures.
Rothemund foresees a series of wafers and standardized DNA origami that could be combined in different spacings and orientations, finding uses in a variety of fields.
“Some people are experts in carbon nanotubes, some in silicon nanowires, some in metal nanoparticles, some in biological proteins,” he says. “We want them all to be able to use it.”
Originally published October 12, 2009