Gene machines

DNA "origami" is opening the door to the smallest structures ever made
June 19, 2013

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Clockwise from top left, Seeman’s DNA cube; Rothemund’s smiley face; a map of the world; DNA cubes with opening lids. Clockwise from top left © Courtesy of Nadrian C. Seeman, New York University; © Paul Rothemund; © California Institute of Technology; © Jørgen Kjems, Lundbeck Nanomedicine Center (Luna)

James Watson and Francis Crick’s paper in Nature on the structure of DNA, published 60 years ago, anticipated the entire basis of modern genetics. The structure they postulated is both iconic and beautiful: a double helix, composed of two entwined strands of conjoined molecular material, each consisting of a sequence of genetic building blocks. The two strands are bound to one another by chemical bonds and, as Watson and Crick realised, for the binding to be secure there must be a perfect match between the sequence of building blocks on each strand. Any errors in this matching make the double helix apt to separate again into its component strands. DNA, packaged in an organism’s genome, carries information essential to the organism’s functioning and replication. But the details are complex and still being unravelled, and this picture of a molecule whose chemical structure encodes instructions for zipping up only with the right partner has been seized by the field of nanotechnology—engineering matter at the scale of nanometres (millionths of a millimetre), the dimensions of molecules.

Here it becomes immensely hard, if not impossible, to arrange and manipulate objects using the techniques that work at larger scales. However, the ability to programme assembly instructions into strands of DNA offers a powerful new alternative, raising the possibility of tiny structures and machines that “make themselves” from their molecular-scale components.

Research in nanotechnology has been propelled partly by the race to miniaturise transistors and other components of microelectronic circuitry. Computer processors and memories are now so small that conventional methods of carving and shaping materials are stretched to the limits of their finesse.

DNA nanotechnology offers one way for scientists to replace such methods of production. Rather than taking a lump of material and sculpting it into the desired shape, nanotechnologists can instead use the selective bonding characteristics of DNA to assemble objects at the molecular level—and perhaps even to dictate their movements.

For example, chemists have now created molecular machines from bespoke pieces of DNA that can move along surfaces. They have made molecular-sized cubes and meshes, and have figured out how to persuade DNA strands to fold up into almost any shape imaginable, including Chinese characters and maps of the world smaller than a single virus. They are devising DNA computers that solve problems mechanically, by the patching together of little “sticky” tiles. They are using DNA tagging to hitch other molecules and tiny particles into unions that would otherwise be extremely difficult to arrange, enabling the chemical synthesis of new materials and devices. In short, scientists are finding DNA to be the ideal nanotechnological construction material, capable of being programmed to assemble itself into structures with a precision and complexity otherwise thought unattainable.

Although this research places DNA in roles quite unlike those it occupies in living cells, it all comes from the direct application of Watson and Crick’s original insight. A single strand of DNA is composed of four types of molecule, whose chemical names are shortened to the labels A, T, C and G, and in the double helix they tolerate only one kind of partner: A pairs with T, and C with G. This means that the sequence on one strand exactly complements that on the other.

So a DNA strand will pair up securely with another only if their sequences are complementary. If there are mismatches along the double helix, the resulting bulges or distortions make the double strand prone to falling apart. This pickiness about pairing means that a DNA strand can find the right partner from a mixture containing many different sequences.

Chemical methods for making artificial DNA, first developed in the 1970s, have reached the point at which strands containing millions of A, T, G and C bases can be assembled in any sequence. These techniques, developed for genetic engineering and biotechnology, are being used to create DNA strands designed to assemble themselves into exotic shapes.

The potential of the approach was demonstrated in the early 1990s by the chemist Nadrian Seeman of New York University and his collaborators. They created DNA strands designed such that, when they were mixed together, they twisted around one another not in a single helical coil, as in Watson and Crick’s famous model, but as a framework of short, interconnected double helices that formed the struts of tiny, cube-shaped cages (opposite, bottom left). No one had any particular use for a DNA cube; Seeman was demonstrating a proof of principle, showing that a molecular shape that would be extremely hard to fashion using conventional chemistry could be engineered by figuring out how to program its components to build themselves.

Although regarded for some years as little more than a clever curiosity, Seeman’s work was visionary. It showed how nanotechnologists might build very small objects from the bottom up, starting with individual atoms and molecules.

Unlike most other molecules, DNA will do precisely what it is told. Researchers have worked out how to program DNA strands to weave themselves into webs and grids, like a chicken-wire mesh, onto which other molecules or objects can be attached. In February, a team at Marshall University in West Virginia showed that giant molecules called carbon nanotubes—nanometre-scale tubes of carbon which conduct electricity and have been proposed as ultra-small electronic devices—can be arranged in parallel pairs along a strip of DNA origami. The carbon nanotubes were wrapped with single-stranded DNA, which attached to corresponding strands fixed to the DNA circuit board, anchoring the nanotubes in place.

The astonishing versatility of DNA origami was revealed in 2006 when Paul Rothemund at the California Institute of Technology in Pasadena unveiled a new scheme for determining the way it folds. His approach was to make single strands programmed to crumple into back-and-forth hairpin-like turns by the pairing-up of bases so as to create a two-dimensional shape. The folds were pinned in place with staples made from short DNA strands with appropriate complementary sequences.

Rothemund developed a computer algorithm that could work out the sequence and stapling needed to define any folding pattern, and showed experimental examples ranging from smiley faces (opposite) and stars to a map of the world (opposite) about a hundred nanometres across (a scale of 1:200,000,000,000,000). These complex shapes could take several days to fold up properly, allowing all kinks and mistakes to be ironed out, but researchers in Germany reported last December that each shape has an optimal folding temperature (typically around 50-60 degrees centigrade) at which folding takes just a few minutes—a speed-up that could be vital for applications.

Last March, Hao Yan of the University of Arizona took the complexity of DNA origami to a new level. He showed how the design principles pioneered by Seeman and Rothemund can be tweaked to make curved shapes in two and three dimensions, such as hollow spheres just tens of nanometres wide. Meanwhile, in 2009 a Danish team saw a way to put DNA cubes to use: they made larger versions than Seeman’s, about 30 nanometres across, with lids that could be opened an closed using a “gene key.” This development was especially exciting because it suggested a potential way to store drug molecules until an appropriate genetic signal releases them for action. In this way, the possibility arises of being able to deliver a drug directly to the particular cells within a human body that require treatment, or which is released only when certain genes become activated.

As aficionados of Lego and Mecano know, once you have a construction kit the temptation is to give it moving parts: to add motors. Molecular-scale motors are well-known in biology: they make muscles contract and allow bacteria to swim. These biological motors are made of protein, but researchers have figured out how to produce controlled movement in artificial DNA assemblies too. One approach, championed by Bernie Yurke of Bell Laboratories in New Jersey and Andrew Turberfield at the University of Oxford, is to make a DNA “pincer” that closes when a complementary DNA strand sticks to the arms of the pincer and, acting as a kind of “fuel” to power the device, pulls them together. A second strand strips away the first and opens the arms wide again. Using similar principles, Turberfield and Seeman have made two-legged “DNA walkers” that stride along DNA tracks, while a “DNA robot” devised by Turberfield and colleagues can negotiate a particular path through a network of such tracks—it is directed by fuel strands that prompt a right- or left-hand turn at branching points.

They and others are also working out how to implement the principles of DNA self-assembly for computing. For example, pieces of folded-up DNA representing binary 1s and 0s can be programmed to stick together to encode information, and can be shuffled around to carry out calculations—a sort of mechanical, abacus-like computer at the molecular scale.

There is even the tantalising—some might say scary—possibility that DNA structures and machines could be programmed not only to self-assemble but to copy themselves. It’s not outrageous to imagine at least some products of DNA nanotechnology acquiring this life-like ability to reproduce, and perhaps to mutate into better forms. Right now such speculations recede rapidly into science fiction; but then, no one guessed 60 years ago where the secrets of DNA self-assembly would take us today.