Friday, October 31, 2014

Michael White - Why DNA Is One of Humanity’s Greatest Inventions

From Pacific Standard, this is an interesting article on how humans are using DNA -- ours and other species' -- to change the world. One wonders if that is such a good thing considering how little we still know about how DNA functions.

Why DNA Is One of Humanity’s Greatest Inventions

By Michael White • October 24, 2014 

(Photo: Renzo.luo/Shutterstock)

How we’ve co-opted our genetic material to change our world.

Humans and their ancestors have been using tools for millions of years. We owe our prolific capacity for making tools to our DNA, and now we’ve reached the point were we’ve made DNA itself into a tool. We use DNA as a crucial research tool in the lab, we use it to engineer food crops and biofuel-producing microbes, we use it as a forensic tool and a medical diagnostic, and we use it to access our ancient history. We’ve even put DNA to uses that have nothing to do with biology whatsoever, as a nanomaterial with amazing chemical properties. Our genetic material is turning out to be one of our most useful high-tech tools.

It didn’t have to be this way. Before the 20th century, scientists didn’t expect the physical make-up of our genes to be something as simple, elegant, and useful as DNA. Darwin, for example, proposed that our genetic material was basically a chemical soup, made of different kinds of molecules that were secreted by each body part and gathered in the reproductive cells. Like the diffuse nebular gases that self-organize into solar systems, our genetic material was often thought to be a complex mix of ingredients that spontaneously organize themselves to direct the development of a new organism.

If this theory were true, the science of genetics—and our society—would now be very different. It would be much more difficult, if not impossible, to do many of the things we do with DNA, such as engineer microbes to make drugs or biofuels, or discover our relationship with Neanderthals. Paternity tests and viruses wouldn’t exist. Perhaps life wouldn’t exist either; in the 1930s and ’40s, physicists convincingly argued that a genetic chemical soup was thermodynamically impossible.

By that time, biologists were already well on their way to discovering what genes actually are: segments of giant molecules of DNA. Our genetic material turns out to be surprisingly similar to a text, with genes spelled out in a linear string of chemical letters. The analogy to a text isn’t perfect, but it’s remarkably good and partially explains why DNA is such a useful tool. The ability to represent genes as a text on our computers is a boon to biologists, who now analyze genomes with the same text-parsing algorithms that go into spam filters. One of the most basic tools of a molecular biology lab are enzymes that cut, copy, and paste DNA text; without these, much of the last 40 years of biological research would have been impossible. So would commercial genetic engineering, which, aside from its role in agriculture, is increasingly important for producing drugs and chemicals using processes that are more efficient and less environmentally damaging.

Because of DNA’s useful properties, “molecular biology” is not only a scientific discipline, but also a set of essential tools used by biologists of all sorts. By manipulating DNA, scientists tackle questions that have little to do with DNA’s biological role. They modify DNA to test hypotheses or to insert chemical sensors into an experimental organism, and they use DNA as a convenient way to read the outcome of an experiment. In my own work, I use DNA “barcodes,” short, easy-to-read sequences of DNA that tag the process I’m interested in. In paternity testing and forensics DNA is merely an identifier; its molecular function is irrelevant. That DNA is a tool with many different biological applications explains the enormous impact of the recent, dramatic improvements in technologies to read and synthesize DNA—DNA science dominates biology more than ever before.

We’ve now extended the uses of DNA beyond biology. DNA is not only life’s hackable source code; it’s a nanomaterial with very useful chemical properties. In particular, DNA is a programmable polymer that reliably folds into very small and fantastically intricate shapes. Engineering shapes from folded DNA is called, appropriately enough, DNA origami. Two key properties of DNA make this molecular origami possible: With its 4-letter chemical alphabet, the number of possible designs is huge. There are over a trillion variations of even a very short, 20-unit long DNA segment. And second, strands of DNA like to stick to each other in predictable ways, typically forming the iconic double helix.

Using DNA origami, engineers have built all sorts of miniature DNA widgets: motors, sensors, rulers, stencils, boxes, smiley faces, and “dolphin-shaped structures with flexible tails.”

These aren’t just demonstration pieces; DNA origami is key element of nanotechnology. In a paper published this month, researchers from MIT and Harvard’s Wyss Institute for Biologically Inspired Engineering describe how they built DNA “molds” to cast precisely shaped gold and silver nanoparticles. These nanoparticles are used in a variety of technologies, and they are typically etched using beams of electrons. But this process is slow and limited in its resolution. By building small molds out of strands of DNA and filling them with gold or silver particles, the researchers were able to cast nano-spheres, triangles, and cubes. They argue that their strategy “points to a new kind of manufacture framework: DNA-directed, digitally programmable fabrication of inorganic nanostructures and devices”—essentially 3-D printing on a nanometer level.

As a tool-using species, we’ve long been making tools out of whatever materials we can get our hands on. We’re lucky that we’ve got the DNA to build tools. We’re also lucky that DNA itself makes such a great tool.

Michael White
Michael White is a systems biologist at the Department of Genetics and the Center for Genome Sciences and Systems Biology at the Washington University School of Medicine in St. Louis, where he studies how DNA encodes information for gene regulation. He co-founded the online science pub The Finch and Pea. Follow him on Twitter @genologos.

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