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DNA: It's Not Just for the Living Anymore

The smiley-faced DNA above is the work of Paul Rothemund of CalTech. In March 2006, Rothemund achieved what became known in the science world as "DNA origami."


To people who say that true nanomachines — those that assemble themselves from the bottom up — are impossible, the best answer true believers can give is simply to present their own existence as proof of concept. We are self-assembled out of simple building blocks.

For many, this settles the argument quickly. I do not believe it does, but I’ll get into that further down if you’ll stay with me. For now, for the sake of argument, let’s say that all that is left is for us to figure out how nature manages this bottom-up self-assembly. But you do not necessarily need to figure out how this feat was accomplished. You can take a shortcut and use DNA, the gift handed down to us via nature’s laboratory and a few billion years of evolution.

DNA exists to self-assemble and its strands are a scaffolding upon which we can build more and more complex structures. DNA can give us not only the physical frame but also the template by which we can learn how to program synthetic versions to obey our commands. This is outlined in a recent paper co-authored by CalTech’s Paul Rothemund, a DNA nanotech pioneer, in Nature Chemistry.

British scientist Richard Jones, author of “Soft Machines,” noted just this week on his blog that DNA nanotechnology is fast becoming the place to watch for truly amazing developments. Jones writes:


For many years DNA nanotechnology could have been viewed as a marvelous technical tour-de-force with little potential for real applications, but the continuing exponential falls in the cost of synthetic DNA and the increasing sophistication of the devices being created in the growing number of laboratories working in this field makes this conclusion less certain.

Jones was referring specifically to the work of NYU’s Nadrian Seeman, who for a decade or so was pretty much the only person working on the amazing possibilities of DNA nanotechnology. More background on his “DNA Walker” and other cool stuff from Seeman’s lab can be found here.

I’m from Michigan where, once upon a time, we were pretty good at engineering and assembling machines that went places and changed the world. Part of the process of creating these machines was to map them out first on CAD/CAM software. So, a few years ago, I met the creator of a Motor City company that was way ahead of its time. Nanorex, based in suburban Detroit, was a company that set out to create CAD software to help engineers design these new DNA nanostructures.

I first met its founder, Mark Sims, in 2004 just after I had won that year’s prize in communication from the Foresight Institute, a nanotechnology think tank. Mark and I found ourselves sitting next to each other on the plane ride back to Michigan from Washington, D.C., and we got to talking about both of our obsessions — nanotechnology. The difference between us was that I just wrote about it and he was actually doing something useful.


I wrote about his company for a Detroit-area tech magazine called X-OLOGY a little while ago:

When Sims founded the company in 2004, it was focused purely on creating software for the “design, simulation and analysis of atomically precise molecular machine systems.” In other words, taking atoms and using their naturally occurring covalent bonds to stick them together and create just about anything. The problem, Sims says, is that nobody really knows how to actually build these molecular machine systems yet. Maybe they’ll figure it out in 20 years, he predicts, and then commercialize it a few years later.

In the meantime, his shorter-term plan is to create design software for researchers working on another promising branch of nanotechnology.

Rather than create entirely new materials out of nothing but atoms, many leading-edge nanotech researchers have found something better – the beneficiary of 3.6 billion years of evolutionary research: DNA.

“The thing that’s exciting about DNA is that they’re doing it now,” Sims says. “Here you have a material and a system with it that is programmable and capable of bottom-up self-assembly from nanoscale to literally microscale.” More here (PDF 158 KB)

I wrote to Mark a few weeks ago to ask how things were going at Nanorex. He told me that, unfortunately, his company closed shop in 2008 for a number of reasons, but it was primarily that it was entirely self-funded and the economic downturn made it increasingly expensive to keep afloat. But the company was never meant to go anywhere, since so few people were actually doing any DNA nanotechnology. It was purely a labor of love by Sims.


But what Nanorex accomplished during its five-year mission, Sims says, was develop an “interactive modeling tool for nanoscale design in order to generate curiosity about nanotechnology and ‘bend the minds’ of young students and scientists. I’m satisfied Nanorex achieved that goal to a significant degree and I’m proud of that.”

He also did create a real CAD system that was used to design and fabricate a nanoscale structure. His open-source software product, Nanoengineer-1, designed DNA origami — a process pioneered by Rothemund’s CalTech lab — from scratch. His design was the first step in fabricating a NAND gate using bottom-up self assembly. “Ultimately, we wanted to create a functional 1-bit adder using DNA and carbon nanotubes,” Sims says. “It was very ambitious, but I’m convinced we could have taken this very far. At least we made the initial NAND gate tile which was a huge achievement. I’m very proud of this.”

So, Nanorex is no more, but DNA nanotechnology continues to develop, as the work of Seeman and Rothemund are expanded upon by other researchers. And Nanoengineer-1, Nanorex’s free open-source software, has been downloaded more than 10,000 times. The seeds are there for continued experimentation and growth.


Just this past October, Seeman developed artificial structures out of DNA strands that can self-replicate, another important step along the way to self-assembling, self-replicating nanomachines. This is no longer science fiction. The naysayers of a decade ago have already been proved wrong many, many times.

Think nanobots are just science fiction? Well, maybe, but a group of Dutch scientists recently took a single-molecule car out for a spin. The car, itself, is just what we here in Detroit like to call a prototype. They’re playing around to see what they can do. Tibor Kudernac, a chemist now at the University of Twente, the Netherlands, and lead author of the paper, tells the BBC: “There are ways to play around,” he said. “That’s what we chemists do — we try to design molecules for particular purposes, and I don’t see any fundamental limitations.”

Now, here’s where I depart a little bit with true nanotech believers. As I hinted at the beginning of this column, I do not necessarily believe that the existence of life is, in itself, proof that we can build molecular machines. It is not a good argument to use. Maybe someday, in the far-distant future, we can create a toaster-size “molecular assembler” that can build whatever we want one atom at a time. But, the fact is, after you hit the “print” button, you still only have a model of the thing … and not the thing, itself.


This might be primitive of me, but I believe life is analog. Not digital. With DNA, we are not inventing a nonexistent digital reality. We are beginning with the true building blocks of life. What we create after that is up to us.

(Thumbnail on PJM homepage by Shutterstock.com.)

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