UA Profs Pursue DNA Engineering

Three professors at the University of Arkansas are working on an engineering project that is sort of like Mary Shelley’s Dr. Frankenstein in reverse.

Instead of creating life from dead matter and machines, they’re looking at ways to make machines out of living material. Specifically, the team is looking at deoxyribonucleic acid, commonly known as DNA.

Russell Deaton, Jin-Woo Kim and Steve Tung all work in various capacities and disciplines at the UA College of Engineering. They’ve been collaborating on a three-year, $699,000 research grant from the National Science Foundation to create a library of reliable DNA sequences.

Each sequence can be thought of as a word, or a letter in a giant alphabet, which can then be used as a form of code for computing, or for database storage, or — because of the element of control — even to build nano-scaled products.

“Nano” is a prefix, meaning one-billionth of a unit. Therefore, take a measurement and move the decimal nine places to the left and that’s nano scale. A nanoparticle ranges in size from about 1/1,000th to 1/10,000th the width of a human hair.

Deaton, a computer science and computer engineering professor and the conceptual father of the DNA project, said the three-year study is nearing its end and the team has developed a library of about 100,000 unique sequences. And, he believes it is about to fine-tune a way to mass-produce each sequence in a reliable, predictable way.

“What me and my collaborators are trying to do, is to explore the possibilities of using biological materials for non-biological purposes,” Deaton said. “We’re not necessarily concerned with what we can compute with this, we’re more concerned with how we can make this practical, reliable. What’s the real potential of the technology?”

But why dabble in the squishy world of DNA when diode and silicone-based computing power has taken enormous leaps and bounds in the past 50 years?

There are inherent benefits in DNA, such as the potential capacity for a phenomenal amount of storage, Deaton said. Think about what it stores naturally, the most complicated computer of all, human heredity traits.

Something like the entire contents of the Internet could be stored within a droplet of water if the right approach is taken, Deaton said. That’s near 10 to the 18th power of bytes of information, he said.

Plus, the stuff is really, really small.

Miniaturization

The trio has proposals before the NSF for two related studies on DNA. Deaton said they hope to hear if they’ve landed more money, though he couldn’t say how soon.

One proposal is to explore the potential of DNA as a storage device for databases. The other will look at how viable it is to construct nano-sized components with the team’s DNA sequence library.

“Everybody thinks that by 2010 or 2012 traditional micro-electronic manufacturing techniques will have hit a wall,” Deaton said. “That is primarily because the device dimensions become so small, that optical ways of making the patterns that become the circuits will no longer work.”

Traditional micro electronics, such as a computer’s processor, are built from the top down, Deaton said, whereas, nano-scaled electronics may have to be built from the bottom up, and that may start at the level of DNA.

Nano technology, he said, is all about manipulating individual molecules. At this point in technology, a machine to build at that scale isn’t feasible.

“One technique of manipulating these individual molecules is to associate them with DNA molecules,” Deaton said. “And then to use that DNA molecule and the way that it interacts with other DNA molecules to assemble something useful,” he said.

This could benefit the electronics industry by furthering miniaturization of products, such as shrinking the typical-sized tower computer down to, say, the size of a micro cassette recorder (about 2.5 by 4.5 by 1 inches).

“We’re working on ways to make DNA molecules come together in a way that the engineer — the nano technology person — wants, and eliminates unplanned ways that they come together,” Deaton said.

Deaton has designed a great deal of sequences on computers. He’s been thinking about these problems for about a decade, he said. But in the last three or four years, the team has successfully made the transformation to the test tube as well.

He thinks with a few more tweaks and one more control experiment, the team ought to have a technique that will allow them to be able to manufacture very large sets of sequences that will react with one another in only one way.

Tube Tested

Though they office in the same building, Deaton and Kim, an assistant professor of biological and agricultural engineering, might as well come from different planets.

Deaton, an English undergrad turned computer engineer, has three desks that are covered with various hard-core science books and a layer of “professordom.”

Kim’s office is immaculate. Books are stacked just-so, and the room is more like a banker’s office than a researcher’s. He started as a chemical engineer and has ended up in biology.

What their offices share, however, are easels for drawing equations and graphical representations of their ideas.

Kim does the wet work on the project. That is, he takes Deaton’s computer generated models and simulates them in the lab.

So far, the team has been able to make the models work in the lab with a fair amount of success.

They can replicate DNA sequences and make them useful by separating them from each other.

“We don’t even really have to know what the sequences are,” Deaton said. “We just really have to know that they don’t interfere with each other, that they’re independent of each other, that we’ve got a certain number of them and that we’ve separated them.”

Kim agrees that developing practical nano-scale fabrication technology through this project is probably the first and most significant commercial application, though he thinks it will be several years before its time.

Hybridization

Tung, assistant professor of mechanical engineering, said his job in the collaboration is to gather up all the information from the other two and build small devices.

He said matching carbon nanotubes and DNA is a good platform for a computer and a “link between the computation and the biological device.”

Carbon nanotubes are nano-sized tubes of graphite that have similar properties to silicone, in that they can either conduct electricity or be semi-conductive to electricity.

A jar of the stuff looks like very black ash.

By weight, it’s more expensive than gold and it may one day serve as the base element for a nano-sized computer processor.

So far, Tung has been able to attach strands of DNA to carbon nanotubes end-to-end. But he wants to be able to attach them to the sidewalls. This will give engineers of the future greater control over manipulation and may facilitate nano-scaled fabrication.

Tung also talked of a possible cancer-screening test that would operate much like an over-the-counter pregnancy test. Though he doesn’t see that it will ever be available at the pharmacy, he said a drop of blood on spot may serve as a preliminary, and virtually instant, pre-screen before patients undergo futher tests.

Between the three, the application possibilities of engineered DNA sequences seem virtually endless.

“To me it’s really a reliability question, and we think that we’ve done that,” Deaton said.