Scientists report advance in DNA computing

Scientists have taken DNA computing from the free-floating world of the test tube and anchored it securely to a surface of glass and gold. In so doing, they have taken a small but important step forward in the quest to harness the vast potential of DNA to perform the same tasks that now require silicon and miniature electronic circuits.

Aboove: Chemistry professors Lloyd Smith, left, and Robert Corn, right, along with graduate student Liman Wang, are co-authors of a new paper that describes a technique for applying DNA to gold-plated glass, another step toward creating DNA computers capable of solving the same kinds of problems conventional computers now handle routinely. Below: The gold chip shown here contains millions of DNA molecules capable, with the help of enzymes that act like software, of solving a relatively complex problem. Putting DNA computing on a solid surface makes the technology simpler, more accessible and more amenable to being scaled up to make computers. Photos: Jeff Miller.

The accomplishment, reported in the Thursday, Jan. 13 issue of the journal Nature by a group of scientists from the UW–Madison, is an important demonstration that shows DNA computing can be simplified and scaled up to tackle complex problems, says Lloyd Smith, a UW–Madison professor of chemistry and a co-author of the paper.

DNA computing is a nascent technology that seeks to capitalize on the enormous informational capacity of DNA, biological molecules that can store huge amounts of information and are able to perform operations similar to a computer’s through the deployment of enzymes, biological catalysts that act like software to execute desired operations.

The Nature paper describes the development of novel surface chemistry that greatly simplifies the complex and repetitive steps previously used in rudimentary DNA computers. Importantly, it takes DNA out of the test tube and puts it on a solid surface, making the technology simpler, more accessible and more amenable to the development of larger DNA computers capable of tackling the kinds of complex problems that conventional computers now handle routinely.

“It demonstrates DNA computing on surfaces, which provides a relatively simple pathway to upscaling DNA computing to solve large problems,” Smith says.

In the Wisconsin experiments, a set of DNA molecules were applied to a small glass plate overlaid with gold. In each experiment, the DNA was tailored so that all possible answers to a computationally difficult problem were included. By exposing the molecules to certain enzymes, the molecules with the wrong answers were weeded out, leaving only the DNA molecules with the right answers.

The appeal of DNA computing lies in the fact that DNA molecules can store far more information than any existing conventional computer chip. It has been estimated that a gram of dried DNA can hold as much information as a trillion CDs. Moreover, in a biochemical reaction taking place in a tiny surface area, hundreds of trillions of DNA molecules can operate in concert, creating a parallel processing system that mimics the ability of the most powerful supercomputer.

The chips that drive conventional computers represent information as a series of electrical impulses using ones and zeros. Mathematical formulas are used to manipulate that binary code to arrive at an answer. DNA computing, on the other hand, depends on information represented as a pattern of molecules arranged on a strand of DNA. Certain enzymes are capable of reading that code, copying and manipulating it in predictable ways.

Conventional computing, with ever more and smaller features packed onto the silicon chips that power it, is approaching the limits of miniaturization. DNA computing, says Smith, is one potential way around that barrier.

But current DNA computing technology, Smith emphasized, is still far from overtaking the silicon chip. The new method reported by the Wisconsin scientists, he says, is simply a testbed for working out an improved and simpler chemistry for DNA computing.

Nevertheless, Smith says, the new surface chemistry provides an opportunity to harnessing DNA to make the biggest nonconventional computer yet.

“We’re interested in scale up. We believe that based on the principles we’ve worked out here, we can see scaling up within a few years a factor of a trillion or more.”

In addition to Smith, co-authors of the Nature paper, include Qinghua Liu, now of Gen-Probe, Inc., San Diego, Calif.; Liman Wang, UW–Madison department of chemistry; Anthony G. Frutos, now with Corning, Inc., Corning, N.Y.; Anne E. Condon, now a University of British Columbia professor of computer science; and Robert M. Corn, a UW–Madison professor of chemistry.