Fifty years after the discovery of the structure of DNA, a new use has been found for the very molecule of life – as fuel for a molecular computer.
Ehud Shapiro of the Weizmann Institute of Science has, for many years, been working on developing the information technology inherent in DNA to power complex calculations. In the longer term, measured in decades, we might find autonomous, programmable molecular computers in vivo, sensing biochemical anomalies, consulting their programmed medical knowledge and synthesizing the appropriate drug molecules in response, Shapiro told Spotlight.
DNA provides one of the most compact and efficient digital information systems known. With just four basic building blocks it can represent the ingredients and blueprint for making a microscopic algae or an elephant in a molecule-sized space. A decade ago, researchers such as Leonard Adleman of the University of Southern California began to find ways to make laboratory-scale DNA manipulation solve mathematical puzzles, such as the travelling salesman problem. More recently, Shapiro demonstrated that a molecular-scale system that exploits the processing power of enzymes could carry out calculations without human intervention.
However, as with any electronic device, these molecular computers need a power supply. Obviously, connecting up a conventional power source, would be one option but Shapiro working with Yaakov Benenson, Rivka Adar, Tamar Paz-Elizur, and Zvi Livneh wanted a more frugal solution. They have now found that the single DNA molecule that encodes the input to the computation can provide all the power requirements too. In terms of speed and size, DNA computers may eventually surpass conventional computers that use silicon microchips.
Previously, the researchers had used the well-known energy molecule of living things – ATP, or adenosine triphosphate, as chemical energy for their DNA computers. In the new approach they have designed out this independent power supply so that the DNA input molecule spontaneously releases energy for the computational operations to take place. In each computational step, two complementary DNA molecules – an input molecule and a software molecule – spontaneously bond together. The software molecule then directs a DNA-cleaving enzyme to cut a piece of the input molecule. The enzyme, FokI, breaks two bonds in the DNA double helix, releasing the energy stored in these bonds as heat, sufficient to trigger the next step in the computation.
The computer itself is similar to the earlier system devised by the team. It is a special case of a Turing machine, a two-state, two-symbol finite automaton. It can answer simple questions about binary strings, which are encoded as DNA strings, such as Does a binary string of a’s and b’s contain an even number of a’s? or Is the length of the string even or odd?
This may seem trivial but such logical operations are at the heart of the computational process allowing much more sophisticated questions to be asked by linking many individual devices. Ultimately such computers could provide biological data analysis in vitro, without the need to convert the information to electronic format (i.e. sequence the DNA), Shapiro told us.
Astoundingly, a single teaspoon of Shapiro’s computer soup might contain 15000 trillion DNA computers, together performing 330 trillion operations per second with what he says is 99.9% accuracy per computation step. The overall process produces just 25 millionths of a Watt of waste energy. Shapiro’s work was recently awarded the Guinness World Record as the world’s smallest biological computing device.
Proc Natl Acad Sci (USA), 2003, 100, (5), 2191-2196