Thursday, May 23, 2013

DNA Computing: Is It Here Yet?


In 1994, Leonard Adleman, a computer scientist at University of Southern California, introduced the concept of DNA based computing in a paper in the journal Science. (1) He used DNA strands to solve the well-known traveling salesman problem (given a number of cities, what is the shortest route for a salesman to take without going to any city more than once?) The entire process took days and required a lot of human intervention. Since then logic gates, essential elements of any computer, have been created using DNA code with a variety of approaches. The circuits can solve simple mathematical problems, recognize patterns, play games and even detect disease states inside a cell.

All modern computers have three basic functions: storing, transmitting and performing logical operations. In 2012, Endy et al. made the headlines by announcing the development of the first two of those functions for DNA computers. (2) Now they announced the last component, that of computation.

In a paper published March 28, 2013 in Science (3) a team of Stanford University bioengineers led by Endy describe a biological transistor made from DNA and RNA which they named a “transcriptor.” This transcriptor uses proteins called integrases to digitally control the flow of RNA polymerase along a strand of DNA, analogous to the flow of electrons along a circuit in electronic transistors. Using these transcriptors, the team has created “logic gates” that can function inside a living cell.

The theoretical advantages of a DNA computer are many. One pound of DNA can conceivably store more information than all the electronic computers ever built. The computing power of a teardrop-sized DNA computer will be more powerful than any supercomputer existing today. More than 10 trillion DNA molecules can fit into an area of 1 cubic centimeter, which would hold 10 terabytes of data and perform 10 trillion calculations at a time. If more calculations are required, more DNA can be added. The DNA system works in parallel, in contrast to most conventional computers that work in series. In addition, DNA is clean, abundant, and uses no toxic materials, unlike electronic chips. It will require little or no energy to run and there will be no overheating problem. And there is one unique trait that a DNA computer has which will make it invaluable in the future: it can work inside living cells.

DNA computing is in the very early stages, to be sure. Researchers do not expect DNA computers to replace laptops any time soon, if ever. What they are aiming for instead is a biologically based computing system that can be inserted inside living cells to study and reprogram genetic systems (for example, monitor the presence of specific chemicals, deliver drugs to specific cells, count the number of divisions a cell undergoes and destroy it if it goes beyond a certain number of divisions, thus avoiding cancer). Similar DNA based computers could be used in microbes and plants to greatly expand our ability to monitor the environment. Into the future, one can envision inserting a genetically engineered microbe into our system which could monitor specific measurements of “health” and then synthesize the appropriate medicines when necessary, a kind of embedded pharmaceutical laboratory ready to produce anything on an as needed basis. 

3.     Jerome Bonnet, Peter Yin, Monica E. Ortiz, Pakpoom Subsoontorn, and Drew Endy. Amplifying Genetic Logic Gates. Science, 28 March 2013 DOI: 10.1126/science.1232758