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Computing with DNA

DNA encodes information. It happens to be used primarily to encode the information necessary to make living organisms, but there’s no rule dictating that that is the only information it can encode. DNA stores  information in its four nucleotide bases much like computer chips store it in zeros and ones; the information can be manipulated and transmitted by designing specific genetic sequences that hybridize with one another and using enzymes that recognize certain sequences to link stretches of DNA together or break them apart. These enzymes work simultaneously, not sequentially, rendering DNA “computers” – actually aqueous solutions of molecules in test tubes – good at solving problems that require parallel computations.

The first use of DNA as computer was by Leonard Adleman in 1994. He used DNA strands to solve the travelling salesman problem: if a salesman needs to visit a number of cities, each of them once and only once, how to find the shortest route?

Adelman generated short DNA sequences corresponding to each of seven cities, and other sequences that served as linkers between them. He mixed these short stretches together and allowed them to hybridize in various ways. He then looked for the longest strands that started and ended with the sequences corresponding to the proper cities, confirmed that they contained the sequences for each of the intermediate cities, and read out the order.

Thus far it has been difficult to get an electrical current to flow through long DNA molecules, and this has been a hurdle in molecular computing. But this week, a team at Hebrew University’s Institute of Chemistry and Center for Nanoscience and Nanotechnology managed to do just that. The researchers measured currents of travelling down DNA molecules for over a hundred nanometers. Interestingly, they needed DNA molecules made of four strands wound together, instead of the usual two. DNA might thus be helpful in reducing the distance between transistors, a step which is currently a bottleneck in further miniaturizing electronic devices.

One thing that DNA computers can do that silicon chips cannot is exist and work inside cells. Molecular sensors made of DNA can sense if a cell has turned cancerous; if it has, the sensor then releases an anticancer drug inside the cell. DNA computers might also one day be used to program stem cells to mature along different lineages, becoming skin cells, muscle cells, or brain cells as needed.

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