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The History of the DNA computer

written by: Robyn Broyles•edited by: Leigh A. Zaykoski•updated: 7/22/2008

The history of DNA computing is short, but full of amazing technological achievements. It has tantalizing potential for advances in computing speed and miniaturization. Medical applications may one day treat diseases and even cure cancer by installing computational genes directly into patients' DNA.

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    Molecular model of DNA
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    History of DNA computing


    DNA computing started in 1994 when Leonard M. Adleman, a University of Southern California researcher, solved a version of a mathematical problem called the “traveling salesman problem” using DNA in a test tube. The problem is to find a route that passes through a certain set of cities exactly once, given the constraint that only certain routes between cities are possible. This first DNA computer found the solution for a seven-city version of this problem by simple trial and error, without using the logic circuits found in traditional microprocessors.

    The problem itself is not difficult to solve -- conventional computers can solve the traveling salesman problem for thousands of cities. Adleman's achievement was significant because it demonstrated that computing can be done using DNA molecules, rather than by electrical circuits.

    Three years later, University of Rochester researchers created simple Boolean logic gates made from DNA. Logic gates are the basis of modern computers' processing abilities, and fashioning them from DNA was a major breakthrough. The development of logic gates opened the doors to sophisticated DNA-based processors.

    In 2002, scientists at the Weizmann Institute of Science in Israel unveiled a working microprocessor made not of silicon, but of protein structures and DNA molecules. A year later, they had engineered a computer made of a single strand of DNA.This amazing device was vanishingly small, since DNA is nothing more than a large molecule, yet could perform 330 trillion operations per second (0.33 PFLOPs). Compare this to the (current) world's fastest supercomputer, the IBM Roadrunner, which can perform about 1.03 PFLOPs.

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    Potential of DNA computer technology


    DNA computing is a form of parallel computing, in which processes are undertaken simultaneously. Conventional processors complete solve problems by completing their constituent tasks one at a time. Parallel computers can dramatically outperform conventional computers in solving some types of problems. Silicon-based parallel computers are the cutting edge of high-performance computing technology, but they are large and draw enormous amounts of electrical power. Compared with traditional parallel computing hardware, DNA computers have the advantages of being much smaller and of not requiring electricity.

    Just as traditional computers make use of microchip hardware, DNA computers have their own version of microchips, which are already in wide use. These devices are called DNA microarrays or “gene chips,” and are manufactured by several companies, including Affymetrix and Illumina. Gene chips evolved from a DNA-analysis technique called Southern blotting. In a gene chip, short segments of DNA called probes are attached to a glass or silicon surface; these then “hybridize” (pair up) with fragments of the DNA being analyzed. Gene chips are used in bioinformatics, with applications ranging from forensic analysis to cladistics. In computing, they may become especially useful for reading the output of a DNA processor.

    Because they utilize parallel processing, DNA computers will likely be useful in fields that use “fuzzy logic,” such as encryption. Specialized computers called computational genes will have wide-ranging medical applications in detecting and treating diseases. DNA may replace silicon as the next king of miniaturization and speed in computing.