Scientists in the United States have taken a major step forward in using DNA, the building blocks of life that carry the human genetic blueprint, to process information and solve mathematical problems. DNA computing has sparked intense interest because more information can be stored on molecules of DNA than any silicon computer chip. Scientists estimate that a dried gram of DNA can store more information than a trillion CDs.
Lloyd Smith and his colleagues at the University of Wisconsin-Madison describe how they have transferred a set of DNA molecules from the test tube to a glass plate. "It demonstrates DNA computing on surfaces, which provides a relatively simple pathway of upscaling DNA computing to solve large problems," Smith said. "It shows that DNA computing can be put in a form which is very amenable to automation."
Instead of retaining information as ones and zeros and using mathematical formula to solve a problem, DNA computing uses data represented by a pattern of molecules arranged on a strand of DNA. Specific enzymes act like software to read, copy, and manipulate the code in predictable ways. Smith says DNA is a potential way of getting around the problem of the silicon chip, which scientists believe cannot be scaled down much further.
Smith cautions that DNA computing is still in its infancy and a long way from challenging chip technology. Only about a dozen centers around the world are working on DNA computing and much more needs to be done. "The interest in the community of computer people is more as exploration or new models for computing than in actual practical consequences in the near term," Smith said.
Leonard Adleman of the University of Southern California came up with the idea of using DNA for computing in 1994. It was while reading a text on DNA that Adleman had a revelation. The mathematician was struck by a resemblance between the way polymerase enzymes "read" DNA and the principle behind the Turing machine, a computational model proposed in the 1930s by theorist Alan Turing.
In 1995, Adleman opened the Laboratory for Molecular Science at USC, where research on DNA computing continues. They are challenging the National Security Agency's Digital Encryption Standard. The problem is beyond the scope of most modern supercomputers, but in theory, DNA's huge parallel-computing capacity is ideally suited to complete the task. USC molecular biologist Myron Goodman, an expert in DNA error correction and transcription, is Adleman's collaborator in the lab.
In 1998, Discover award finalist Nanogen Corporation developed DNA Optical Storage Media. If it works, it will be possible to cram a thousand times more information on a CD-ROM. On a CD, each digital bit is represented as a dot etched on the disk. But the dot can be no smaller than the laser beam used to read it, about four hundred-thousandths of an inch.
To get around this limit, Nanogen's Michael Heller built synthetic DNA containing chromophores, molecules that glow when a laser shines on them. The presence or absence of the glow would represent a 1 or a 0 of binary data. Chromophores respond to specific frequencies of lasers, so many different dots could be packed into a single spot and be read individually by separate laser flashes.
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