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Biocomputing for Bioinformatics: Olympus Develops DNA Computer for Expression Analysis

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Olympus Optical of Tokyo said last week that it is developing the first DNA-based computer for applications in gene expression analysis.

Olympus is developing the DNA computer in collaboration with University of Tokyo professor Akira Suyama and NovusGene of Tokyo, a 51 percent-owned spin-off of Olympus. The project began last March with 400 million Yen ($3 million) in financing. Performance testing of a development prototype has begun using biological samples at NovusGene’s facilities, and full-scale analytical services are expected to come online in 2003.

Olympus spokesman Nobuhiko Morimoto described the DNA computer as “a fully automated reactor of DNA which autonomously reacts and solves combinatorial problems by its nature.” This computing-in-a-test-tube approach is expected to provide advantages such as huge computational capacity, massively parallel processing capabilities, and low energy consumption when fully developed.

In the first encoding step, Morimoto explained, the input cDNAs are converted into artificial DNA fragments with regular physicochemical properties and perfect specificity so that quantitative and accurate reactions take place. A traditional device such as a microarray, electrophoresis, or PCR is used in the final decoding step.

“Gene expression analysis consists of two steps,” said Morimoto. “The first is analysis by DNA experiments. The second is numerical analysis of the result of the experiments by an electronic computer. Our DNA-based computer will be a good alternative for the first step, but it can be applied to the second step … in the future.”

The DNA computer incorporates Magtration, a patented magnetic DNA extraction technique developed by Tokyo-based Precision System Science, to separate the DNA molecules from solution in the test tubes.

While DNA computers should be useful in a range of areas, Morimoto said that Olympus decided to make gene expression analysis the first use of the computer “because expression analysis has a big demand and was a simple application for our first approach.”

The technique should also provide some advantages over traditional microarray technology, Morimoto said, because current technology requires changing the chip format when switching between species, which is very expensive. “Our DNA computer requires only one chip for arraying artificial DNA fragments,” he said. “You don’t need the microarrays for each species of samples.”

NovusGene is now beginning to test the computer to quantitatively profile gene expression, and plans to publish its results at DNA8, the 8th International Meeting on DNA-Based Computers at the University of Hokkaido in June.

— BT

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