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Is DNA the new silicon?

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CIOL Bureau
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Ben Hirschler and Patricia Reaney

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LONDON: News last month that scientists had built the first programmable

computer made from the molecule that carries our genes has brought the vision of

computing with DNA one step nearer.

Israeli researchers have developed a DNA computer so tiny that a trillion of

them could sit in a drop of water and perform a billion operations per second.

The idea of following Mother Nature's lead and using DNA to store and process

information took off in 1994, when Leonard Adleman of the University of Southern

California first used DNA in a test tube to solve a simple mathematical problem.

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Since then a dozen research groups around the world have jumped into the

field -- which fuses biology and information technology -- in a bid to harness

the inherent ability of strands of DNA to perform trillions of calculations at

the same time.

That massive simultaneous problem solving at a nanoscale is a potential way

of getting round the limits of the silicon chip, which scientists believe cannot

be scaled down much further. The famous double-helix molecule found in the

nucleus of all cells can hold more information in a cubic centimetre than a

trillion music CDs, with data stored as a code of four chemical bases --

adenine, thymine, cytosine and guanine, or A, T, C and G.

These chemical "letters" like to link up with particular other

ones, which means strands with complementary letters stick together. These

linkages can then be "read" using naturally occurring enzymes, giving

scientists a way of finding hidden patterns in complex datasets.

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The achievement of researchers at Israel's Weizmann Institute in getting DNA

to perform calculations automatically follows a breakthrough last year by a team

at the University of Wisconsin who successfully anchored strands of DNA to a

glass slide, opening the door to eventual DNA computer chips.

But harnessing DNA's potential as a microprocessor remains a challenge and

many scientists believe it will only ever complement rather than replace

silicon-based computers.

Hybrid machines



"I think in the future we might have hybrid machines that use a lot of

traditional silicon for normal processing tasks but have DNA co-processors to

take over specific tasks for which it is best suited," said Martyn Amos, a

lecturer at the University of Liverpool who wrote the first PhD in DNA

computing.

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While a conventional desktop PC is designed to perform one calculation very

fast, DNA strands produce billions of potential answers simultaneously, which

may make them suitable for solving "fuzzy logic" problems that have

many possible solutions rather than the either/or logic of binary computers.

Although DNA offers an intriguing new medium for computing, scientists have

yet to crack the problem of "scalability," or the capacity to expand

to solve huge problems that existing computers now do.

Adleman's initial test-tube calculation solved the so-called "travelling

salesman problem" by working out the shortest route between seven cities

linked by 14 one-way roads. All possible permutations were created in a test

tube and the correct ones filtered out using biochemical reactions. The snag is,

the bigger the problem the more DNA you need -- and, with current techniques,

the numbers can get out of hand.

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"It has been estimated that if you scaled up Adleman's problem to 200

cities from seven, then the weight of DNA required to represent all the possible

solutions would exceed the weight of the Earth," said Amos.

That is one the reasons why computer giant International Business Machines

Corp is focusing on other ideas such as carbon nanotubes and quantum computing,

based on atoms rather than biological material.

Clever cells



If it seems unlikely we will be popping down to the local PC store for a DNA

computer any time soon, the clever molecule may yet have other applications that

could bring the technology closer to the pharmaceutical industry.

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Professor Ehud Shapiro of the Weizmann Institute, the head of the Israeli

research team, believes DNA nanomachines could in the future operate within

human cells, monitoring potentially disease-causing changes and synthesising

drugs to fix them.

"The living cell contains incredible molecular machines that manipulate

information-encoding molecules such as DNA and RNA (its chemical cousin) in ways

that are fundamentally very similar to computation," he said.

"Since we don't know how to effectively modify these machines or create

new ones just yet, the trick is to find naturally existing machines that, when

combined, can be steered to actually compute."

Another use could be in building diagnostic tests inside a "smart"

bacterium by re-engineering its genome to include a small logic circuit that

could, for example, be activated by the presence of a certain chemical. The

whole field of DNA computing remains at the very early

"proof-of-principle" stage but could start to become a reality in the

next five to 10 years, Amos believes.

(C) Reuters Limited.

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