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DNA Computer Could Fight Cancer

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by Charles Choi
New York (UPI) Apr 29, 2004
New computers made of biological molecules that react to DNA hold the promise to diagnose and treat diseases such as cancer by operating like doctors inside the body, Israeli scientists said.

The devices, used in test-tube experiments, already have demonstrated the ability to identify and then destroy prostate and lung cancer cells, but their creators cautioned it could be decades before such biological computers find their way into medicine.

"The hope is that someday this direction will help lead to a new concept of 'smart drugs,'" said researcher Ehud Shapiro, a computer scientist at the Weizmann Institute of Science in Rehovat, Israel.

"Today's drugs are like carpet bombing -- you take a large amount of drug molecules and they go all over the body," Shapiro told United Press International from Brussels. "A smart drug would onl y operate where the condition of disease holds."

Shapiro and colleagues have created a series of biological computers in the past five years -- several trillion of which can fit in a drop of water. Their software is made of DNA, while the hardware is made of DNA-manipulating enzymes.

The computers work on genetic material, specifically ribonucleic acid or RNA, the smaller cousin of DNA. The body uses RNA often to transmit messages in the cell. Strands of DNA and RNA can bind if the sequences of molecules that make both up match.

Diseases such as cancer leave their own chemical fingerprint in the body, including over-producing or under-producing specific RNA sequences. The computer's enzyme hardware chops up the RNA it finds. If those bits bind to a computer's DNA software -- which is encoded to look for cancer sequences -- the computer then can release a drug.

In the lab experiments at the Weizmann Institute, the drugs in question were short DNA molecules known to interfere with tumors by suppressing key cancer genes, making those diseased cells self-destruct.

"I think it's really a wonderful landmark piece of work. It certainly merits a lot of interest," computer scientist John Reif at Duke University in Durham, N.C., told UPI. "The goal would be to do this in a cell, to have a doctor in a cell. This experiment doesn't do that. It does it in a test tube -- sort of a doctor in a test tube -- so it's a really cool idea but there's a major hurdle next.

"This is the first step, the biggest and most significant piece of work to date that indicates DNA computing techniques can be really important to therapeutic medicine," Reif said.

The scientists presented their findings Wednesday in Brussels at a symposium where Nobel laureates discussed the future of the life sciences. Their data also appears in the April 29 issue of the British journal Nat ure.

"We're sort of running ahead of ourselves. Had you asked me a year ago when we started how long it would take to reach the milestone we reached today, I'd have said 10 to 15 years," Shapiro said. "We are still overwhelmed by what we achieved. It took us less time than we thought."

The research team ensured more than just one chemical marker of a disease is required to activate drug output from one of the microscopic computers. A lone symptom could just be a temporary, insignificant phenomenon in the body.

"In our particular design, we can diagnose the presence of a disease by looking in a relatively straightforward way for eight symptoms of a disease, and can go up to 16," Shapiro said.

Shapiro's team originally designed biological computers to compete against electronic computers. The field began in 1994, when computer scientist Len Adleman at the University of Southern California proposed how DNA could be used in solving certain important mathematical calculations, such as the so-called "traveling salesman problem," critical in planning any kind of deliveries in a complex network, from shipping freight to scheduling airline flights to transmitting data packets on the Internet.

The problem is that although a single drop of water can have trillions of biological computers working on a single problem, they moved slowly compared with electronics "and unreliably also," Bennett explained.

Because the biological computer concept did not look as if it could vie with electronics on general computing and win, Shapiro said he decided to "go back and do something useful with it."

"Electronic computers can talk very easily with other electronic devices -- a printer, a DVD player -- but they cannot talk very easily with biological molecules. We opened with biological computers instead to talk with biological molecules," he explained.

The new computers still have a long way to go before they can find use in the body, Shapiro cautioned.

"What we demonstrated is just small enough and smart enough to do the job in a test tube. Making sure it works inside a tissue culture, let alone a living organism, is going to be a challenge," Shapiro said.

"They're not packaged right now," he added. "They'd probably degrade too soon in the body to be active or effective. They'd have to be protected in some way. Also, the enzyme we used here as hardware, Fok1, cuts DNA. If it finds its way into the nucleus of a cell, it'd just chop the entire genome to pieces, and that particular cell would not be too useful afterwards," Shapiro said.

"It's a very cute idea to have chemicals within the system you're working on doing computations on that system," said physicist Charles Bennett of IBM Research in Yorktown Heights, N.Y. "Instead of having to stick a probe into a mixture of c ells to find out what's happening inside, these have the advantage of having computations right in there. The thing that's doing the measuring is already part of the mixture."

Bennett also suggested expanding the range of molecules the computer could process and the types of drugs it could make.

The Weizmann team envisions future versions that could even release proteins or other compounds.

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