[FoRK] NYTimes.com Article: A Glimpse at the Future of DNA: M.D.' s Inside the Body

khare at alumni.caltech.edu khare at alumni.caltech.edu
Fri Apr 30 11:40:56 PDT 2004


The article below from NYTimes.com 
has been sent to you by khare at alumni.caltech.edu.


Turing machines with tapes, indeed!

RK

khare at alumni.caltech.edu


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A Glimpse at the Future of DNA: M.D.'s Inside the Body

April 29, 2004
 By ANDREW POLLACK 



 

Scientists have developed what they say could become the
world's smallest medical kit: a computer, made of DNA, that
can diagnose disease and automatically dispense medicine to
treat it. 

The computer, so small that one trillion would fit into a
drop of water, now works only in a test tube, and it could
be decades before something like it is ready for practical
use. But it offers an intriguing glimpse of a future in
which molecular machines operate inside people, spotting
diseases and treating them before noticeable symptoms even
appear. 

"Eventually we have this vision of a doctor in a cell,"
said Dr. Ehud Shapiro of the Weizmann Institute of Science,
in Rehovot, Israel, who led the work, published online
yesterday by the journal Nature. 

DNA's role is to store and process information, the genetic
code. So it is not surprising that it can be used for other
computing tasks as well, and scientists have in fact used
it to solve various mathematical problems. But the Israeli
scientists said theirs was the first DNA computer that
could have a medical use. 

The computer, a liquid solution of DNA and enzymes, was
programmed to detect the kind of RNA (a DNA cousin) that
would be present if particular genes associated with a
disease were active. 

In one example, the computer determined that two particular
genes were active and two others inactive, and therefore
made the diagnosis of prostate cancer. A piece of DNA,
designed to act as a drug by interfering with the action of
a different gene, was then automatically released from the
end of the computer. 

Experts called the work ingenious but pointed out that it
had been done in a test tube, to which the RNA
corresponding to the disease genes was added. It is not
clear, they said, whether such a computer could work inside
cells, where there would be many pieces of DNA, RNA and
chemicals that could interfere. 

"I think it's very elegant - it's almost like a beautiful
mathematical proof," said Dr. George Church, professor of
genetics at Harvard Medical School. "But it's not working
in human cells yet." 

DNA has intrigued some computer scientists since 1994, when
Dr. Len Adleman of the University of Southern California
showed that it could be used to solve a mathematical
problem. People in the field then began envisioning
billions of pieces of DNA undergoing chemical reactions in
parallel, solving problems so complex as to stymie
conventional computers. 

Some scientists have since concluded that it will be
difficult to get DNA computers to outmuscle electronic
computers. But Dr. Shapiro, an associate professor of
computer science and applied mathematics who is also in the
Weizmann Institute's department of biological chemistry,
decided to focus on a DNA computer for use in the body,
where silicon would have a hard time competing. 

And rather than trying to build the DNA equivalent of a
supercomputer, or even a wristwatch calculator, he made a
device so simple - from a computer science standpoint, that
is - that it can barely be called a computer. 

It has two states, "yes" and "no," and changes from one to
the other on the basis of a single variable, like the
presence or absence of the RNA it is looking for. If at the
end of a series of steps it is in the "yes" state, the
diagnosis is positive. 

The Weizmann DNA computer encodes both the software and the
data in the four letters of the genetic code, A, C, G and
T. The "hardware," the part of the computer that does not
change, is an enzyme that cuts the strands of DNA in a
particular way. 

The computer is made of double-stranded DNA with ends that
are single-stranded. These so-called sticky ends can bind
to specific other strands of DNA or RNA in the solution
under the usual rules of DNA pairing. If binding occurs,
the enzyme cuts the DNA a certain distance away, exposing
new sticky ends. If those ends find something to bind to,
the enzyme cuts in yet another location, and so on. If the
chain reaction proceeds in a certain way, the enzyme
eventually slices off the piece of DNA that acts as the
drug. 

After the DNA encoding the problem is made and put in the
test tube, the computer works automatically and arrives at
the answer in minutes. 

"Basically," Dr. Shapiro said, "we just drop everything in
solution and see what happens." 

http://www.nytimes.com/2004/04/29/science/29DNA.html?ex=1084350456&ei=1&en=6ed06dfb0d6e1593


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