computer readout glows
Technology Research News
DNA is the ultimate biological code, packing
all the information needed to make life forms as diverse as viruses, turnips
and human beings into a microscopic package that can copy itself and automatically
carry its own instructions.
It's no wonder that biologists and computer scientists are working toward
using DNA for computing. Computers that use the microscopic molecules
have the potential to solve certain types of very large problems, like
finding the most efficient traveling salesman route or circuit board layout,
much faster than conventional computers. This is because many DNA molecules
can be used to work on all possible solutions to a problem at once.
Researchers from the University of Wisconsin-Madison have come up with
a better way to read the results of a microscopic DNA computation once
it is completed.
The challenge to reading DNA computing results is the molecules that represent
the answer to a problem are mixed in with other DNA molecules, and it
is difficult to pick out the right ones. The researchers' method makes
the right molecules stand out by giving them the microscopic equivalent
of the glow sticks people wave around at large outdoor events.
The approach "is a different way of finding out what is there," said Lloyd
Smith, a chemistry professor at the University of Wisconsin-Madison and
a director of Third Wave Technologies, Inc.
DNA molecules are made up of long strings of four types of bases connected
to phosphate backbones. The order of the bases makes up a type of code.
DNA computers consist of large sets of DNA molecules that include all
possible answers to a computational problem. During the DNA computing
process a series of enzymes takes the DNA molecules through the logical
steps needed to compute the correct answer by combining them and breaking
them in different places to form new sequences. At the end of the computation
there is a small subset of DNA molecules that represent the correct solutions
to the problem.
The researchers' readout method involves putting the DNA into a series
of wells that contain an enzyme and other DNA strands that contain inactivated
fluorescent molecules. The combination lights up the correct answers by
a method known as invasive cleavage. The DNA molecule representing the
answer causes the enzyme to cleave, or cut, the fluorescent molecule free
from its DNA strand, causing it to glow. "If a certain DNA molecule is
present... the cleavage makes fluorescence appear," said Smith.
The cleavage method already existed, but it took some work to adapt it
for reading DNA computing answers, said Liman Wang, part of the University
of Wisconsin-Madison team, and now a senior research chemist at Merck
Co. Inc. The researchers had to delete certain portions of the DNA in
order to produce the specific sequence needed for the invasive cleavage
method, said Wang.
The method is simpler and more accurate than previous readout methods,
said Wang. "The signal uniformity has been significantly improved, and
false positive signals are much less -- in other words, the signal-to-noise
ratio is higher."
The method is "an experimental improvement on the way Smith and his colleagues
have been performing DNA-based computation for a number of years," said
Nadrian Seeman, a chemistry professor at New York University. "They have
increased the fidelity of their readout method," he said.
The key issue is whether the general method will work with very large
problems, said Seeman. "The issues involve both the difficulty of setting
up the problem and the accuracy of the results. These authors have improved
the accuracy of the results," he said.
The researchers are working to make fluorescence reaction uniform among
all the different DNA answers, said Wang.
DNA computing is at least 10 years away from being used in practical applications,
Smith and Wang's research colleagues were Jeff Hall of Third Wave Technologies,
and Manchun Lu and Qinghua Lu of the University of Wisconsin-Madison.
They published the research in the November, 2001 issue of Nature Biotechnology.
The research was funded by the National Science Foundation (NSF) and the
Defense Advanced Research Projects Agency (DARPA).
Timeline: Now, > 10 years
TRN Categories: Biological, Chemical, DNA and Molecular
Story Type: News
Related Elements: Technical paper, "A DNA Computing Readout
Operation Based on Structure-Specific Cleavage," Nature Biotechnology,
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