DNA plays tic-tac-toe
Technology Research News
During the time they knew each other as
kids in Belgrade, Serbia, Milan Stojanovic and Darko Stefanovic didn't
play tic-tac-toe, according to Stojanovic. Things are different now that
they are scientists at Columbia University and the University of New Mexico.
The researchers have fashioned a device that uses pieces of artificial
DNA to automatically play tic-tac-toe. And as long as it makes the first
move, the device cannot be beat.
The device is made of nine wells containing solutions where DNA
can react. DNA in the wells acts like logic gates. "The distribution of
logic gates in wells is such that it implements a perfect [tic-tac-toe]
strategy," said Stojanovic. "Tic-tac-toe is a game of perfect information
and guarantees a victory or draw for the first player," he said.
This makes it a good test for an automaton -- a machine that operates
on its own, without human control. The device, dubbed Molecular Array
of YES and ANDANDNOT gates (MAYA), is simpler than a computer, which is
generally capable of storing, organizing and processing data, or controling
other machines, said Stojanovic.
The researchers' method could eventually be used to control nano
devices and in automata that educate people about science, said Stojanovic.
MAYA contains 24 logic gates distributed in the nine wells of
solution. Some of the logic gates in each well perform Boolean calculations
when short single-stranded DNA sequences, or oligonucleotides, are added.
The addition triggers an enzyme to react with DNA. Depending on the result,
the reaction may expose a fluorescent molecule.
DNA is formed from four types of bases - adenine, cytosine, guanine
and thymine -- connected to a sugar-phosphate backbone. Strands of DNA
can combine to form double-stranded DNA when their base sequences match
up: adenine across from thymine, and cytosine across from guanine.
The researchers' device contains two types of gates that perform
two types of Boolean calculations. The DNA molecule that makes up a YES
logic gate has two states, one of which is fluorescent, or active. The
more complicated DNA molecule that makes up a combination ANDANDNOT gate
contains eight physical states, one of which is active.
YES gates change from nonactive to active when a complementary
DNA sequence combines with the DNA in the well to release a loop in the
DNA, which triggers a second reaction that exposes a fluorescent molecule.
The ANDANDNOT gate contains three groups and is activated only if two
of three possible inputs are provided.
MAYA always goes first and always starts in the center. Then the
human challenger adds a DNA sequence to all the wells to represent the
second move. The DNA sequence triggers a positive reaction with the DNA
contained in only one of the wells -- the reaction exposes a fluorescent
molecule, which makes the well glow to indicate the move.
"The game is played like this," said Stojanovic. "[The] human
moves by adding oligonucleotide, takes a fluorescence reading, and adds
[the] next oligonucleotide," he said. The game continues until the automaton
wins, or there are no more spaces on the board, resulting in a draw.
The researchers' method differs from standard DNA computing, which
is aimed at tapping DNA's massively parallel nature. In theory DNA could
be used to test all possible answers to a problem at once in order to
identify those that fit certain criteria. The goal of this type of DNA
computing is to compete with silicon in certain applications that have
large numbers of possibilities, like code-cracking.
In contrast, the researchers' method is aimed at adding relatively
simple logic to nano devices. "We're not taking advantage of massively
parallel processing capabilities," said Stojanovic. "Our approach is silicomimetic,"
he said. The researchers use molecules that behave as logic gates, and
arrange these logic gates into more complicated circuits by mixing them
The researchers are aiming to eventually use the method to control
nano devices in the human body, said Stojanovic. "We hope... in some distant...
future, to use similar [devices] to make decisions in vivo [about] whether
to release a toxic compound or not, [or] to kill a cell not," he said.
Such devices could also be used to monitor in vivo disease signatures
of astronauts on long space flights, he said.
Such uses are probably several decades away, Stojanovic added.
The research is also aimed at constructing automata that could
help popularize science and familiarize young people with advanced concepts
in nanotechnology, said Stojanovic.
The researchers are currently working on improving the tic-tac-toe
device and on connecting DNA networks to sensors, said Stojanovic.
The work appeared in the August 17, 2003 issue of Nature Biotechnology.
The research was funded by the National Aeronautics and Space Administration
(NASA), and the National Science Foundation (NSF).
Timeline: Several decades
TRN Categories: Biological, Chemical, DNA and Molecular
Story Type: News
Related Elements: Technical paper, "A deoxyribosome-Based
Molecular Automation," August 17, 2003.
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