By Sean Henahan, Access Excellence
SANTA FE, NM (6/3/97)- Using a bit of DNA and some commonplace
biological laboratory techniques, researchers have now engineered
the first DNA computer "hardware" ever: logic gates made of DNA.
CAPTION: On the pencil in the foreground is a drop of DNA isolated
from salmon sperm; in the background, an electronic computer's monitor
displays a model of the DNA helix surrounded by a sea of letters representing
the four genetic bases.
"There is absolutely nothing fancy in what we have done," Ray says.
"The techniques we've used are the same ones that thousands of biologists
use every day in their labs."
The breakthrough could form the basis for powerful DNA -based computers.
The DNA logic gates rely not on electrical signals to perform logical operations
-- as do logic gates in today's computers -- but rather on DNA codes.
Logic gates are tiny structures that convert the binary data coursing
through every computer into a series of signals that a computer uses to
perform its operations. Today's logic gates process electronic signals
from transistors made of materials like silicon, converting two input signals
into one output signal in a way that allows a computer to perform complex
operations. Up to now, the only logic gates used for computing have been
electronic structures that detect signals coming from transistors.
The new DNA logic gates are tiny DNA processing centers that detect
specific fragments of the genetic code as input, then splice together the
fragments to form a single output. For instance, a genetic And gate links
two DNA inputs by chemically binding them so they're locked in an end-to-end
orientation -- much as two Legos might be fastened end-to-end by a third
Lego stuck on top. A DNA ligase seals the gap between the ends of the two
input strands, yielding a single new strand.
Using regular gel electrophoresis, the length of this new strand can
be precisely measured, providing the DNA computer's "answer" or output
to the two input strands. For example, with the DNA And gate, a final DNA
sequence that's as long as the input strands linked together indicates
that an And operation has occurred. A similar system of two short DNA strands
work together in Ray and Ogiharas Or gate, whose answers are likewise read
in the length of the resulting DNA strands.
Other researchers have focused on building DNA computers to complex
math problems that traditional computers cannot solve, such as the famous
"traveling salesman" problem. The Rochester team is one of the first to
seriously consider whether DNA computers might be used for problems now
routinely done by electronic computers, and to emulate the way electronic
Ogihara showed mathematically that a computer consisting of a series
of DNA-filled test tubes can work more efficiently than a digital computer
in analyzing the information cascading in from a tangled web of
logic gates. This includes the type of calculations now done every
day, as well as more complex arrangements. A DNA computer would need just
a few hours to analyze a flood of information that would take today's
conventional computers hundreds of years to solve.
The Rochester researchers believe that when coupled with new DNA microchips
now in development, the
gates will usher in a wave of breakthroughs in DNA computing. Ray says
such chips could make DNA computation even faster by speeding the tally
of the DNA strands that serve as answers to computations. Rather than running
the DNA through a slow gel electrophoresis, researchers could add labeled
strands to a DNA chip, which consists of hundreds of squares containing
different known strands of DNA. The added DNA would quickly bind to the
strands in the square containing its complementary DNA sequence, and
scientists could use the labels to detect the DNA answers.
Ray and Ogihara believe that DNA could serve as a very compact, efficient,
and accurate form of memory
in computers -- just as it does in the cells of the human body. The
potential benefits of a DNA computer are astounding: One pound of DNA has
the capacity to store more information than all the electronic computers
ever built, and the computing power of a teardrop-sized DNA computer
using the new DNA logic gates could dwarf that of the world's most powerful
supercomputer, which is the size of a house. Ogihara believes DNA will
prove useful on problems that now require vast networks of computers, such
as forecasting the weather, designing airplanes, or cracking complex security
The research was announced at the First International Conference
on Computational Molecular Biology in Santa Fe, N.M.
Related information on the Internet
Language of Recombinant DNA