Technology Research News
The DNA molecule is the mechanism nature
uses to construct every living being. Scientists are beginning to use
the same mechanism to compute, but most of the rudimentary DNA computers
built so far require researchers to manually trigger each step of a molecular
Researchers from the Weizmann Institute in Israel have found a way to
automatically carry out several computational steps at once in a test
tube of short, artificially-constructed DNA molecules. They put the DNA
through a series of steps that, once begun, carried through to the end
of a computation.
Although it takes minutes for DNA to do a single computation, many molecules
can compute at once in a very small amount of space. "We get a trillion
computers doing a billion operations per second in [a drop] of solution,"
said Ehud Shapiro, an associate professor in the departments of computer
science and biological chemistry at the Weizmann Institute of Science
This computation DNA, like biological DNA, is made up of four types of
bases attached to long sugar-phosphate chains. Two of these chains, with
bases attached, zip together, pairing up the bases on each chain to form
DNA's classic double-helix shape.
Biological DNA uses specific sequences of the bases as blueprints to build
the many proteins involved in the chemical reactions of life. The same
sequences can represent numbers and be manipulated mathematically to compute.
The computation method uses two types of DNA molecules: software, or computation
molecules, which are about 40 base pairs long and contain the instructions
for the computation, and input molecules, which contain strings of six
bases that represent the problem to be solved. A computation happens when
these two types of molecules interact. Each has a sticky end, meaning
one strand of the double helix is longer than the other, exposing a sequence
of bases that are not paired.
When the sticky end of an input molecule bumps into a software molecule
that has a sticky end that fits, the bases of the two sticky ends join
together, and an enzyme present in the solution seals them together. The
molecule is then cut in a different place by a second enzyme, exposing
another sticky end so that a second step can take place. The number of
steps depends on the number of computations coded into the software DNA
For example, to answer the question 'does the sequence of letters "bab"
contain an even number of b's?' the input DNA molecules would represent
each of the three letters using a segment of DNA six bases long. The software
molecules would contain a logical series of steps for determining whether
the input has an even number of b's.
When the computation ends, the remaining sticky ends connect to one of
two marker molecules of different lengths. One of the marker molecules
contains a sequence of bases that will stick to the computation molecules'
sticky end if the answer turned out to be even, and the other contains
the correct sequences if the answer turned out to be odd.
Once the microscopic reshuffling of DNA bases is done, the researchers
read the answer using gel electrophoresis, a process that involves putting
DNA on a gel, and passing electrical current through electrodes attached
to the gel. "[You] place the DNA near the minus electrode. The DNA travel
slowly inside the gel towards the plus electrode at a speed that is a
function of the molecule size. If you stop the process at the right time,
you have a spread of the molecules according to... length," which makes
it apparent which marker molecule has connected to the computation molecule,
The researchers' DNA computer can run 735 sample programs made up of sequences
of the eight basic operations that are possible using six-base input strings.
Previous experiments that used DNA to compute had to be designed to solve
a single problem, although some could handle varied inputs, said Nadrian
Seeman, a chemistry professor at New York University. "Here, several different
questions can be asked of the same system," he said. The work could lead
to more generally programmable approaches to DNA-based computation, he
In the researchers' experiments, the DNA took nearly 17 minutes to carry
out each operation; eventually DNA will probably be able to carry out
an operation in a few seconds, said Shapiro.
Compared to silicon computer chips, which compute in millionths or billionths
of a second, this would still be very slow, but because millions or trillions
of DNA molecules could compute in parallel, this type of DNA computer
could handle very large problems; more important, it works in a test tube.
The work is "different from most experimental work on DNA computers in
that we do not attempt to compete with silicon computers by solving difficult
problems faster. The potential is... operation in a biochemical environment,"
The method is "an ingenious construction that provides the capability
of a basic sort of computation at the molecular scale," said John Reif,
a computer science professor at Duke University. It is not new to use
the molecular configuration of DNA to store the result of a computation,
but this work provides a very general mechanism for using that result
to then compute a further result, he said.
This type of work could eventually lead to molecular computers that could
be used to control molecular processes like complex assemblies and molecular
robotic devices, Reif said.
The method could be used to screen libraries of DNA in five to ten years,
and could eventually be used to carry out more complicated tasks like
detecting DNA anomalies and synthesizing drugs to fix them, Shapiro said,
adding that this use is decades away.
Shapiro's research colleagues were Yaakov Benenson, Tamar Paz-Elizur,
Rivka Adar and Zvi Livneh from the Weizmann Institute, and Ehud Keinan
from the Weizmann Institute and the Scripps Research Institute. They published
the research in the November 22, 2001 issue of Nature. The research was
funded by the Weizmann Institute.
Timeline: 5-10 years, several decades
TRN Categories: Biological, Chemical, DNA and Molecular
Story Type: News
Related Elements: Technical paper, "Programmable and Autonomous
Computing Machine Made of Biomolecules," Nature, November 22, 2001.
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