DNA computing
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DNA computing, commonly called biomolecular computing, is an emerging field that
uses DNA and biochemistry instead of silicon-based electronics.
The first proof-of-concept use of DNA to perform computation was carried out by Professor
Leonard Adleman at the University of Southern California in 1994.
The original goal of the field was to use biomolecules to beat electronic computers at solving
large complex problems.
"Today, most people believe that biomolecular computing will not beat electronic computers
in the foreseeable future," admitted Professor Ehud Shapiro of the Weizmann Institute of
Science in Israel.
Instead, said Professor Shapiro, the new goal is to try to use DNA computing to do things that
traditional silicon cannot.
"What we offered in our work was a different vision," he said.
In particular he is trying to develop smart drugs that are capable of computation.
"You want a drug that can sense the biochemical environment, analyse it and, in response,
release a molecule which is the appropriate drug for that particular situation," he said.
Cancer buster
In 2002, Professor Shapiro unveiled a programmable molecular device composed of enzymes
and synthetic strands of DNA.
Two years later, the same team showed off another DNA computer so small that roughly a
trillion of them could fit into a microlitre (a millionth of a litre).
The device was able to detect signs of cancer, and release drugs to treat the disease.
"This soup of DNA and enzymes implements a well know mathematical model of
computation known as finite automaton," he explained.
"This finite automaton knows how to do very simple computation such as recognising
whether a list of zeros and ones has an even number of ones."
In the case of his 2004 computer this method of computation was used to analyze ratios of
specific molecules related to prostate cancer and a specific type of lung cancer.
The "computer" consisted of a chain of three segments of DNA and an enzyme which could
cut the strands.
If the first segment of the DNA detects ratios of certain molecules that indicate the presence
of cancer, it tells the second segment to release the third segment, which is an anti-cancer
drug.
Since then, other researchers have shown off new computational systems that make use of
enzymes that naturally occur in a living cell, whilst Professor Shapiro has attempted to make
a more practical device.
"We have continued working in this direction trying to make this molecular system to work in
living cells," he said.
DNA computer 'answers questions'
A computer with DNA as its information carrier can solve classic logic conundrums,
researchers say.
DNA has been used to do simple number crunching before, but a system developed by Israeli
scientists can effectively answer yes or no questions.
Strands of DNA are designed to give off a green light corresponding to "yes".
In Nature Nanotechnology, the team also describes a program which bridges the gap between
a computer programming language and DNA computing code.
The team, led by Tom Ran and Ehud Shapiro of the Weizmann Institute in Israel, has been
developing DNA-based computation systems for a number of years, including "computers"
that can diagnose and treat cancers autonomously.
But the current approach is fundamentally different, Professor Shapiro told BBC News.
"Using more sophisticated biochemistry, we were able to implement simple logic programs,
which are more akin to the way people program electronic computers," he said.
Sticky proposition
The system devised by the researchers uses molecules to represent facts and rules. In this
way, the team was able to use it to answer simple molecular "questions".
First, they tried the system with simple "if then" propositions. One of these went as
follows: "All men are mortal. Socrates is a man. Therefore, Socrates is mortal."
Without computer robotic support to this process, we would not have finished this in
our lifetime
Professor Ehud Shapiro Weizmann Institute of Science
When fed a molecular rule (all men are mortal) and a molecular fact (Socrates is a man), the
DNA computing system was able to answer the question "Is Socrates mortal?" correctly.
The team went on to set up more complicated queries involving multiple rules and facts. The
DNA devices were able to deduce the correct answers every time.
The answer was encoded in a flash of green light. Some of the DNA strands were equipped
with a naturally glowing fluorescent molecule bound to a second molecule which keeps the
light covered.
A specialised enzyme, attracted to the part of the molecule representing the correct answer,
would then remove this cover to let the light shine.
Life's work
Professor Shapiro said the fact this system was based on clever biochemistry meant it was no
less a computer than the conventional kind.
"Of course when the examples are simple, as in today's logic program, one can pre-compute
the answer with pencil and paper. But in principle there is no difference between simple and
complex computer programs; they can compute only what they programmed to compute.
"It is important to note that, while bio-molecular computing trails behind electronic
computing - in terms of actual computing power, maturity of the technology, and sheer
historical progression - at the conceptual level they stand side-by-side, without one being a
more 'preferred' embodiment of the ideas of computation," he said.
To save time and effort, the researchers developed a robotic system to set up the DNA-based
propositions and queries.
The system can take in facts and rules as a computer file of simple text. The robotic
"compiler" can then turn those facts and rules into the DNA starting products of a logical
query.
"We had to do many, many experiments to develop, debug, and calibrate the molecular
computing system, and without computer robotic support to this process, we would not have
finished this in our lifetime," Professor Shapiro said.
While the current work may raise the bar for programmable, molecular computing, Professor
Shapiro said: "the ultimate applications are in programmable autonomous computing devices
that can operate in a biological environment."
In other words, computers that go to work inside a cell.