DNA computing is a form of computing which uses DNA and biochemistry and molecular biology, instead of the traditional silicon-based computer technologies. DNA computing, or, more generally, molecular computing, is a fast developing interdisciplinary area. R&D in this area concerns theory, experiments and applications of DNA computing.

History

This field was initially developed by Leonard Adleman of the University of Southern California. In 1994, Adleman demonstrated a proof-of-concept use of DNA as a form of computation which solved the seven-point Hamiltonian path problem. Since the initial Adleman experiments, advances have been made and various Turing machines have been proven to be constructible.

In 2002, researchers from the Weizmann Institute of Science in Rehovot, Israel, unveiled a programmable molecular computing machine composed of enzymes and DNA molecules instead of silicon microchips. The computer could perform 330 trillion operations per second, more than 100,000 times the speed of the fastest PC. ^[1]

On April 28, 2004, Ehud Shapiro, Yaakov Benenson, Binyamin Gil, Uri Ben-Dor, and Rivka Adar at the Weizmann Institute announced in the journal Nature that they had constructed a DNA computer. This was coupled with an input and output module and is capable of diagnosing cancerous activity within a cell, and then releasing an anti-cancer drug upon diagnosis.

What is really a DNA Computer?

DNA replicates according to its sequences. So, based on initial input sequences (the problem to be solved), DNA replicates and create trillions of new sequences. The solution to the problem is one of those new sequence strands created that could be achieved by an elimination process.

Practically, the DNA computer looks like a solution in a test tube. There is no mechanical device. Instead of showing up on a computer screen, results are analyzed using a technique that allows scientists to see the length of the DNA output molecule.

In order to enable a convenient input of sequences and present the output to the naked eye, human manipulation is needed. In other words, no I/O devices exist yet for this kind of computer. This kind of computer is not practical yet and is in its initial stages.

Capabilities

DNA computing is fundamentally similar to parallel computing in that it takes advantage of the many different molecules of DNA to try many different possibilities at once.

For certain specialized problems, DNA computers are faster and smaller than any other computer built so far. But DNA computing does not provide any new capabilities from the standpoint of computational complexity theory, the study of which computational problems are difficult to solve. For example, problems which grow exponentially with the size of the problem (EXPSPACE problems) on von Neumann machines still grow exponentially with the size of the problem on DNA machines. For very large EXPSPACE problems, the amount of DNA required is too large to be practical. (Quantum computing, on the other hand, does provide some interesting new capabilities).

DNA computing overlaps with, but is distinct from, DNA nanotechnology. The latter uses the specificity of Watson-Crick basepairing and other DNA properties to make novel structures out of DNA. These structures can be used for DNA computing, but they do not have to be. Additionally, DNA computing can be done without using the types of molecules made possible by DNA nanotechnology (as the above examples show).

Examples of DNA computing

MAYA-II (Molecular Array of YES and AND logic gates) is a DNA computer, developed by scientists at Columbia University and the University of New Mexico.

Replacing the normally silicon-based circuits, this chip has DNA strands to form the circuit. It is said that the speed that such DNA-circuited computer chips can attain will rival the silicon-based ones, they will be of use in blood samples and in the body and might part-take in single cell signaling.

It is the successor to the MAYA I which was composed of only 25 logic gates and could only complete a partial game of tic-tac-toe. MAYA-II has more than 100 DNA circuits and can now thoroughly play a game of tic-tac-toe. It is very slow - one move in a game of tic-tac-toe can take up to 30 minutes making it more of a demonstration than an actual application.^[1]

The arrangement of this device looks like that of a tic-tac-toe grid and consists of nine wells coated with culture cells. The cell-containing wells are filled with a solution that contain DNA strands coding for red or green fluorescent dyes.

This technology was used to deepen the quality of diagnostics given to patients infected with the West Nile virus. Joanne Macdonald, a Columbia University virologist, hopes this device can be implanted in the human body and control the presence of cancer cells or the levels of insulin for diabetic patients.^[2]

One of the suggested uses put forward by MAYA's creators is that technology such as this can be used in situations where fluid is involved, such as in a sample of blood or a body, since it does not use traditional silicon components. ^[3]

See also

• Peptide computing
• Parallel computing
• Quantum computing

References

External links

• How Stuff Works explanation
• Physics Web
• Ars Technica
• A Bibliography of Molecular Computation and Splicing Systems
• NY Times DNA Computer for detecting Cancer
• Bringing DNA computers to life, in Scientific American
• Japanese Researchers store information in bacteria DNA