DNA computers

DNA computing with DNA and enzymes
Image by Mk2010 via WikiCommons

DNA stores a massive amount of information inside the tiny nuclei of living cells. It encodes all the instructions needed to make every living creature on earth. Therefore, DNA forms the basis of the most complex computers that exist: humans. So it makes sense that we are trying to use DNA to make artificial computers.

This post is part of a series on bio-computers. I’ve already talked about using DNA to store information, essentially to form computer memory. Now I want to talk about using DNA to make computer circuits. There are two ways that scientists are doing this. Firstly, just using DNA. Secondly, using DNA and the enzymes that naturally process DNA inside living cells: nucleases and polymerases. In both these methods DNA (+/-) enzymes are used to create a series of logic gates. 

The circuits that form standard non biological computers are made up of logic gates. In PCs logic gates are turned on and off by voltage, so high and low voltage controls whether gates are open or closed. The gates are connected into complex circuits to become memory cells and microprocessors inside computers.

Computers circuits made up entirely of DNA use a method called DNA strand displacement. In this method each logic gate is a DNA sequence. When input DNA is added to the circuit, it binds to a logic gate and displaces a second DNA sequence. In a multi-gate circuit, this second sequence then binds to another gate, and on and on until the reaction at the final gate liberates the output DNA sequence. The output sequence is usually attached to a fluorescent molecule so it is easy to read.

Alternatively, enzymes can be used to liberate DNA sequences after input DNA binds to a logic gate.

The beauty of these systems is that they can be self-powering as they use the energy stored in the DNA backbone to power the DNA binding reactions.

These DNA-based computing methods require new programming languages. Microsoft has been quick to create such a language called, unsurprisingly DNA Strand Displacement tool. This language can be used to design DNA sequences that will form efficient computing circuits and also to model how the reactions will occur with a given set of ingredients.

One of the major problems with current DNA-computing technology is that it is incredibly slow compared with normal computers. Also there are a number of viruses that can attack DNA sequences. So just like non-biological computers, bio-computers will be susceptible to viral attack. However, with time, these things will most likely be overcome. The reason it’s worth the effort is because DNA is so much smaller than current computer parts. Therefore it can be used to make tiny computer components and thus create super-computers the same size as our current tablets.

The Scientific Papers:

Benenson et al. DNA molecule provides a computing machine with both data and fuel. PNAS. 2003. (free and open access)

Qian and Winfree. Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades. Science. 2011.

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