DNA sequencing in one easy step

Photo / Thinkstock

Opinion

This post originally appeared on Sciblogs.co.nz.

DNA sequencing has been around for a while now. Its success is down to a wonderfully unlikely collaboration between molecular biology and computer science.

Basically, in simple terms (apologies to molecular biologists if I get this wrong - feel free to correct me) to sequence your genome, you take your DNA, chop it into bits, replicate those bits, attach clever fluorescent molecules to the bases (a different colour attaches to each base) then read the sequence of bases by looking at the fluorescent colours. This gives you lots of little bits of the whole sequence - you then throw these into your computer programme which works out what the complete sequence has to be.

Is there a quicker way? What about making a DNA reading machine - just feed your entire DNA strand through the machine and it reads it automatically - rather like swiping your credit card through the magnetic reader. The physicists and chemists are working towards that point, as described by Philip Ball in December's PhysicsWorld magazine, and blogged about here.

A way of doing this is with the nanomaterial graphene. Graphene is a form of carbon, and can be considered to be a single layer of graphite. It's a sheet of carbon atoms, arranged hexagonally - just one atom thick. The idea is to punch a hole into a graphene sheet, just large enough to feed a DNA strand through. The strand almost blocks the hole, but not quite, so it is possible for small ions to pass through the hole as well, when an electric field is applied. This flow of ions constitutes an electric current, which can be measured.

But here's the clever bit: each base of the DNA has a slightly different size and shape, which means it blocks the hole to a slightly greater or lesser extent compared to another base. This change in the unblocked hole area means an increase or decrease in the amount of current that can flow through it. So by measuring the current that flows, one can determine which base is in the hole. Just pull the strand through the hole, measure the variations in the ionic current, and, hey-presto, you have read the entire strand.

That's the idea, anyway. Why use graphene, not another membrane with a small hole? Graphene offers extreme strength and is very thin, and low-cost too. It's so thin that only a single base can get into the hole at one time, meaning it really does have the potential to read a strand of DNA, base by base. It's a candidate to watch for the X PRIZE Foundation's $10 million for a machine that can read 100 human genomes in 10 days (at less than $10,000 a genome).

Dr Marcus Wilson is a lecturer in the Engineering Department at Waikato University. View his work and that of 30 other scientists and science writers at Sciblogs, New Zealand's largest science blogging network.