Wetenschap - 29 september 2011

Heavy-duty machine decodes DNA in a jiffy

It is the ultimate status symbol. It has to run fast, look smart and, of course, be better than the neighbour's. Which doesn't make it any easier to choose the perfect DNA sequencer.

 With the help of the virtual equipment bank CAT-AgroFood, Wageningen UR is now purchasing two new machines that will be able to decode DNA strands faster than ever.
The total DNA of a cell, otherwise known as the genome, contains all the genetic information about a person, potato, cow or bacterium. This information is coded in the sequence of the four bases which DNA is made up of. Like a script with an alphabet of only four letters. And that is how it appears on the computer after decoding: an endless line of As, Ts, Cs and Gs which, thanks to decades of research, we can translate into concrete information about genes, proteins and functions. All this information is valuable to researchers.
There are already plans to decode the DNA of 100 tomato plants in Wageningen in the near future. The apparatus will also be used to chart biodiversity. ‘With this new purchase', says researcher Elio Schijlen, ‘we are ahead of the field in Europe, certainly in the AgroFood sector.'

Illumina Hiseq 2000
For the real speed addict the Illumina Hiseq 2000 is on the market for a mere 500,000 euros. The technique under the bonnet of this monster dates back to 2005, but has not yet been overtaken. To do the sequencing, broken DNA is stuck onto a chip and multiplied by one million times. Then fluorescent bases are added in order to be recorded with the help of a laser and an ultrasensitive camera. This enables the precious machine to illuminate up to 50 billion base pairs per day: 16 times the human genome. This is a different ballgame to the snail's pace at which the previous generation of machines achieved the same thing.
- Up to 50 billion base pairs per day
- Fragments of between 50 and 100 base pairs
- 10 million bases for one euro
- Price tag: 500,000 euros

PacBio RS

Nice toy, that Hiseq, but the real trendsetters want more than just brute force. For them there is the PacBio RS, the first machine to be able to decode a single DNA molecule. So it does not require any multiplication stage which could influence the results. The machine does this trick using a chip full of holes on a nanometre scale, each with one enzyme. This enables it to sequence fragments of up to 6,000 base pairs and to decode simple genomes.
- 1 billion base pairs per day
- Fragments of between 2 and 6 thousand base pairs
- 15,000 bases for one euro
- Price tag: 700,000 euros

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