Wednesday, 18 April 2012

The MinION Nanopore USB DNA Sequencer


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Your favourite TV detective may soon be pointing at a whole new way of showing DNA, instead of the iconic electrophoresis bands (right [6]), if Oxford Nanopores’ new MinION device takes off. Typically, working out the DNA code in an organism involved cutting the DNA up into many pieces, amplifying (copying) many copies of the same molecule, and then sorting them using the electrophoresis technique, creating the aforementioned image.[1][5] As the picture may imply, working out the actual code for DNA is a tedious and time-consuming process.




This is where the MinION comes in. Shaped like a USB drive, it plugs into the any computer’s USB port and features a unique way of sequencing (or reading) genetic code. The MinION’s internals feature nanopore channels (made of protein) embedded in a membrane. There is a membrane potential (an electrical charge) is held across the membrane, meaning the sides of the membrane are charged differently (positive and negative).[4] As one strand of the entire DNA molecule – not cut into pieces as previously done – passes through the protein channel, the different nucleotide components which form the ‘code’ of DNA alter the charge on the membrane.[4] The level of these disturbances is different for each of the four nucleotides in DNA and as such, whichever nucleotide passes through can be recognized by the change in electrical state.[4]

Although the process is confusing, the main benefits of this new technique are simple; entire DNA molecules can be sequenced without the need for the ‘solving’ the jigsaw electrophoresis provides, and the process of sequencing DNA is much faster. The cost of $900 is also considered cheap in terms of research applications, since the investment is quite low, and it is a ‘pay as you go’ scheme, rather than a large upfront investment in a sequencing machine.[3][2]

The speed of this process naturally causes people to consider mass uses of DNA sequencing. While sequencing the DNA of every person in the world may seem intrusive, many are likely to support using sequencing to track convicted criminals, and assist in making convictions. Other uses could be diagnosing genetic diseases quickly, or indexing animal genomes.

Despite all the excitement – from scientists at least – such mass use of genetics is still a way off. A large deterring factor would be the $900 cost of each MinION device, and its one use limit. Despite it being beneficial to researchers, the price currently seems to negate the obvious benefit of the technology – the speed and potential for widespread use.[3] Another drawback is the accuracy of the device, claimed to be 4%. This is currently not accurate enough to be used in diagnosis of diseases.[3]
However, as production costs drop, and the technology improves, the nanopore technology could become the preferred method of DNA sequencing.

References:
1.     DNA sequencing 2012. Encyclopædia Britannica Online. Retrieved 19 March, 2012, from http://www.britannica.com/EBchecked/topic/422006/DNA-sequencing
2.     Oxford Nanopore introduces DNA 'strand sequencing' on the high-throughput GridION platform and presents MinION, a sequencer the size of a USB memory stick, retrieved 19 March, 2012, from http://www.nanoporetech.com/news/press-releases/view/39
3.     Company Unveils DNA Sequencing Device Meant to Be Portable, Disposable and Cheap, New York Times, Retrieved 19 March 2012, from http://www.nytimes.com/2012/02/18/health/oxford-nanopore-unveils-tiny-dna-sequencing-device.html
4.     Nanopore DNA sequencing, Oxford Nanopore Vimeo. Retrieved 19 March 2012, from http://vimeo.com/36907534
5.     Campbell, Reece, Meyers et al (2011). Biology. 9th ed. San Francisco: Benjamin-Cummings Publishing Company. p407-408.
6.     Electrophoresis Image, University of Cincinnati, Retrieved 20 March, 2012 from http://biology.clc.uc.edu/fankhauser/labs/genetics/DNA_Electrophoresis/DNA_Electrophoresis.htm
7.     $1000 genome might be just around the corner, Life Scientist. Retrieved 20 March 2012 from http://www.lifescientist.com.au/article/415927/_1000_genome_might_just_around_corner/

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