DNA sequencer in the palm of your hand
A DNA decoder in the form of a USB flash drive is entering the market
Leonid Popov, Membrane
The UK has created the tiniest automatic genome decoder in the world. It will appear on the shelves this year, and with a rather attractive price tag. And he will be accompanied by an equally interesting DNA analyzer enclosed in the server.
Oxford Nanopore Technologies has introduced a miniature disposable base sequence determinant in the DNA molecule – MinION.
A fully autonomous device, slightly larger in size than a memory stick, connects to the USB port of a laptop or PC. It contains all the elements necessary for complete genome sequencing: microthreading systems, a unique sensor and specialized electronics.
The accuracy of the novice's work is at the level of existing sequencing systems, according to the creators of the device.
The device directly reads the "letters" of DNA and reflects them on the screen in real time, as well as writes them to the computer memory.
Researchers can determine in advance how much information they need for the purposes of a particular experiment, or which fragment of the genetic code they are looking for, and stop decoding immediately after reaching the result in order to quickly move on to a new experiment.
Preparing samples for the MinION system also does not require much effort. The device works with double-stranded DNA, and it does not require pre-amplification.
In some cases, the sensor can isolate the molecule immediately from a blood or serum sample, and sometimes a small pretreatment of the mixture may be necessary.
Even more interesting is that the MinION device is a side project that was born when creating a larger and more powerful reusable sequencing system – GridION. Both use the same genome decoding technology, which a group of biochemists from Britain and the USA have been working on for about 20 years (counting from the appearance of the bare idea).
The mechanism is based on a polymer membrane with embedded nanopores. This part of the device is obtained by a combination of natural (proteins) and synthetic molecules.
Nanopores in the membrane are designed to pass strictly defined molecules.
A specially developed enzyme added to the sample solution picks up the DNA molecule
and consistently pushes it through the pore, as through a die.
At this time, an electronic circuit connected to the pore registers electrical vibrations. According to their specific profile, the device calculates each past base pair, and with high accuracy even for very long fragments of the "molecule of life".
Protein nanopore in the membrane. An ion current flows through it, in which "interruptions" occur,
different depending on the type of molecules passing through these "gates".
By the degree of current deviation, electronics identifies the basic DNA bases.
Unlike its tiny counterpart, the GridION system is something like a complex of decoder servers (the company calls them nodes - GridION node).
Each such node has a slot for a disposable cartridge. The latter contains the entire set of reagents necessary for a complete DNA analysis, and the actual chip analyzer with two thousand nanopores described above.
The GridION node measures the ion currents inside the chip with high accuracy, decodes them and displays the sequencing result. In parallel, the sequence of the genetic code is written to an external hard drive or another computer (via USB or Network).
In a day, one GridION node is able to output tens of gigabytes of data on the sequence of bases in the studied DNA.
The GridION device can be configured to search not only in the sample and DNA analysis,
but also other molecules – proteins needed by scientists or, for example, explosive compounds.
Although the GridION node "server" is capable of operating as an independent desktop equipment, the most impressive result is achieved when several such devices are combined into a server rack (standard width 19 inches) and act in concert, exchanging data directly during decoding. By the way, the sizes and connectors of the GridION node correspond to a regular server.
In 2013, the GridION node version should be released already at 8000 nanopores, and it should work faster than the previous model.
According to the developers, 20 such machines in one server rack will be able to decode the entire genome of a person in just 15 minutes.
Both devices, the GridION (in the first version) and the striking MinION, are scheduled to be released to the market in 2012. The manufacturer intends to set competitive prices, in comparison with the latest technologies of high-speed genome decoding.
In particular, the "DNA flash drive sequencer" will cost less than $900, Technology Review reports.
The "server" is a GridION node and a set of such nodes in the server rack.
One GridION node consumes less than 50 watts of power,
the company emphasizes one of the advantages of the device
(here and above are illustrations by Oxford Nanopore Technologies).
Here we need to remember that a little more than a year ago, the American company Life Technologies introduced a desktop personal genome decoder Personal Genome Machine, which costs less than $ 100 thousand.
The principle applied in it differs from the GridION technology, but there is also a common feature: for automated sequencing, scientists have also developed a microchip that combines electronics with chemistry.
In January 2012, Life Technologies (or rather, its subsidiary Ion Torrent) showed its new genome decoder model called Ion Proton. This machine is already valued at $149 thousand, but the chip analyzer hiding inside is 1000 times more powerful than the previous sample.
The Ion Proton device is able to read the complete human genome in one day
with the cost of "consumables" at $ 1000 (photo by Ion Torrent Systems/Life Technologies).
All these devices should eliminate, as scientists say, one of the bottlenecks in a number of biological and medical research – slow decoding of the genome.
Now relatively small laboratories can take on such a task, and in the case of a flash drive decryptor, we can say that DNA decoding technology is on the verge of coming to almost every home, just as people now independently analyze blood sugar.
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21.02.2012