Drawing individual strands of DNA through nanoscopic pores in a chip could do in a matter of minutes what the human genome project took more than a decade to achieve – sequence an entire human genome.
Known as solid state nanopore sequencing, the technique identifies DNA base pairs by measuring their electrical properties as they pass through a tiny hole – relying on the fact that DNA nucleotides each possess distinct electrical signatures. It marks a radical move away from the traditional biochemical and optical approaches to genome sequencing, and according to IBM and Roche Applied Science, who are teaming up to develop the technology, it could slash the cost of sequencing a genome from over $US10,000 to as little as $US100.
The technique was developed by Stanislav Polonsky’s team at IBM’s Watson Research Centre in Yorktown Heights, New York state. They built a 10-nanometre-thick membrane, composed of three layers of titanium nitride separated by insulating layers of silica, then punched a 3-nanometre-wide hole through it.
When a voltage is applied across the membrane the negatively charged strands of DNA are drawn towards it and one passes into the pore, says Polonsky. Once trapped, the voltage is shut off and an electric field is applied across each metal layer, trapping a base pair in the central layer to identify it. Finally, by flipping the field’s polarity the DNA strand is ratcheted along so the next base pair sits in the central layer for identification.
To date, the team has built the membrane and shown that DNA molecules can be drawn into the nanopore – they have yet to classify the base pairs, however. “But our modelling shows that it is doable,” says Polonsky. Furthermore, preliminary unpublished experiments with DNA suggest the ratchet mechanism works, he says.
Nanopore sequencing is by no means a new idea. Research groups in the US and UK have spent 15 years developing and improving versions of the technology. In the UK, Hagan Bayley’s work at the University of Oxford has spawned a company – Oxford Nanopore – that is now in the process of trying to commercialise nanopore sequencing.
But Oxford Nanopore, and others in the sector, use biological mechanisms to fashion the nanopores and thread DNA through them. Oxford Nanopore’s technology involves an enzyme called alpha hemolysin (AHL), which sits on the membrane’s surface, chopping off DNA base pairs one at a time and feeding them through the pore to be measured, says the company’s CEO Gordon Sanghera.
“But they cannot control the speed,” says Ulrich Schwoerer of Roche Applied Science in Branford, Connecticut. “It is dependent upon the speed of the enzyme.” A non-biological, solid-state approach should make it possible to process DNA strands at rates of 1000 base pairs per second, per pore – a 30-fold increase on the enzyme approach, he says. Furthermore, because pores can be packed densely, several strands could be read simultaneously.
The advantages of solid-state systems are encouraging Oxford Nanopore to explore replacing its protein pores with non-biological versions, says Sanghera. “If it can be made to work, this really is a significant leap in the industry,” he says.