Molecular detection

Identifying the sequences of bases in DNA is among the most significant of scientific tasks. Yet, despite its importance to life science research, it is still a laborious and expensive process. That is why Oxford Nanopore Technologies is trying to revolutionise molecular detection and analysis.

The company is developing techniques using nanopores as biosensors. It has already demonstrated that it can read the four bases (C, G, A and T) of a single DNA molecule without having to use amplification and tagging, as happens in current methods. It has also made a working electrical interface for the system.

Now it has licensed exclusive rights to develop and commercialise breakthrough technologies from three US laboratories that will help it clear the final hurdle — cutting the base molecules from the double-helix structure.

‘There is a key chemical-biological challenge left for us,’ said Dr Gordon Sanghera, chief executive of Oxford Nanopore Technologies. ‘DNA is in a duplex helical strand but we want to present to our sensor system single base molecules. The intellectual property we have licensed involves an enzyme that acts like a pair of scissors, cutting the strand.’

The concept work has been developed over nearly 15 years in labs at Harvard, University of California Santa Cruz and the National Institute of Standards and Technology, an agency of the US Department of Commerce. Sanghera said: ‘We are proud to collaborate with this world-class research team. Harvard’s long record of excellence in nanopore research means that this agreement encompasses many aspects of nanopore technology.’

He claimed: ‘Through this partnership and agreements with other prestigious institutions, Oxford Nanopore takes the leading position in transforming nanopores from science into technologies that will benefit researchers and people everywhere.’

The nanopore used for the detection and analysis system is formed by a protein pore set into a membrane. It has an inner diameter of 1nm, which is on the same scale as a single DNA molecule. The inside of the hole is engineered and coated with a molecule, which allows individual DNA bases to bind with it and accurate measurement of their passage through the nanopore. ‘We put a small bias voltage across, so current flows only through the hole and then our target molecule of interest enters the pore through electrophoretic flux,’ said Sanghera. ‘This is where the clever engineering comes in because it is transiently held by the pore and then it’s released, to give an on-off event.’

Without modification to the nanopore, the DNA molecule would naturally block the pore for only microseconds — too short for detection and analysis. ‘We engineer the pore to slow this down and give us targets within the millisecond timeframe,’ said Sanghera. ‘So we hold the molecule for one to 10 milliseconds.’

The degree to which the molecule blocks the pore and the time it stays there gives researchers vital information about that molecule.

When the technology is fully proven, the company expects to be able to fabricate arrays of sensors on a suitable substrate, much like computer chips. The process of sequencing will be speeded up by the multiplicity of sensors. No time would be required to amplify samples and there would be no need to fluorescently label the bases with four different tags. A process that can take five days would be shortened dramatically and be a lot cheaper, said Sanghera. ‘Direct electrical read, which our system has, has huge implications in terms of cost, speed, throughput and quality of signal,’ he added.

There are also potential applications beyond DNA sequencing. ‘It could be used for point-of-care diagnostics, because it’s very easy to build a single-use reader and a disposable chip,’ he said. ‘There’s a great deal of interest in looking at counter-bioterrorism applications and also at small molecule matabolites for companion diagnostics in drug efficacy research.’

So when does Oxford Nanopore Technologies expect to launch its finished product? ‘We have a timeline but this is an incredibly competitive field and very commercially sensitive,’ said Sanghera. ‘I hate to say this but ‘watch this space’ because we’re getting very close to achieving our goal.’

Max Glaskin