Oxford Nanopore Technologies ("Oxford Nanopore") today announced the publication of new research in Nature Nanotechnology, demonstrating accurate and continuous identification of DNA bases using nanopores.
The system can also directly identify methylated cytosine, important in the study of epigenetics. This research marks significant progress towards Oxford Nanopore's goal of developing the first label-free, single molecule DNA sequencing technology.
A method of identifying single molecules that does not rely on expensive and complex fluorescent labelling is central to achieving the next dramatic improvement in the cost and speed of genome analysis. It is possible to achieve this goal by monitoring a simple electrical current passing through a nanopore. As single DNA bases pass through the nanopore, each base causes a characteristic disruption of current that allows the molecule to be identified.
Today's Nature Nanotechnology paper describes the use of nanopore technology to identify DNA bases with very high confidence for integration into a highly competitive new DNA sequencing system. Results were achieved through modification of a protein nanopore, including the permanent attachment of an adapter molecule to its inner surface.
The publication also demonstrates that methylated cytosine can be distinguished from the four DNA bases using the same method. This is important in the study of cancer, where genome methylation is implicated but existing study techniques require complex labelling of the DNA sample.
"The science of nanopore DNA sensing is now accurate and reliable enough to support a breakthrough industrial technology," said Professor Hagan Bayley, founder of Oxford Nanopore and an author of the paper. "The simplicity and versatility of nanopores as a sensing system has intrigued academic researchers for nearly two decades. We anticipate that with the fast pace of the science, nanopore devices will soon be used for the measurement of DNA and many other molecules."
"The findings from this paper provide validation of the high performance of the nanopore sensing element of our DNA sequencing system," said Dr Gordon Sanghera, CEO of Oxford Nanopore Technologies. "We continue the rapid development of this technology, whose advantageous cost, speed and versatility promise to enable a new paradigm of DNA analysis."
The research includes other outcomes essential for an integrated nanopore sequencing system. For its BASETM Technology, Oxford Nanopore couples a protein nanopore with a processive exonuclease enzyme. This enzyme cleaves individual DNA bases from a strand of DNA and introduces the individual bases into the nanopore for identification. This study shows that the operating conditions of the nanopore are compatible with those of an exonuclease. In addition there is a high probability that each DNA base translocates the nanopore so that a base is not read twice.
Discrimination of nucleotides:
The accuracy of identification of DNA bases was determined as follows: The distributions of bases as dNMPs were fitted to Gaussians and the areas of peak overlap were determined to give confidence values for base identity. The percentages of binding events that could be assigned to each base with a confidence approaching 100% at a high salt concentration (800 mM) were 99.9% (G), 99.7% (T), 99.8% (A) and 99.99% (C). Where there is ambiguity in a base call, the identities of the only two possible alternative bases are known.
This research was concluded in the summer of 2008 at the University of Oxford and Oxford Nanopore, where scientists continue to improve on this performance.
About Oxford Nanopore Technologies Ltd.
Oxford Nanopore was founded in 2005 on the science of Professor Hagan Bayley of the University of Oxford. Since its inception, the Company has focused on developing nanopore technology into a mass producible biochip and reader system for molecular analysis. Nanopores have been researched for more than 15 years at a number of the world's most prestigious academic institutions including Harvard, MIT, NIST, the University of Massachusetts, Texas A&M University, and the University of Oxford.
BASETM (Bayley Sequencing) Technology uses an adapted protein nanopore coupled with a processive exonuclease enzyme to sequence DNA. The enzyme cleaves individual bases from a strand of DNA, and sequentially introduces the bases into the aperture of the nanopore. An ionic current is continually flowing through the nanopore, and as individual bases travel through the nanopore, each one creates a characteristic disruption in this current. This signal is recorded electronically and interpreted to identify the DNA base. Future generations of nanopore sequencing technology may sequence DNA polymers directly or utilize nanpores made of synthetic materials.
The technology is label-free and sensitive at the single-molecule level, meaning that it removes the need for fluorescent labels, optical imaging and instrumentation, and the need for complex sample preparation including DNA amplification. By scaling up into a massively parallel sequencing process on an array chip, this method has the potential to deliver dramatic improvements in cost, speed, simplicity and versatility of sequencing.
In January 2009, Oxford Nanopore announced a strategic alliance with Illumina, Inc, including a commercialization agreement and equity investment to accelerate the development of BASE Technology. Under the terms of the commercialization agreement, Illumina will exclusively market, sell, distribute, and service BASE Technology products developed by Oxford Nanopore for DNA sequencing into the research and diagnostic markets on a worldwide basis.
Nanopores for the detection of other analytes
Nanopores offer a modular sensing system. Through chemical or genetic modifications to the pore, the biosenor can be adapted for the analysis of other molecules of interest. These might include medical biomarkers, drugs of abuse, agents of bioterrorism and many more analytes. The technology that supports the analysis of nanopores might also be used for ion-channel screening, with applications in drug development.