Oxford Nanopore moves closer to label-free, single molecule DNA
23 February 2009
Oxford Nanopore Technologies has 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, which is 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
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
“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 BASE 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
1. James Clarke, Hai-Chen Wu, Lakmal Jayasinghe, Alpesh Patel, Stuart
Reid1 & Hagan Bayley. Continuous base identification for single-molecule
nanopore DNA sequencing. Nature Nanotechnology. Published online: 22
February 2009 | doi:10.1038/nnano.2009.12
The abstract is available at:
Bookmark this page