For DNA sequencing to become a routine part of patient care, it needs to become cheaper and faster. A company called Oxford Nanopore hopes to bring down both the cost and the time required for sequencing using a technique called nanopore sequencing. The company has now made an important demonstration of its technology: for the first time, researchers were able to identify DNA bases with near total accuracy. In addition to identifying the four bases of DNA, the technique can also detect a modified version of one of the bases, which may be responsible for causing cancer and other diseases.
The new technique allows for the direct identification of bases without the fluorescent labels and imaging equipment used for conventional high-speed sequencing. Direct reading of DNA should not only be faster and cheaper, but it should also make it possible to perform more complex analysis, says Jeffrey Schloss, program director for technology development at the U.S. National Human Genome Research Institute. The Oxford Nanopore system’s ability to detect the DNA modifications catalogued by an emerging field called epigenetics is particularly exciting, says Schloss. For example, the addition of organic molecules called methyl groups to one of the bases has been shown to play a role in the development of diseases such as cancer. But it is arduous to detect these modifications using conventional sequencing methods, so the full effects and why they happen are still not well understood.
Oxford Nanopore researchers have not yet demonstrated that they can process complete DNA sequences using their system. However, the new results, published this week in Nature Nanotechnology, are an important proof of concept for nanopore sequencing. “They’ve shown the feasibility of all the steps,” says Schloss.
The system that the company used to identify DNA bases is a tunnel-like protein embedded in a membrane very similar to that which surrounds biological cells. The flow of ions across the membrane and through the pore creates a current that can be measured using an electrode similar to those used to study neurons in the lab. By applying a strong electrical potential across the membrane, researchers drive DNA bases through the pore. As each base passes through, it modifies the current flowing across the pore in a characteristic way.
The key to making the method work is controlling the flow of the bases through the protein pore. DNA bases are “too small to be identified on their own: they would fly through,” says James Clarke, a scientist at Oxford Nanopore. So a sugar molecule lining the opening bulks it up so that the DNA doesn’t zip through too rapidly. In previous versions of the nanopore system, this sugar molecule was rather loosely associated with the pore, moving in and out. Company researchers led by founder Hagan Bayley, who is also a professor of chemistry at the University of Oxford, made it possible to read DNA bases one after the other by chemically bonding the sugar to the inside of the nanopore.