In nanopore-based sequencing, the word “tunneling” does not refer to the threading of a single strand of DNA through a nanopore, as one might expect. It is, rather, a novel detection technique, the measurement of tunneling current. Tunneling occurs when an electron exploits a quantum mechanical loophole and passes through a potential barrier that would be great enough to repel a classical electron.
Quantum tunneling detectors are still the stuff of experiment, but they may find their way into commercial nanopore sequencing platforms, which typically rely on measuring the ionic current that passes across a pore as DNA passes through it. Quantum tunneling detectors could reduce the cost and increase the scale of nanopore sequencing, but they require nanopores that are fabricated from synthetic materials, rather than proteins, which have already been shown to be optimizable and reliable nanopore components.
In 2005, tunneling as a means of determining DNA base sequences was first proposed. In 2010, tunneling was used to identify single bases in short DNA molecules. As late as 2015, tunneling developers were still striving to achieve single-base resolution by controlling how quickly the DNA passes through the nanopore.
The kinks in tunneling are still being worked out, but at Osaka University it has been used to distinguish between chemically modified bases, demonstrating how it may be advantaged in certain applications. Specifically, Osaka scientists used a single-molecule quantum sequencing method to determine exactly where an anticancer agent, trifluridine, becomes incorporated into DNA. Although trifluridine can take thymine’s place in DNA, it cannot bind to thymine’s partner, adenine. Consequently, when trifluridine gets incorporated into DNA of cancer cells, it inhibits cell proliferation and tumor growth.
In Scientific Reports, the Osaka scientists described how they used tunneling to distinguish drug molecules from normal nucleotides in short strands of DNA. The analysis of long strands of DNA, the scientists noted, will require better “flow-dynamics control techniques.”
Eventually, tunneling could lead to a “better understanding of the mechanism involved in DNA damage,” said the article’s senior author, Masateru Taniguchi, PhD. “This technology,” he added, could “aid in the development of more effective anticancer drugs.”