The Nanopore Project

Nanopore detectors are instruments built around a membrane containing a tiny pore called an ion channel, just big enough to allow a single strand of DNA to pass through. A voltage applied across the membrane generates an ionic current and pulls the negatively charged DNA molecules through the pore. When the DNA molecule blocks the opening of the nanopore, it causes a characteristic decrease in the current, allowing discrimination between individual DNA molecules. A computer trained by machine-learning techniques recognizes the signals generated by different DNA molecules.

The nanopore project at UC Santa Cruz has pioneered the use of ion channels for the analysis of single RNA and DNA molecules. Nanopore technology makes it possible to measure DNA structure and dynamics with precision at the angstrom level. Thus, it is possible to rapidly discriminate between nearly identical strands of DNA and investigate their physical properties. Nanopore technology is well suited to analysis of the terminal ends of double-stranded DNA, and it is amenable to high throughput experiments.

In the future, it may be possible to develop a durable solid-state or protein-based nanopore device that would allow the measurement of several different genomic factors from one cell without amplification:

• gene expression
• single-nucleotide polymorphisms (SNPs), common, minute variations in genes that can be used to track familial inheritance
• point mutations in single RNA or DNA molecules

Using machine learning tools developed at UCSC, each molecule could be identified in real time and in less than 50 milliseconds. Such a device would have broad clinical utility in diagnosing inherited traits such as hearing disorders and drug sensitivity and in tracking disease progression at the level of single cells.