Right now, there is a race to the bottom – to develop new technology that both reduces the cost and improves the speed of sequencing DNA. Today, a lot of the cost and time associated with sequencing DNA is attached to the chemistry required to amplify DNA; that is to say, making multiple identical copies of the DNA to accommodate the chemistry involved in sequencing.

Winning idea?

Sequencing DNA with a nanopore is a revolutionary concept that one day may enable us to sequence a single molecule of DNA, eliminating the need for amplification and reducing the cost to <$1000 for a genome.

A nanopore is a hole, which is comparable in size to a DNA molecule, in a thin (nanometre-thick) membrane made from a material such as silicon or silicon nitride. When the hole is immersed in electrolyte and a voltage applied across the membrane, a current flows through it. In addition to electrolytic ions, highly charged DNA molecules also try to electrophoretically migrate through the pore, but the hole is so small that only one molecule fits in the pore at a time.

Detecting base pairs

The key principle for sequencing DNA involves the electrical detection of each base pair as the DNA molecule translocates through the pore by measuring either the voltage across the membrane or the current through the pore. One of the main challenges is the signal-to-noise ratio required to discriminate between base pairs. The signal detection is limited by the bandwidth of the measurement and the corresponding electrical noise.

For high-speed, high-fidelity sequencing, low-noise electrical measurements at high frequency are required because the signal used to discriminate between bases is typically only at a microvolt or picoamp level, and because the molecule translocates through the pore at a velocity of ~1 base pair per 10 ns.

Noise reduction

Recently, scientists from the University of Illinois, US, have shown that they can engineer nanopores in which the high frequency noise is reduced. They accomplish this feat in three different ways: increasing the membrane thickness; miniaturizing the membrane area to reduce the parasitic capacitance; and by compensating for the membrane capacitance using an external electrical circuit. In each case, the reduction of the membrane capacitance is the key element to improving the overall electrical performance for sequencing DNA. Miniaturization is the easiest strategy. It leverages the same photolithography tools that are used to define conventional integrated circuits: they define a micron-scale pattern in a thick layer of dielectric (~5 µm) material on top of the membrane to reduce the area.

Device upgrade

The Illinois group has also modelled the performance of its nanopore devices to show that further improvements in bandwidth and noise can be easily achieved by using thicker dielectric layers on top of the membrane. This finding is especially important given that both the high-frequency noise and the response speed of nanopores is inexorably tied to the capacitance of the pore-membrane system. Reducing the capacitance leaves the electrical resistance to the flow of electrolyte inherent to the nanopore as the only active element in the total impedance of the system, which has negligible high-frequency noise and reduced frequency cut-off.

More information can be found in the journal Nanotechnology.