“Not only could we distinguish between double-stranded and single-stranded nucleic acid molecules, we could also see the difference between the two main classes of RNA bases – purines (adenine) and pyrimidines (cytosine and uracil),” team member Gary Skinner told nanotechweb.org. For the moment, the researchers can only do this for long molecules where the bases are all the same, but the technique is an important step towards using solid-state nanopores for RNA and DNA sequencing.

Skinner and colleagues begin by immersing the nanopore into a bath of salt solution and then apply a voltage across it. This produces a small, measurable, electric current resulting from the flow of salt ions through the pore. The size of the current depends on the amount of ions flowing.

If a molecule, such as DNA, now enters the pore and blocks the flow of some of the ions, this results in a current drop, which can be measured. The amount of ions blocked depends on the size of the molecule in the pore, explains Skinner. “Therefore, double- and single-stranded molecules produce different values of blocked current because they have different sizes.”

The Delft team, led by Nynke Dekker, says that the technique is simple in principle and requires only a nanopore, electrodes and a suitable amplifier/current meter. Measurements can be made extremely rapidly and only a few milliseconds are needed to quantify an individual molecule. An entire solution can thus be analysed in just minutes. This is in contrast to conventional techniques, such as gel electrophoresis, that require several hours.

The method might be used to make a molecular-scale Coulter Counter, a device routinely used in hospitals to measure white and red blood cell counts. “In our approach, the pore is orders of magnitude smaller and could be used to rapidly quantify mixed molecular populations with different concentrations in a single electrical measurement,” said Skinner. “And again, since we detect single molecules, we require much less material than that needed in other methods.”

The results were published in Nano Letters.