Nanotech News

September 26, 2005

Detecting Single Stranded DNA with a Solid State Nanopore

In an effort to develop methods for rapidly sequencing genes of individual cancer cells, researchers are turning to methods based on nanopore detectors. The basic idea is to create nanometer-scale holes in a material such as silicon dioxide and develop methods to force a single strand of DNA through the hole. In theory, as each base passes through the hole, the sensor produces an electrical current that reflects the identity of that base.

Now, new work from a team of investigators at the University of Arkansas has defined some of the physical parameters that determine how DNA molecules move through such a pore. These results, published in the journal Nano Letters, should speed efforts to refine nanopore sequencing methods. The research team was led by Jiali Li, Ph.D.

Working with nanopores designed to guarantee that only single-stranded DNA can traverse the pore in sequential, single file order, the investigators studied the effects of pH and pore size on DNA passage through the nanopore. The key result of their study was that under alkaline conditions – between pH 7 and 13 – and at room temperature, DNA would pass through pores with a variety of sizes in strict, single file fashion. Most importantly, the researchers found that under these conditions, single-stranded DNA did not fold up on itself prior to passing through the hole, which means that single-stranded DNA will not form tangles that could clog the nanopores during a sequencing experiment.

This work is detailed in a paper titled, “Detecting single stranded DNA with a solid state nanopore.” This paper was published online in advance of print publication. An abstract is available at the journal’s website.
View abstract.