Nanopore detector shows discriminating taste in DNA molecules

Santa Cruz, CA--Researchers at the University of California, Santa Cruz, have devised a method of analyzing DNA molecules that can rapidly discriminate between nearly identical DNA strands. The technique may someday find applications in clinical settings to test patients for certain genetic traits. But for now, the ability simply to distinguish individual DNA molecules in a mixed solution is a notable achievement, said David Deamer, professor of chemistry and biochemistry at UC Santa Cruz.

The instrument used to perform the analysis, called a nanopore detector, is built around a membrane containing a tiny pore just big enough for 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. A characteristic decrease in the current occurs when a DNA molecule temporarily blocks the opening.

Deamer's lab has been working on this prototype nanopore detector for several years. The group's latest results, published in the March issue of Nature Biotechnology, come from experiments with a variety of synthetic DNA molecules. Using machine learning techniques, a computer program was "trained" to recognize the signals generated by different DNA molecules. The detector was able to analyze a mixed sample and indicate the proportions of each type of molecule present in the sample.

"It's almost like the detector is tasting the solution, pulling in one molecule at a time, spitting it out, sampling another molecule, and it's doing this hundreds of times a second," Deamer said.

The pore in this nanopore detector is actually a kind of toxin, known as the alpha-hemolysin ion channel, produced by Staphylococcus bacteria to punch holes in cell membranes. Because of the toxin's role in staph infections, it has been studied extensively and its structure is known in great detail.

"We know the environment of the ion channel very well, wh

Contact: Tim Stephens
University of California - Santa Cruz

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