Researchers use virus to reveal nanopore physics

Nanopores could provide a new way to sequence DNA quickly, but the physics involved isn't well understood. That's partly because of the complexities involved in studying the random, squiggly form DNA takes in solution.

Researchers from Brown have simplified matters by using a stiff, rod-like virus instead of DNA to experiment with nanopores. Their research has uncovered previously unknown dynamics in polymer-nanopore interactions.

Nanopores may one day lead a revolution in DNA sequencing. By sliding DNA molecules one at a time through tiny holes in a thin membrane, it may be possible to decode long stretches of DNA at lightning speeds. Scientists, however, haven't quite figured out the physics of how polymer strands like DNA interact with nanopores. Now, with the help of a particular type of virus, researchers from Brown University have shed new light on this nanoscale physics.

"What got us interested in this was that everybody in the field studied DNA and developed models for how they interact with nanopores," said Derek Stein, associate professor of physics and engineering at Brown who directed the research. "But even the most basic things you would hope models would predict starting from the basic properties of DNA -- you couldn't do it. The only way to break out of that rut was to study something different."

The findings, published today in Nature Communications, might not only help in the development of nanopore devices for DNA sequencing, they could also lead to a new way of detecting dangerous pathogens.

The researchers looked at fd, a harmless virus that infects e. coli bacteria. Two things make the virus an ideal candidate for study with nanpores. First, fd viruses are all identical clones of each other. Second, unlike squiggly DNA, fd virus is a stiff, rod-like molecule. Because the virus doesn't curl up like DNA does, the effect of drag on each one should be essentially the same every time.