Threading DNA through a nanopore
If a nanopore is sufficiently wide, folded DNA molecules can squeeze through. But where do the folds form?
January 10, 2013Published: January 10, 2013
Nanoscale pores are showing increasing promise as tools for DNA analysis, including size determination, folding studies, and base sequencing (see Physics Today, November 2012, page 29). When threading a sewing needle, some people pass the end of the thread through the eye, while other people fold the thread first and then pass the fold through. Similarly, when a nanopore's electrophoretic forces capture a DNA molecule, the 2-nm-diameter DNA can be pulled through from one of its ends or, if the pore is wide enough, can form a fold somewhere along its length and be pulled through from there. Derek Stein and colleagues at Brown University now offer a statistical study of the fold locations in DNA passing through a voltage-biased 8-nm-diameter nanopore fabricated in silicon nitride. From the observed variations in the electrical current across the pore, the team could readily discern the positions of folds in transiting DNA molecules. The experiments show a strong bias favoring the capture of molecules near their ends. A simple physical model explains the data in terms of configurational entropy: The closer the fold is to the end of the molecule, the more numerous are the molecule's possible physical configurations, and the more likely it is for one of those configurations to be observed entering the pore. Molecules, the team concludes, do not search for an energetically favorable configuration beforehand. (M. Mihovilovic, N. Hagerty, D. Stein, Phys. Rev. Lett. 110, 028102, 2013.)—Richard J. Fitzgerald