Oct 22, 2013
Probing an individual DNA molecule thousands of times with a nanopore
Research on DNA translocation through solid-state nanopores has received intense attention in recent years, not least thanks to its potential for DNA sequencing and single-molecule analysis. In a typical experiment, DNA molecules pass through a nanopore and their properties are determined by the resulting ionic current blockade. Once a molecule has passed through the nanopore it randomly mixes with other DNA molecules in the fluidic chamber and any individual molecule cannot be identified again. In a new study, however, researchers at the Delft University of Technology in the Netherlands have shown that they can measure the same individual molecule thousands of times.
By actively detecting the passage of an individual DNA molecule as it passes through the nanopore and quickly reversing the electric field, single molecules can be recaptured over 1000 times. This allows the researchers to obtain statistics on the translocation process for an individual DNA molecule. The technique reveals short translocation times and very strong folding when molecules are recaptured at timescales below their characteristic "Zimm" relaxation time. At longer recapture times, when the molecule has had sufficient time to relax, these values approach those seen in non-recapture experiments.
These insights into a novel, so-far not well explored non-equilibrium regime, means that researchers can assess the importance of the (non)equilibrium state of the molecule during translocation processes. Furthermore, such repeated interrogation of single-molecules could allow for more accurate measurements and might be used in the future to explore time-dependent processes.
More information can be found in the journal Nanotechnology (in press).
About the author
Calin Plesa is a PhD candidate in Prof. Cees Dekker’s laboratory in the Department of Bionanoscience of the Kavli Institute of Nanoscience at the Delft University of Technology in the Netherlands. The group carries out a variety of research investigating the properties and applications of solid-state nanopores.