Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix

Utkur Mirsaidov, Jeffrey Comer, Valentin Dimitrov, Aleksei Aksimentiev, and Gregory Timp
Nanotechnology 21(39) 395501 (2010)
DOI:10.1088/0957-4484/21/39/395501  PMID:20808032  BibTex


The image of the double helix of DNA has become an icon of biotechnology and genetics. However, this double helix is more than just an aesthetically pleasing image: it gives double-stranded DNA peculiar mechanical properties that are pertinent to biology and biotechnology. We have previously shown that molecules of double-stranded DNA can be electrically driven through tiny pores smaller in diameter than the double helix. How is this possible? Our computer simulations show that the DNA double helix stretches and distorts as it passes through a pore smaller than itself—a situation somewhat like forcing a drinking straw through the small hole in a drink box. With this knowledge, the researchers in the Timp and Aksimentiev groups have invented a method to trap DNA by driving the molecule into the pore using a strong electric force and then reducing the electric force while the DNA is still in the pore. Using molecular dynamics simulations, we have examined the process of trapping a DNA double helix in atomic detail, providing our experimental collaborators with the estimates of the forces and time scales involved. Using a special purpose electric circuit, the researchers in the Timp group have demonstrated the trap machanism in practice. The results of this study suggest the possibility of controlling the motion of double-stranded DNA through a solid-state nanopore. Such control could facilitate nanopore sequencing, which has the potential to reduce the cost of DNA sequencing to the extent that you and your doctor could make medical decisions based on the unique information in your genome. This work is described in a report that appeared in Nanotechnology.


It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a nanopore, smaller in diameter than the double helix, in a solid-state membrane. By applying an electric force larger than the threshold for stretching, dsDNA can be impelled through the pore. Once a current blockade associated with a translocating molecule is detected, the electric field in the pore is switched in an interval less than the translocation time to a value below the threshold for stretching. According to molecular dynamics (MD) simulations, this leaves the dsDNA stretched in the pore constriction with the base-pairs tilted, while the B-form canonical structure is preserved outside the pore. In this configuration, the translocation velocity is substantially reduced from 1 bp/10 ns to approximately 1 bp/2 ms in the extreme, potentially facilitating high fidelity reads for sequencing, precise sorting, and high resolution (force) spectroscopy.