Slowing the Translocation of Double-Stranded DNA Using a Nanopore Smaller than the Double Helix

摘要

It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a solid-state nanopore smaller in diameter than the double helix. 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, while the B-form canonical structure is preserved outside the pore. In this configuration, the translocation velocity is substantially reduced from 1bp/10ns to ~1bp/2ms in the extreme, potentially facilitating high fidelity reads for sequencing, precise sorting, and high resolution (force) spectroscopy.