Controlled transport of DNA through a Y-shaped carbon nanotube in a solid membrane

Abstract

We investigate the possible ratcheting dynamics of double-stranded DNA (dsDNA) driven through a Y-shaped carbon nanotube (Y-CNT) in a solid membrane, using all-atom molecular dynamics (MD) simulation. By applying constant or alternating biasing voltages, we found that the dsDNA molecule can be unzipped at the junction of the Y-CNT. Because of the energy barrier (a few k_BT per base-pair), the motion of the entire DNA molecule was alternatively in a trapped state or a transiting state. We show that during each transiting state the same number of nucleotides were transported (DNA ratcheting). An analytical theory that is mathematically equivalent to the one for Josephson junctions was then proposed to quantitatively describe the simulation results. The controlled motion of DNA in the Y-CNT is expected to enhance the accuracy of nanopore-based DNA sequencing.