Dynamics of DNA translocation in a solid-state nanopore immersed in aqueous glycerol

Abstract

Nanopore-based technologies have attracted much attention recently for their promising use in low-cost and high-throughput genome sequencing. To achieve single-base resolution of DNA sequencing, it is critical to slow and control the translocation of DNA, which has been achieved in a protein nanopore but not yet in a solid-state nanopore. Using all-atom molecular dynamics simulations, we investigated the dynamics of a single-stranded DNA (ssDNA) molecule in an aqueous glycerol solution confined in a SiO2 nanopore. The friction coefficient ξ of the ssDNA molecule is found to be approximately 18 times larger in glycerol than in water, which can dramatically slow the motion of ssDNA. The electrophoretic mobility μ of ssDNA in glycerol, however, decreases by almost the same factor, yielding the effective charge (ξμ) of ssDNA being roughly the same as in water. This is counterintuitive since the ssDNA effective charge predicted from the counterion condensation theory varies with the dielectric constant of a solvent. Due to the larger friction coefficient of ssDNA in glycerol, we further show that glycerol can improve trapping of ssDNA in the DNA transistor, a nanodevice that can be used to control the motion of ssDNA in a solid-state nanopore. Simulation results of slowing ssDNA translocation were confirmed in our nanopore experiment. © 2012 IOP Publishing Ltd.