Effect of Valence and Concentration of Counterions on Electrophoretic Mobility of DNA in a Solid-State Nanopore

Abstract

Controlling the electrophoretic mobility of DNA in a solid-state nanopore is critical to the development of the nanopore technology for sequencing DNA because, under typical experimental conditions, DNA moves through a nanopore too fast for its sequence to be detected. One could expect that increasing the electrostatic screening of the DNA charge in a nanopore would reduce the force driving DNA through and consequently the DNA translocation velocity. In free solution electrophoresis experiments, increasing either the valence or the concentration of counterions in an electrolyte was shown to affect mobility of DNA. Through extensive all-atom molecular dynamics simulations, we investigated the feasibility of controlling electrophoretic mobility of DNA in a solid-state nanopore. In our simulations, a double stranded DNA molecule is placed in the center of a 3-nm-radius nanochannel. The system is solvated in an electrolyte containing either Na(+), Mg(2+), spermidine(3+) or spermine(4+) ions. An external electric field is applied and the resulting displacement of DNA is recorded. We have found that the valence and concentration of counterions can dramatically alter the electrophoretic mobility of DNA in a nanopore. In monovalent or divalent electrolytes, increasing the concentration was found to decrease the electrophoretic mobility, whereas in spermidine and spermine electrolytes, the direction of the DNA motion could be reversed. Analysis of the interaction between DNA and the surrounding electrolyte revealed that the reduction of the electrophoretic mobility is caused not only by the presence of counterions, but also by the hydrodynamic drag of an electro-osmotic flow near the DNA surface.