Counterion-Hopping along the Backbone of Single-Stranded DNA in Nanometer Pores: A Mechanism for Current Conduction

Molecular dynamics calculations are performed to investigate ionic current conduction through nanopores in the presence of single-stranded DNA. We find the counterions to be strongly attracted to the phosphate groups of the DNA, with resident time on the order of nanoseconds, while coions are strongly excluded. The diffusion constant of the counterions is calculated and used to estimate the ionic current through the pore, which gives a similar magnitude as in experiment. The results suggest a counterion-hopping mechanism along the ssDNA backbone in the current conduction through nanopores.

Figure 1

The average number of counterions bound to the ssDNA. (a) C20: blue line, the phosphate group; red line, the oxygen atom connected to C2 of the cytosine base; black line, the rest of the atoms; pink squares, C2 atom; green circle, N3 atom of the cytosine base. (b) A20: blue line, the phosphate group; red line, the rest of the atoms. Green diamond, N3 atom; pink square, C4 atom of the adenine base, respectively. Black circle, $\mathrm{O}{5}^{\prime }$ of the sugar ring. (c) Abasic DNA: the peaks correspond to the phosphate groups.

Figure 2

The continuous residence time correlation function of the ${\mathrm{Na}}^{+}$ around the phosphate groups of C20 (solid line), A20 (long-dashed line), and the abasic DNA (dashed line) and the fitting functions (thin dashed lines).

Figure 3

The mean square displacement of ${\mathrm{Na}}^{+}$ in the axial direction in the presence of ssDNA in nanopore and the fitting functions.