DNA in Nanopores: Counterion Condensation and Coion Depletion

Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule inside. In the presence of DNA, the counterions condense on the stretched macromolecule effectively neutralizing it, and nearly complete depletion of coions from the pore is observed. The implications of our results for experiments on DNA translocation through $\alpha$-hemolysin nanopores are discussed.

Figure 1

(a) The time history of the numbers of counterions ($N_{+}$), coions ($N_{-}$), and the total charges [$Q=e(N_{+}-N_{-})$] contained in the empty pore (no DNA) is shown. (b) The time history in the presence of DNA (with $N_{-}^{\mathrm{DNA}}\approx 12$) in the pore. The total instantaneous charge in the pore is $Q=e(N_{+}-N_{-}-N_{-}^{\mathrm{DNA}})$. In both cases ${\epsilon }_m=2$.

Figure 2

Snapshot of the ion distribution with ssDNA in the pore for ${\epsilon }_m=2$ (a) and ${\epsilon }_m=80$ (b). Green and red spheres are counterions and coions, respectively, and orange spheres represent the charged phosphate groups of DNA (the neutral sugars and bases are not shown).