Translocation of DNA through nanopores: Electrostatic effects for ion diffusion process

We present our molecular dynamics studies of translocation of DNA through nano-size pores which emulate cellular membrane pores [PRL 94, 148103, 2005], Due to low dielectric constant of the membrane (ε=2) compared to water (ε=80), electrostatic energy of charges in the pore are intensified, thus cations and anions always make pairs in the pore. A single-stranded DNA, which is a negatively charged polymer, is neutralized by counterions, and takes a stretched configuration due to electrostatic effects. Coions are almost depleted from the pore. The diffusion time of coions is reduced when the DNA exists in the pore, which is consistent with the experiment at Harvard Univ. that observed reduction of the pore current when the pore is stuffed with single-stranded DNA.