title: DNA in nanopores: counterion condensation and coion depletion.
abstract: 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.
authors.affiliation: Institute for Mathematics and Its Applications, University of Minnesota, Minneapolis, Minnesota 55255, USA.
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Rabin
authors.forename: Motohiko
authors.initials: M
authors.lastname: Tanaka
mesh_terms: D003198:Computer Simulation; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000378:metabolism; D008956:Models, Chemical; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D004277:DNA, Single-Stranded