Coarse-grained simulation of polymer translocation through an artificial nanopore

Abstract

The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of semiconductor--based nanopore devices for ultra--fast DNA sequencing. The polymer is represented by a simple bead--spring model designed to yield an appropriate coarse-grained description of the phosphate backbone of DNA in salt--free aqueous solution. A detailed analysis of single translocation event is presented to assess whether the passage of individual ions through the pore can be detected by a nanoscale field--effect transistor by measuring variations in electrostatic potential during polymer translocation. We find that it is possible to identify single events corresponding to the passage of counterions through the pore, but that discrimination of individual ions on the polymer chain based on variations in electrostatic potential is problematic. Several distinct stages in the translocation process are identified, characterized by changes in polymer conformation and by variations in the magnitude and direction of the internal electric field induced by the fluctuating charge distribution. The dependence of the condensed fraction of counterions on Bjerrum length leads to significant changes in polymer conformation, which profoundly affect the dynamics of electrophoresis and translocation.Comment: 37 pages Revtex, 11 postscript figure