Molecular Dynamics Study of a Rapid DNA Sequencing Device

Christina Payne, Vanderbilt University

High-throughput, low-cost (sub-$1000) DNA sequencing techniques are crucially important in the advancement of individualized medicine. One proposed nanotechnology concept offering the possibility of such rapidity is based on sequencing techniques utilizing transversal DNA conductance measurements as DNA translocates through a rectangular nanopore created by two nanoscale electrodes. The device, consisting of two nonconductive plates and housing the two metallic electrodes, will contain a DNA strand in solvent driven to translocate by the application of electric fields. Based on our previous molecular dynamics simulations of this device, we implemented a charge dynamics based method to properly represent the metal/non-metal interactions. Using this improved methodology, we examine device design characteristics and their influence upon the transport properties of DNA. Results from this theoretical implementation will, ideally, be combined with ab initio calculations of the differences in tunneling electron transport of nucleotides to yield valuable insight into the experimental fabrication of the actual device.

Abstract Author(s): Christina M. Payne, Xiongce Zhao, Lukas Vlcek and Peter T. Cummings