Tuesday, November 6, 2007 - 10:30 AM
207e

Dynamics Of Single-Stranded DNA Translocation In Nanometer Pores

S. T. Cui, Chemical Engineering, University of Tennessee, Knoxville, TN 37966-2200

There is a growing interest in using nanometer sized pores to detect the biological molecules by measuring the ionic current. The quasi one-dimensional geometry of the nanopores provides a natural environment for confining the linear molecules such as DNA. The experiments on single-stranded DNA (ssDNA) using the α-hemolysin pore, a self-assembled heptameric transmembrane pore of Staphylococcal α-hemolysin proteins with a diameter ~2.0 nm, and length of 10 nm, raised the possibility for DNA base type detection. There are currently many research efforts to use nanopore devices for detection of electric current as the ssDNA passes through the nanopore. Although double stranded DNA structure is well known. For single stranded DNA, however, many aspects of their behaviors are not well understood, especially in nanopore confinement environement. In this study we investigate the behavior of ssDNA in nanopore under applied electric field and the effect of the interaction between the ssDNA and small ions. The system consists of ssDNA in aqueous solution containing small ions confined in a nanopore of diameter ~ 2 nm. The nature of the pore models silica to correspond to experimental effort. We characterize the various conformational properties of the ssDNA molecules; the effect of a transverse field on the orientation of the ssDNA bases; the effect of different ionic species on the behavior of ssDNA; the translocation of the ssDNA driven by an electric field; and the dynamics of the ssDNA backbone and the base re-orientation.