Asymmetric Dynamics and Current Signals of DNA Entering and Exiting a Strongly Confining Nanopore

In nanopore sensing, changes in ionic current are used to analyse single molecules in solution. The translocation dynamics of polyelectrolytes is of particular interest given potential applications such as DNA sequencing. In this study, we determine how the dynamics and current signatures of voltage driven DNA translocation can be affected by the nanopore geometry and hence the available configurational space for the DNA. Using the inherent geometrical asymmetry of a conically shaped nanopore, we examine how DNA dynamics and current signals depend on the directionality of transport. The total translocation time of DNA when exiting the extended conical confinement is significantly larger compared to the configuration where the DNA enters the pore from the open reservoir. By using specially designed DNA molecules with positional markers, we demonstrate that the translocation velocity progressively increases as the DNA exits from confinement. We show that a hydrodynamic model can account for these observations. The current signatures also depend on the DNA translocation direction and we used a finite simulation method to explain the observed current signatures. Our analysis shows that over a wide range of geometries, voltages, and salt concentrations, we are able to understand the ionic current signals and dynamics of DNA in asymmetric nanopores, enabling signal optimization in molecular sensing applications. References [1] N. A. W. Bell, K. Chen, S. Ghosal, M. Ricci, and U. F. Keyser. Nature Communications, 8(380), 2017. [2] K. Chen, N. A. W. Bell, J. Kong, Y. Tian, and U. F. Keyser. Biophysical Journal, 112(4):674-682, 2017. [3] K. Chen, M. Juhasz, F. Gularek, E. Weinhold, T. Yu, U. F. Keyser, and N. A. W. Bell. Nano Letters, 2017, 17, 5199-5205.