Abstract
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 paper, we determine how the dynamics 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 depends 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.
Highlights
In nanopore sensing, changes in ionic current are used to analyse single molecules in solution
Quantitative experiments on the dynamics of the translocation process, in particular the trajectory profiles of DNA passing through solid-state nanopores, are still lacking[14]
Solid-state nanopores can be fabricated in a wide variety of three-dimensional (3D) geometries and provide an ideal platform for investigating the effects of nanopore geometry on translocation
Summary
Changes in ionic current are used to analyse single molecules in solution. Using the inherent geometrical asymmetry of a conically shaped nanopore, we examine how DNA dynamics depends on the directionality of transport. Quantitative experiments on the dynamics of the translocation process, in particular the trajectory profiles of DNA passing through solid-state nanopores, are still lacking[14]. Several strategies have been investigated for modifying geometric constraints on translocating polymers by integrating porous fibre networks or agarose gels on one side of a membrane[26, 27] This is in part motivated by the need to reduce the velocity of DNA translocation thereby potentially improving resolution. We demonstrate how DNA translocation speed can be affected by solid-state nanopore geometries which create restrictions on the available DNA conformations. Our findings demonstrate a comprehensive understanding of DNA dynamics through conical nanopores
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