Pulling a DNA through a Double-Nanopore system: A Brownian Dynamics Study

We study translocation of a model DNA polymer captured in a double nanopore (DNP) system using Brownian dynamics (BD). We consider two different configurations as reported in recent experimental studies. In the first case, the direction of translocation is parallel to the vector connecting the two pores (X. Liu et al., Small 2019, 1901704). In the second case, the direction of translocation is perpendicular to the vector connecting the two pores (S. Pud et al., Nano Lett. 2016, 16, 8021-8028). In the former case we demonstrate that in the absence of a time dependent feedback mechanism, the velocity of the segment in between the pores is not constant, which hinders the mapping of the data from the time domain into genomic length. In the second case, we investigate parameters for optimal translocation of the chain through the DNP system. We consider limiting cases, where the distance between the pores is much shorter than the contour length of the chain, and show that one can use scaling results for single nanopore translocation to interpret results for the DNP translocation.