Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device

We report Brownian dynamics simulation results with the specific goal to identify key parameters controlling the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. First, we validate the simulation scheme in silico by reproducing and explaining the physical origin of the asymmetric experimental dwell time distributions of the oligonucleotide flap markers on a 48 kbp long dsDNA at the left and the right pore. We study the effect of the electric field inside and beyond the pores, critical to discriminate the protein tags based on their effective charges and masses revealed through a generic power-law dependence of the average dwell time at each pore. The simulation protocols monitor piecewise dynamics at a sub-nanometer length scale and explain the disparate velocity using the concepts of nonequilibrium tension propagation theory. We further justify the model and the chosen simulation parameters by calculating the Peclet number which is in close agreement with the experiment. We demonstrate that our carefully chosen simulation strategies can serve as a powerful tool to discriminate different types of neutral and charged tags of different origins on a dsDNA construct in terms of their physical characteristics and can provide insights to increase both the efficiency and accuracy of an experimental dual-nanopore setup.

Automated summary

This study reports the results of Brownian dynamics simulations aimed at identifying key parameters that control the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. The simulation scheme is validated by reproducing and explaining the asymmetric experimental dwell time distributions of the oligonucleotide flap markers on the dsDNA. The effect of the electric field inside and beyond the pores is studied to discriminate protein tags based on their effective charges and masses. The simulation protocols and chosen parameters are justified by calculating the Peclet number, which agrees closely with the experiment. It is demonstrated that the carefully chosen simulation strategies can effectively discriminate different types of neutral and charged tags on a dsDNA construct and provide insights to improve the efficiency and accuracy of an experimental dual-nanopore setup.