Electrokinetic Brownian dynamics of current blockade of a dsDNA through a nanopore

Brownian Dynamics (BD) simulation has been shown to be effective for understanding and providing physical insights into the complex processes of long dsDNA translocation through nanopores [1-3]. We expand our BD study by considering the movement of the co-ions and counter-ions along with a short-chain dsDNA decorated with oligo-flap markers through a nanopore. The inclusion of the ions and counterions enables us to calculate the current blockade (CB) directly from the electrokinetic Brownian dynamics (EKBD) simulation and compare it to a simpler but computationally efficient model of CB that uses the volumetric occupancy of the species in the nanopore. By comparing both CB data sets, we finally tune the adjustable parameters of the volumetric CB model, which enables us to construct the CB data for a very long dsDNA strand (~Mbp) with high accuracy but at a much lower computational cost. We further compare the Peclet number of both the simulation and experiments to validate our findings. Moreover, we investigate the effect of mono-and divalent ion concentration on the noise levels in the current blockade and the translocation speed, which we believe to be helpful for improving the signal-to-noise ratio of the nanopore current blockade data.



[1] Seth, S., & Bhattacharya, A. (2021). RSC Advances 2021, 11 (34), 20781–20787.

[2] Seth, S., & Bhattacharya, A. Sci Rep 2021, 11 (1), 9799.

[3] Seth, S., Rand, A., Reisner, W., Dunbar, W. B., Sladek, R., & Bhattacharya, A. Sci Rep 2022, 12 (1), 11305.