Modeling current blockade in a dual nanopore device

We study current blockade (CB) of molecular features (markers) on a dsDNA construct translocating through a multiscan dual nanopore (NP) setup [1] using a volumetric occupation model of the CB for species inside or in the vicinity of the NP. The simulated reconstruct of the current traces in silico using Brownian dynamics (BD) obtained for different types of markers of various architecture contain relevant information that we later deconvolute by improving the signal-to-noise ratio and accounting for the velocity corrections [2]. These in-silico studies are important to understand the effect of tension propagation [2,3] on the current traces when multiple tags of different origins are present on a Kbp long dsDNA. The volumetric CB algorithm is quite general, and we choose the model parameters by comparing the exact CB data from simulation of an electrokinetic BD model (EKBD) where the co-ions and counter-ions flow through the NP provides the CB directly. We further validate our simulation results by comparing the experimental CB data for a 16.5 μm long λ-phage DNA with 15 oligo-tags [4] to further fine tune our BD model.

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

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

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

[4] Rand, A., et al., ACS Nano 2022, 16, 5358-5273.