Exact current blockade maps of dsDNA bound motifs driven through a solitary nanopore using electrokinetic Brownian dynamics

TL;DR

This study uses electrokinetic Brownian dynamics to precisely map current blockade signals of DNA motifs during nanopore translocation, revealing the critical role of counter-ion condensation in current modulation and translocation dynamics.

Contribution

It provides an exact simulation approach to understand current blockade mechanisms and introduces a volumetric model to replicate these signals without explicit ions.

Findings

Counter-ion condensation causes current drop during translocation.

Divalent ions increase condensation, slowing DNA movement.

Volumetric ansatz can replicate current blockade characteristics.

Abstract

We report current blockade (CB) characteristics of molecular motifs residing on a model dsDNA using electrokinetic Brownian dynamics (EKBD) and study the role of the valence of the counterions as the dsDNA translocates through a solitary nanopore (NP) driven by an electric field. We explicitly incorporate all the charges on the DNA backbone, co- and counter-ions, and investigate CB characteristics of two charged sidechain motifs exactly. Our simulation brings out the details of binding and unbinding of the counter-ions and the time dependent counter-ion condensation on the translocating DNA for mono- and di-valent salt conditions. An important and less intuitive finding is that the drop in the conventional (positive) current through the pore is due to the condensation of the counter-ions on the translocating DNA and not so much due to drop in the co-ions passing through the pore. This finding aligns with previous studies conducted by Tanaka et al. [Phys. Rev. Lett. 94, 148103 (2005)], Cui [J. Phys. Chem B 114, 2015 (2010)], and Holm et al. [Phys. Rev. Lett. 112, 018101 (2014)]. We further find that this condensation is larger for the divalent ions leading to a slowing down of the translocation speed and yielding a longer dwell time for the motifs. Finally, we use the exact CB characteristics from the EKBD simulation to reconstruct the same CB characteristics using a volumetric ansatz on the segment inside and in the vicinity of the pore using on the ordinary BD model without the explicit presence of co- and counter-ions. Refinement of this ansatz will allow us to obtain the CB characteristics for longer genome fragments using low-cost ordinary BD simulation.