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

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.