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We report current blockade (CB) characteristics of molecular motifs residingon a model dsDNA using electrokinetic Brownian dynamics (EKBD) and study therole of the valence of the counterions as the dsDNA translocates through asolitary nanopore (NP) driven by an electric field. We explicitly incorporateall the charges on the DNA backbone, co- and counter-ions, and investigate CBcharacteristics of two charged sidechain motifs exactly. Our simulation bringsout the details of binding and unbinding of the counter-ions and the timedependent counter-ion condensation on the translocating DNA for mono- anddi-valent salt conditions. An important and less intuitive finding is that thedrop in the conventional (positive) current through the pore is due to thecondensation of the counter-ions on the translocating DNA and not so much dueto drop in the co-ions passing through the pore. This finding aligns withprevious 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 forthe divalent ions leading to a slowing down of the translocation speed andyielding a longer dwell time for the motifs. Finally, we use the exact CBcharacteristics from the EKBD simulation to reconstruct the same CBcharacteristics using a volumetric ansatz on the segment inside and in thevicinity of the pore using on the ordinary BD model without the explicitpresence of co- and counter-ions. Refinement of this ansatz will allow us toobtain the CB characteristics for longer genome fragments using low-costordinary BD simulation.

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