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. Author manuscript; available in PMC: 2013 Feb 9.
Published in final edited form as: J Phys Chem C Nanomater Interfaces. 2012 Jan 9;116(5):3376–3393. doi: 10.1021/jp210641j

Figure 15.

Figure 15

Ion current through a nanopore blocked by a single DNA basepair. (A) All-atom model of the system. The K+ and Cl− ions are shown by yellow and green spheres, while the A and T nucleotides of the A·T basepair are shown in blue and red, respectively. The atoms of water are not explicitly shown, but represented by a a blue translucent surface. The phantom pore is shown by a purple semitransparent surface. The electric field is applied such that K+ ions passing through the pore approach the A nucleotide before the T nucleotide. (B, C) Simulated dependence of the nanopore ion current on the sequence and orientation of the DNA basepair. The data shown in panels B and C are for bulk concentrations of 0.1 and 1.7 M. The tilting of the basepair makes it possible, in principle, to measure a different current for X·Y than for Y·X. The systematic deviation of the ARBD currents at 1.7 M is attributable to the higher conductivity of bulk electrolyte in the ARBD method if compared with all-atom MD. In the high-salt regime, ARBD is expected to be in a better agreement with experiment than MD in predicting the absolute nanopore currents, see Figure 13A.