Effects of Nanopore Charge Decorations on the Translocation Dynamics of DNA Ining Jou, Murugappan Muthukumar Biophysical Journal Volume 113, Issue 8, Pages 1664-1672 (October 2017) DOI: 10.1016/j.bpj.2017.08.045 Copyright © 2017 Biophysical Society Terms and Conditions
Figure 1 (a) The αHL protein pore, showing the location of mutations to add additional positive charges in the β-barrel region. The mutated amino acid residue is represented by blue beads that are positively charged. The red beads are negatively charged and the gray beads are neutral. (b) The ssDNA is modeled using three beads per nucleotide. To see this figure in color, go online. Biophysical Journal 2017 113, 1664-1672DOI: (10.1016/j.bpj.2017.08.045) Copyright © 2017 Biophysical Society Terms and Conditions
Figure 2 Electrostatic potentials along the center of the αHL pore from the cis to the trans side. The vestibule entrance at z=−48 Å and the β-barrel end at z=48 Å are marked by dashed lines in the plot. The bulk concentration is 1M KCl and the applied potential difference is 120 mV. The nanopore shown is a CG WT showing the direction of the z axis along the center of the pore. To see this figure in color, go online. Biophysical Journal 2017 113, 1664-1672DOI: (10.1016/j.bpj.2017.08.045) Copyright © 2017 Biophysical Society Terms and Conditions
Figure 3 Distribution of the translocation time per nucleotide of the DNA. This is the time taken for the entire chain of DNA to exit the β-barrel divided by the number of nucleotides. The most likely translocation time is taken as the maximum of the Gaussian fit shown in the insets and in Table S1. To see this figure in color, go online. Biophysical Journal 2017 113, 1664-1672DOI: (10.1016/j.bpj.2017.08.045) Copyright © 2017 Biophysical Society Terms and Conditions
Figure 4 Comparison between simulation and experimental results (34) of the most likely translocation time per nucleotide (tn) for different charge decorations of the nanopore. The simulated system was performed for 1M KCl at 300 K with an external potential difference of +120 mV. To see this figure in color, go online. Biophysical Journal 2017 113, 1664-1672DOI: (10.1016/j.bpj.2017.08.045) Copyright © 2017 Biophysical Society Terms and Conditions
Figure 5 Ionic current trace through an RL2 nanopore as DNA translocates through the RL2 nanopore. The snapshots S1–S4 show the positions of the DNA during the various stages of translocation. To see this figure in color, go online. Biophysical Journal 2017 113, 1664-1672DOI: (10.1016/j.bpj.2017.08.045) Copyright © 2017 Biophysical Society Terms and Conditions
Figure 6 Ionic current trace as DNA translocates through an RL2-M113R-N123R nanopore. The blue spheres are the positively charged amino acid residues added by the mutations. The stages of DNA translocation are shown in snapshots M1–M4 at the corresponding current values. To see this figure in color, go online. Biophysical Journal 2017 113, 1664-1672DOI: (10.1016/j.bpj.2017.08.045) Copyright © 2017 Biophysical Society Terms and Conditions
Figure 7 Segments a, b, and c of the DNA. Segments a–c correspond to nucleotide numbers 1–5, 31–35, and 41–45, respectively. To see this figure in color, go online. Biophysical Journal 2017 113, 1664-1672DOI: (10.1016/j.bpj.2017.08.045) Copyright © 2017 Biophysical Society Terms and Conditions
Figure 8 Distribution of the translocation times through the β-barrel per nucleotide for segments a (a), b (b), and c (c) of the DNA. The insets show the Gaussian fit to the corresponding distribution. To see this figure in color, go online. Biophysical Journal 2017 113, 1664-1672DOI: (10.1016/j.bpj.2017.08.045) Copyright © 2017 Biophysical Society Terms and Conditions
Figure 9 The average translocation speed of each nucleotide in the z-direction when inside the β-barrel are shown in a. The standard deviations of each nucleotide for the cases of WT and M113R-N123R are shown in b. To see this figure in color, go online. Biophysical Journal 2017 113, 1664-1672DOI: (10.1016/j.bpj.2017.08.045) Copyright © 2017 Biophysical Society Terms and Conditions