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. Author manuscript; available in PMC: 2013 Aug 28.
Published in final edited form as: ACS Nano. 2012 Jul 13;6(8):6960–6968. doi: 10.1021/nn3019943

Figure 3.

Figure 3

Simulated effect of arginine mutations on DNA transport rate. (a) Averaged over 16 independent trajectories, the transport rate of cytosine homopolymers is plotted versus the simulation time for M1 and M1 L88R nanopores. The error bars represent the standard deviation of the mean. The inset shows the average permeation rates for triple mutants M1 L88R/T83R/S116R and M1 L88R/A96R/S116R. A break marked by ‘//’ indicates a switchover between linear and logarithmic scales. (b) The number of persistent contacts between the DNA and the arginine residues as a function of simulation time, averaged over 16 independent trajectories. To count as a persistent contact, non-hydrogen atoms of the same DNA nucleotide must reside within 4 Å of the same arginine residue for 10 ns at least 80% of the time. The inset shows the corresponding plot for the single 4-microsecond trajectory of the M1 L88R/T83R/S116R system. (c–d) Cut away view of the M1 L88R/T83R/S116R nanopore showing contacts between (c) a phosphate group of the DNA backbone and an arginine residue and (d) a cytosine base and an arginine residue. The DNA backbone and bases are shown as vdW spheres and bonds, respectively; the MspA protein is shows as a semitransparent surface; the arginine residues are shown in all-atom detail.