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. Author manuscript; available in PMC: 2017 Dec 14.
Published in final edited form as: Nano Lett. 2016 Dec 1;16(12):8021–8028. doi: 10.1021/acs.nanolett.6b04642

Figure 4.

Figure 4

Force-differential control over DNA escape from a double-pore trap. (a) Sequence of snapshots illustrating escape of a DNA molecule from a symmetric double-pore-trapped conformation. At t = 0, a DNA molecule (blue) is threaded through both pores such that the DNA fragments that extend from the two pores to the trans side are of equal length. The backbone beads of the DNA residing within the left and right nanopores experience total net forces FL and FR, respectively, directed from cis to trans side, normal to the membrane. In this particular simulation, FL = FR = 10 pN. (b) Ensembles of DNA conformations observed during CG MD simulations of DNA escape from a double-pore trap. Shown in blue are 200 instantaneous conformations of DNA overlaid with each other. At t = 0, the DNA molecules are symmetrically threaded through the two pores, similar to the conformation shown in the top snapshot in panel a. (i) Ensemble of conformations adopted by DNA right after escaping (at t = tesc) to the trans compartment in the case the driving forces in the two nanopores are equal (FL = FR = 10 pN). Note that individual escape times vary from one replica to the other, see panel d. DNA escape through either left or right nanopore is equally likely. (ii) Same as above, except that the driving force in the right nanopore is 0.5pN larger than in the left nanopore. The majority of the DNA now escapes through the right pore. (c) The percentage of 200 replica simulations where DNA is seen to escape through either right or left nanopore as a function of the nanopore force differential, ΔF. The force at the right pore was fixed to 10 pN. (d) Distribution of the DNA escape times. The DNA escape time is defined as the time elapsed from the beginning of the simulation until the moment the entire DNA molecule moves to the trans side of the system. The force at the right pore was 10 pN. Bin size of the histograms is 50 μs. (e) Average DNA escape time versus the force differential. The force at the right pore equals 5 pN (grey bar), 10 pN (red bar), and 20 pN (blue bar).