Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations - Nanopores: Sensing and Fundamental Biological Interactions - page 347

Fig. 14.4 Snapshots of MD simulations in which the phosphorus atom of the terminal base is pulled
downward at a rate of 1 nm/ns. The pores have minimum diameters of (a)1.0nm,(b) 1.3 nm,
(c) 1.4 nm, and (d) 1.6 nm. In all cases, the double helix, which has a diameter of 2.5 nm must be

distorted to pass through the pore; however, the mode of passage is much different for the 1.6 nmpore
than for the 1.0 and 1.3 nm pores. Figure adapted from [ 18 ] by permission of Oxford University Press

maintained, although the double helix was stretched and significantly distorted [ 18 ].
It is known that less force is required to unzip basepairs one-by-one (10-30 pN)
than to stretch the DNA along its contour length (60-70 pN) [ 58 ]. Therefore, the
reduction of the threshold voltage when moving from larger to smaller pores may
be associated with the change in the translocation pathway from unzipping of the
basepairs to stretching and distortion of the double helix.
Furthermore, there was a question as to the orientation of the hairpin DNA when
it entered the pore. The DNA could pass through with the overhanging coil portion
leading, as shown in Fig. 14.4a, b , as well as the with the double helix leading as
shown in Fig. 14.4c . Due to the timescale limitations of MD, it was not possible to
place the hairpin DNA in a random orientation far from the pore and observe which
mode of translocation would eventually occur. Instead, Monte Carlo simulations
were used to show that the probability that the hairpin DNA used in the simulations
(having a 10 basepair double helix and a 50 basepair loop) arrived in the pore with
the loop leading was significant [ 20 ]. We then began MD simulations in which
either the loop of the helix was placed slightly outside the constriction of the pore or
the coil was threaded through the constriction so that the translocation process
could be observed in both orientations.
These MD simulations revealed that the DNA could pass through the pore in
two distinct orientations - one in which the overhanging coil led translocation
and another where the loop connecting the two strands of the double helix led