Biomedical Engineering Reference
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translocation [
20
]. Although a transmembrane voltage was used to drive trans-
location rather than SMD pulling, we observed a similar dependence of the
translocation mode on the pore size. Furthermore, for a 1.6 nm diameter pore,
translocation by unzipping was seen at transmembrane voltages
6.5 V, where
stretching/distortion was seen at
5 V. Figure
14.5a-c
show snapshots from
simulations of hairpin DNA translocation under an applied transmembrane voltage.
Reduction of the constriction size resulted in a higher maximum electric field
magnitude along the pore axis, while also reducing the depth at which the duplex
DNA could move into the pore without unfolding. These competing factors resulted
in dramatically different translocation behavior across different transmembrane
voltages and pore geometries. The diagram in Fig.
14.5d
illustrates which translo-
cation modes were predicted by the MD simulations for a given minimum pore
diameter and transmembrane voltage.
Because the duration of MD simulations is currently limited to a few micro-
seconds for large systems such as DNA in a synthetic nanopore, certain transloca-
tion modes may not be sampled in the MD simulations. For example, spontaneous
thermal unzipping of the hairpin DNA could occur on timescales inaccessible
Fig. 14.5 Possible translocation modes for hairpin DNA in a synthetic nanopore having a
diameter less than that of the double helix. (a) Unzipping of the basepairs one by one with the
overhanging coil leading. (b) Stretching/distortion of the double helix with the overhanging coil
leading. (c) Stretching/distortion of the double helix with the loop leading. (d) Diagram for
predicting which of the translocation modes illustrated in the other
panels
might occur for a
given pore diameter and transmembrane voltage. The
circles
show points that were probed by MD
simulations. Figure adapted from [
20
] with permission from Elsevier
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