Nanopore Force Spectroscopy: Insights from Molecular Dynamics Simulations - Nanopores: Sensing and Fundamental Biological Interactions - page 352

Furthermore, the investigators have demonstrated that the electro-osmotic flow
velocity and, consequently, the viscous force on the DNA depends on the geometry
of the pore and the pore's surface properties [ 62 ]. Figure 14.6b shows the velocity
profile of the electro-osmotic flow in several nanochannels. For 6.0 and 4.5 nm-
diameter nanochannels with atomically smooth walls, the effective charge was
shown to be Q eff ¼

0.5 e , in agreement with experiment. However, in a
nanochannel having a corrugated surface whose diameter varied as dðzÞ¼d 0 þ
A cos

1.07 nm), the effective charge
was substantially higher. Finally, the study has shown that the stall force on DNA in
a nanopore is F z ¼xmE z , where

ð 2 pz=lÞ (where d 0 ¼ 3.0 nm, A¼ 0.2 nm, and l ¼

is DNA's friction coefficient, which can be
determined by measuring the time required for DNA to exit the pore in absence
of electrostatic force, and

x

is the electrophoretic mobility, which can be deter-
mined from DNA translocation experiments.
One might guess that a smaller-diamater pore would exhibit a smaller-magni-
tude electro-osmotic flow under the same bias, and hence the value of the effective
charge would be closer to that of bare DNA. Indeed, van Dorp et al. [ 63 ], presented
experimental evidence that Q eff became closer to Q as the pore size decreased
below 20 nm.
Simulations using 2.9 nm-diameter nanopores corroborated this relation between
pore size and Q eff . Figure 14.7a shows a system that consisted of initially unstrained
DNA placed inside a nanopore having a minimum diameter of 2.9 nm in a
membrane with a thickness of 10 nm. Figure 14.7b illustrates the second system
in which the same molecule was placed in a pore of the same diameter, but here the
membrane had a thickness of 5 nm. The system illustrated in Fig. 14.7c contained
the same pore as the system shown in Fig. 14.7a except that the DNA was initially

m

Fig. 14.7 Influence of the membrane thickness and DNA conformation on the stall force in a
nanopore. In all cases, effectively infinite DNA was attached to a virtual spring, a transmembrane
bias of 1.0V was imposed. (a) Snapshot of unstrained DNA in a membrane having a thickness of
10 nm. (b) Snapshot of unstrained DNA in a membrane having a thickness of 5 nm. (c)Snapshotof
strained DNA in a membrane having a thickness of 10 nm. (d) Force on the virtual spring attached to
the center of mass of the DNA as a function of time after the 1.0 V transmembrane voltage was
switched on for the three systems shown in panels a, b,andc. Figure adapted from [ 23 ]bypermission
of Oxford University Press