Nanopore-Based DNA Sequencing and DNA Motion Control - Nanopores: Sensing and Fundamental Biological Interactions - page 283

ensemble for 2 ns, DNA was pulled by a harmonic spring (mimicking optical
tweezers) of constant k and at a constant velocity of 1 ˚ /ns along the nano-channel.
When the trapping fields are off (Fig. 11.31b ), the pulling force exerted by the
spring can be characterized by F ¼ xv , where v is the pulling velocity and

the
friction coefficient. The large fluctuation in force can be explained by thermal
fluctuations

x

k B T p . When the trapping fields are on (with value 108 mV/ ˚ ), the
force exerted by the spring vs. the position of DNA relative to the DNA transistor
is shown in Fig. 11.31c , indicating the uphill and downhill motions of DNA on
the landscape of a periodic potential of period d . The maximum trapping force is
about 90 pN, corresponding to a trapping potential of about 100 meV, much larger
than the thermal energy 26 meV.
This “harmonic spring” approach can be used to characterize the electrical
trapping force inside the DNA transistor. But for real applications, rather than
using optical tweezers, one will use a biasing electric field across the nanochannel
to drive the DNA through the DNA transistor base by base. As shown in Fig. 11.32 ,
when the biasing field is strong (9.38 mV/ ˚ ), DNA moves through the transistor at
a constant velocity. However, when decreasing the biasing electrical field, the
motion of DNA consists of a stick state and a slip state, as shown in Fig. 11.32 .
The stick-slip motion of DNA in a transistor can also be seen in http://www.
youtube.com/watch?v aLXw2pebWPg . This movie was made from a trajectory

of a 10 ns molecular dynamics simulation. The simulation setup is same as
described above. The biasing electric field is 0.625 mV/ ˚ and the trapping field is
108 mV/ ˚ . This stick-slip motion can be extremely useful for controlling the DNA

¼

Fig. 11.32 Simulation results (time vs. the position of the DNA center of mass) for the stick-slip
motion of DNA in a DNA transistor. DNA is driven by a biasing electric field across the whole
channel while the trapping fields are on. The applied biasing fields vary from 0.625 to 9.375 mV/ ˚ .
The spacing of vertical lines is d , the spacing between neighboring phosphate groups. Adapted
from [ 46 ]