Nanopore-Based DNA Sequencing and DNA Motion Control - Nanopores: Sensing and Fundamental Biological Interactions - page 278

the experiments reported in [ 41 ], a DNA capture event is indicated as an increase
of the ionic current [ 17 , 42 - 44 ]. A 200 mV voltage bias was applied across the
nanopore and a hand-held magnet was employed to drag one DNA-coated magnetic
bead slowly close to the 12 nm nanopore. The ionic current increases when a DNA
is captured by the nanopore. Once this occurs, the magnetic bead becomes immo-
bile. Then the voltage bias was lowered to 50 mV to avoid breakage of the
streptavidin-biotin bond of the captured DNA.
A pair of magnetic tweezers was mounted on a Burleigh Inchworm nano-
positional stage and was moved slowly towards the nanopore chip. In the distance
range over which the DNA is pulled out, the force increase rate is less than 0.2 fN
per step on the Burleigh stage. Once the magnetic force exceeds the electric force
(at 50 mV), the DNA was pulled out from the nanopore, as indicated from the
decrease of the ionic conductance to the baseline value.
The ionic current trace of a DNA being pulled out of the nanopore is shown in
Fig. 11.27 , which reveals that the transitional time is about 19 ms. For comparison,
the inset of Fig. 11.27 shows the histogram of the transitional times of ionic current
increases and decreases for 50 sequential DNA events, in which DNA is captured
into the nanopore and then released from the nanopore due to breakage of strepta-
vidin-biotin bond. All the 100 transitional times are less than 2 ms. (The histogram
peaks at 1.2 ms due to the 1 kHz cutoff frequency set in the ionic current
measurement system.) So the 19 ms is the actual time that it takes for the end of
the DNA to pass through the 60 nm long nanopore channel by the pulling of the

Fig. 11.27 The time trace of the nanopore ionic current as the DNA is being pulled out of the
nanopore by magnetic force. (Note t ¼ 0 is re-defined.) The thick solid line is a smoothed curve of

the same data. For comparison, the inset shows the histogram of the transitional times of ionic
current increases and decreases from 50 sequential events (DNA is captured into the nanopore and
then released from the nanopore due to breakage of streptavidin-biotin bond). Note that the peak at
1.2 ms in the inset is not the actual time that the end of the DNA passes through the nanopore. It is
due to the 1 kHz cutoff frequency set in the ionic current measurement system. Adapted from [ 41 ]