Solid-State Nanopores: Methods of Fabrication and Integration, and Feasibility Issues in DNA Sequencing - Nanopores: Sensing and Fundamental Biological Interactions - page 198

Fig. 8.15 Two nearly identical trimer events are shown in left. On the right are two simulated
translocation events. The simulation was done using a hard rod model consisting of alternating
single and double-stranded DNA regions ( ss-ds-ss-ds-ss ) corresponding to the trimer complex
used. An effective circular nanopore is assumed corresponding to the size of the nanopore used in
the experiment with an effective membrane thickness of 10.68 nm and in 1 M KCl buffer. A white
Gaussian noise was added to the simulated current and then filtered with a Bessel filter with 10 kHz
cut-off frequency. The simulation was done in MATLAB [ 31 ]. Used with permission. Copyright
Nanotechnology 2010
The DNA-bead complex translocation events were collected with a nanopore
setup immersed in an ionic buffer at a pH of 8.0 with 1 M KCl, 10 mM Tris, 1 mM
EDTA (TE) concentration using an Axopatch-200 current amplifier in voltage-
clamp mode. After filling the DNA-bead complex sample in the cis side of the
nanopore, the current was recorded at a voltage of 100 mV until DNA translocation
events were observed. The repeated runs of translocation experiments have yielded
large amount of interesting data. In some time intervals, the events are so dense in
their arrival that it is difficult to identify individual events. Then there are also
relatively isolated, “clean,” events that, with the assistance of computer simulation,
can be reasonably interpreted. Here, two such events are shown in Fig. 8.15 above.
The most striking features of these events are the two double dips at the bottom of
the curves. Using the parameters of the nanopore used here, and the lengths of the
different segments of the DNA, as well as the noise level of the background ionic