Third Generation DNA Sequencing with a Nanopore - Nanopores: Sensing and Fundamental Biological Interactions - page 297

Fig. 12.4 Nano-fluidics Integrated Circuits. Using the same line-rules used for single cell analysis
we implemented with soft lithography in PDMS a 6-valve, 10 input microfluidic circuit shown in
(a). (b) A magnified view of the region highlighted in (a) shows a single cell is trapped in the
microfluidic. (c, d) Magnified view of the same region highlighted by the circle in (a) illustrating the
operation of the valves. By applying pressure to the valves ( lightly colored dye ) in this circuit we can
control the flow of small DNA ( dark colored dye ) to the pore in the cross

DNA are guided to the pore via the valves. The operation of the valves (highlighted
with dye) illustrated in Fig. 12.4c, d allows us to direct a small volume of material
(represented by dark colored dye fluid) toward the pore. Because of the line-rules
we are able to manipulate very small volumes of material (9 pL) and at the same
time gate three different flows into the volume over the pore. For example, using
the valves to gate the flow, a single E. coli bacterium can be positioned in the active
area (Fig. 12.4b ). Using 12 m m line-rules with a concentration of 10 9 molecules/

L,
the volume over the pore shown in Fig. 12.4c contains ~1,000 molecules. Thus, by
leveraging this integrated microfluidic circuitry, a nanopore can be connected to the
products of a single cell analysis.

m

12.2.3 Trapping a DNA in a Synthetic Nanopore

Once inside the pore, there are three main forces that affect the DNA according to
MD simulations [ 55 ]. The first and strongest force is the electric field, acting
primarily on the negatively charged phosphate backbone of DNA, which drives