Solid-State Nanopores: Methods of Fabrication and Integration, and Feasibility Issues in DNA Sequencing - Nanopores: Sensing and Fundamental Biological Interactions - page 197

Fig. 8.14 The schematic of the ssDNA trimer complex translocates through the nanopore, driven
by an applied voltage. For clarity, the length of the single-strands, the bead diameter and the
thickness of the pore have been drawn to scale to illustrate that when the first double-strand region
exits the nanopore, the second region is still far away from the nanopore. The bead is not drawn to
scale, however [ 31 ]. Used with permission. Copyright Nanotechnology 2010

The base-pairings are designed to be stable at room temperature. As such, in
equilibrium, the buffer sample should contain monomers of 142 bases, and dimers of
274 bases and the trimers 404 bases in length respectively. The formation and stability
of the trimers have been confirmed using gel electrophoresis. Figure 8.13b shows the
presence of three different bands, one between 100 and 150, another between 250 and
300, and another one between the 400 and 450 bp bands of a 50-base increment DNA
ladder reference. Also, the UV absorption spectrum measurements at wavelength
260 nm from the single-stranded DNA complex mixture in 1 M SPSC buffer from
25 to 70 C show the melting transitions of the ss1-ss2 and ss2-ss3 DNA segments at
temperatures close to 51 and 57 C, respectively. Themelting transitions of individual
dimers were confirmed from measurements on buffer solutions containing only one
type of dimers. The measured melting temperature is closer for ss2-ss3 double-
stranded segment with the computationally obtained value of 60.8 C while it is
somewhat lower for ss1-ss2 segment, 64.2 C. The calculated contour length of
these individual polymer chains is ~49 nm that is nearly twice the optimum thickness
of the silicon nitride that bears the nanopore. This relatively large contour length
compared to the membrane thickness would allow the location of the second double-
stranded region to be well away from the nanopore when the first double-stranded
segment just exits the nanopore during their electric-field driven translocation.
The nanopore device is fabricated using the TEM “drilling” approach [ 6 ].
For the pore used for collecting the data below, the pore dimensions are 10 nm

7.8 nm obtained from TEM. The measured nanopore resistance is close to the
calculated value using these pore parameters and the optimummembrane thickness.
The open-pore current shows linear I - V characteristics typical of a properly wetted
solid-state nanopore. Two typical translocation events for DNA trimers are shown
in Fig. 8.15 , along with two computer-simulated translocation events.