Biology Reference
In-Depth Information
spectroscopy with PNA probes to be a very promising technique for
portable DNA detection applications.
6.4.2
Modeling of the Signal
The optimization of the EIS signal for DNA sensing can be achieved
through modeling of the DNA layer potential and charge changes
upon hybridization. To consider the effect of discrete charge sites,
a geometry model was composed to represent the DNA structure
at the surface [35, 39]. The ssDNA probe or DNA/DNA duplex
(or PNA/DNA duplex when PNA probe is used) was modeled as
a cylinder with diameter of 2 nm, perpendicular to the electrode
surface and linked by a spacer, as shown in Fig. 6.8a. The negative
charge of the phosphate backbone was considered as a uniform
surface charge evenly distributed on the side of the cylinder. The
DNA strand was spaced from the surface by the linker molecules—
in the case presented, 2.7 nm long to represent a linker consisting
of 6 polyethylene glycol (PEG) groups. As this distance is longer
thantheDebyelengthofsolutionswithionicstrengthabove15mM,
the effect of the metal electrode on the electric field around DNA
strandcanbeneglected.Whenthespacermoleculeisuncharged,the
electricfieldisnotaffectedbytheSAMandasymmetryplanecanbe
Figure 6.8.
Geometry model for the simulation of modification layer with
discrete charged sites: (a) side view of the structure, (b) cross section
showing the simulation plane with dimensions representing probe density
of 3
10
12
molecules/cm
2
.
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