DISSERTATION
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______________________________________________________________________ Introduction<br />
1.2.2 DNA in front of a polarized electrode<br />
In addition to the DNA-ion interaction, it is important to understand the influence of a charged<br />
electrode on the behavior of DNA on its surface for the application in DNA sensing at electrified<br />
surfaces. The GC model of the double layer describes how the ionic strength and the<br />
polarization of the electrode influence the double layer structure and the potential drop in front<br />
of the electrode. The GC equation:<br />
Φ = 2kT<br />
e<br />
ln 1 + γexp ( −d<br />
κ −1)<br />
1 − γexp ( −d<br />
κ −1) (1.12)<br />
γ = tanh ( eΦ 0<br />
4kT ) (1.13)<br />
where Φ0 and Φ are the potentials at the electrode surface and at a distance d from the surface,<br />
respectively, reveals that the potential distribution strongly depends on the ionic strength, where<br />
an increase of the ionic strength leads to a steeper drop of the potential (Figure 1.7, a). Thus, a<br />
few nm away from the surface, Brownian motion prevails over electric forces and dominates<br />
the system response 42 . Furthermore, the model predicts a sharp potential drop for highly<br />
charged electrodes (high Φ0), while the decline is more gradual for lower Φ0 values 43 (Figure<br />
1.7, b).<br />
The DNA conformation on the electrode surface can be manipulated by externally applied<br />
potentials 44,45 . However, this is true only under certain conditions 42 . Namely, as in solutions of<br />
high ionic strength the applied potential decays within a nm distance, the range is too short to<br />
significantly affect grafted DNA molecules. Therefore, both negative and positive potentials do<br />
not affect the conformation of neither ds- nor ssDNA. dsDNA exhibits a rigid conformation,<br />
while ssDNA coils on the electrode surface (Figure 1.8, a). This remarkable difference in<br />
conformation originates from the difference in the persistence length of dsDNA and ssDNA, as<br />
explained in Section 1.2.1. Furthermore, in presence of filler molecules with height comparable<br />
to the length of the DNA spacer, the dsDNA conformation is almost perpendicular with respect<br />
to the electrode surface 42,45 . The reason for the upright conformation is the steric repulsion<br />
between the lowest base pairs and a monolayer that backfills the gold electrode between DNA<br />
strands. In contrast, ssDNA remains lying on the surface since, besides the very weak electrical<br />
interactions, self-repulsion along the DNA strand is suppressed by the high ionic strength.<br />
1.2 DNA 13