DISSERTATION

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