Biology Reference
In-Depth Information
layer [25]. However, the Poisson-Boltzmann theory fails to describe
the physical situation if the electrostatic interactions are strong,
the counterions are multivalent or the density of DNA is high [26].
MonteCarlostudiesofoligonucleotideshaveindicatedthatthelocal
cation concentration is expected to decrease sharply as either end
of the molecule is approached, due to coulombic end effects [27].
Duetoendeffectsanddensepackingofoligoelectrolytes,counterion
condensation may not give an accurate approximation of the charge
fraction for oligomers immobilized in a SAM. Molecular dynamics
studies of single-grafted ssDNA and dsDNA oligomers show that
counterion condensation increased with both longer chain lengths
and added salt [28]. For 16 bases oligonucleotides at zero salt
concentration, 30% of counterions were contained within 1.6 nm
of the oligonucleotide for dsDNA, compared to 15% for ssDNA.
Although dsDNA has a smaller charge fraction, its net charge will
be 65% greater than for ssDNA. Addition of 5 mM salt increased the
fraction of counterions within 1.6 nm of the ssDNA to 45%. Results
on salt addition were not given for dsDNA. In the single-chain limit
studied, a significant portion of counterions lies beyond the chain
lengthfromthesurface.However,forastrongpolyelectrolytebrush,
counterions are expected to be contained within the brush with
electroneutrality satisfied locally [29].
TheDNAchargewillalsobeaffectedbyitsconfinementtoaSAM.
The ionization of acidic or basic groups in a SAM is less favored and
for acid groups p
K
a
will increase by approximately 1unit[30].
6.3.1.3 Quantitation of the field-effect device signal
A variety of different approaches to calculate the shift in the
I
-
V
characteristics upon DNA hybridization or due to charge
redistribution upon antibody-antigen binding have been presented
in the literature. It has been suggested that the accumulation of
charged molecules at a surface might be electronically detected
as responses to a Donnan potential, which is built up during the
attachmentofthemolecules[31].Thisshouldonlybepossibleifthe
sensor exhibits a pH sensitivity smaller than the Nerstian response.
If this is the case, the output signal should depend on the gate
material.
