Biomedical Engineering Reference
In-Depth Information
Also, a change in the bulk concentration has a significant impact on hybridization kinetics.
They analyzed hybridization kinetics on glass substrates. One 22-mer strand (bound DNA)
was immobilized via a phenylene-diisocyanate linker molecule on the glass substrate. The
dye-labeled (Cy3) complementary strand was in solution in a reaction chamber. These
authors further explain that to work efficiently with microarrays a knowledge of kinetics
and thermodynamics is essential.
Figure 11.3a
shows the binding of 10 nM free-DNA in solution to a 22-mer strand (bound
DNA) immobilized via a phenylene-diisocyanate linker molecule on a glass substrate
(
Michel et al., 2007
). A dual-fractal analysis is required to adequately describe the binding
kinetics. The values of (a) the binding rate coefficient,
k
, and the fractal dimension,
D
f
, for
a single-fractal analysis and (b) the binding rate coefficients,
k
1
and
k
2
, and the fractal
dimensions,
D
f1
and
D
f2
, for a dual-fractal analysis are given in
Table 11.2
.
1.2
1.2
1
1
0.8
0.8
0.6
0.6
0.4
0.4
0.2
0.2
0
0
0
500
1000
1500 2000
Time (s)
2500
3000
3500
0
1000
2000
3000
4000
5000
6000
A
B
Time (s)
0.8
0.25
0.2
0.6
0.15
0.4
0.1
0.2
0.05
0
0
0
1000
2000
3000
4000
5000
6000
0
1000
2000
3000
4000
5000
6000
C
D
Time (s)
Time (s)
Figure 11.3
Binding (hybridization) of different concentrations (in nM) of free-DNA in solution to a 22-mer
strand (bound DNA) immobilized via a phenylene-diisocyanate linker molecule on a glass substrate
(
Michel et al., 2007
): (a) 10. (b) 7.5. (c) 5. (d) 2. When only a solid line (--) is used then a single-
fractal analysis applies. When both a dashed (- - -) and a solid (--) line are used then the dashed
line represents a single-fractal analysis and the solid line represents a dual-fractal analysis.
