Biomedical Engineering Reference
In-Depth Information
Table 16.7 Binding rate coefficient and the fractal dimension for a novel molecular beacon (MB)
for surface immobilized DNA hybridization studies (
Feng et al., 1999
)
.
Analyte in
Solution/Receptor
(MB) on micro-array
surface
k
k
1
k
2
D
f
D
f1
D
f2
Complementary target
11686
9435
20554
2.2632
1.8126
2.702
DNA at pH 8.0/Biotinylated
molecular beacon (MB)
1348
436
369
0.0796
0.0868
0.0436
coefficient increases by a factor of 2.18 from a value of
k
1
equal to 9435 to
k
2
equal to 20554.
The changes in the fractal dimension or in the degree of heterogeneity on the microarray sur-
face and in the binding rate coefficient are in the same direction.
Li et al. (2001)
have developed an optical DNA biosensor based on surface immobilization of
an MB by a bridge structure. The use of molecular beacons has already been presented in a
previous example. Another example on MBs is now presented. These authors report that
DNA biosensors exhibit potential for obtaining sequence-specific information when com-
pared to traditional hybridization assays in a rapid, simpler, and less-expensive manner
(
Okahata et al., 1988
).
Li et al. (2001)
provide examples wherein these DNA biosensors have
been developed which include the surface of a modified electrode (
Steel et al., 1998
), a
piezoelectrode quartz crystal microbalance (
Okahata et al., 2000
), a surface plasmon reso-
nance biosensor (
Nilsson et al., 1995
), an optical fiber (
Mehrvar et al., 2000
), and a planar
waveguide (
Derisi et al., 1997
).
Li et al. (2001)
emphasize the two customary fabrication
steps involved in these types of biosensors that include: (a) a chemical modification of the
polymer or the activation of the matrix, and (b) the immobilization of the single-stranded
DNA on the sensor surface (
Mehrvar et al., 2000
).
Li et al. (2001)
have developed an optical DNA biosensor based on a streptavidin-biotin
interaction and is based on a bridge immobilization method. This according to them
enhanced the freedom of the immobilized MB. The MB is a new DNA fluorescence probe
which is a single-stranded oligonucleotide. This oligonucleotide consists of a probe sequence
embedded within complementary sequences that form a hairpin stem (
Kostrikis et al.,
1998a,b
;
Tyagi and Kramer, 1998
).
Figure 16.12a
shows the binding of 50 nMcomplementary target 5
0
-GCGACCATAGCGATT
TAG (A-3
0
) in solution to the MB (5
0
-TMR-CCT AGC TCT AAA TCG CTA TGG TCG CGC
(biotin dT)AG G-DABCYL-3
0
) immobilized using streptavidin-biotin immobilized on a bio-
sensor surface (
Li et al., 2001
) 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 16.8
.
