Binding and Dissociation Kinetics During Hybridization on Biosensor Surfaces - Biosensors and Biosensor Kinetics - page 467

The fit is not good. There is scatter in the data. Only three data points are available. The
availability of more data points would lead to a more reliable fit. The poor fit is also noticed
by the large error in the power to which the fractal dimension D f1 , is raised to.

The binding rate coefficient, k 1 , is very sensitive to the fractal dimension, D f1 , or the degree
of heterogeneity that exists on the microarray biosensor surface as noted by the negative
order of dependence between three and a half and four (equal to 3.65) exhibited.

Feng et al. (1999) have developed a biotinylated ssDNA MB for DNA hybridization studies
at a solid interface. These authors point out that DNA hybridization and molecular interaction
studies assist in the diagnosis of genetic disease. The clinical symptoms are linked to the
alterations in DNA. MBs were first developed by Tyagi and Kramer (1998) . These are
single-stranded oligonucleotides that possess a stem-and-loop structure. Feng et al. (1999)
explain that the loop portion of the molecule can report the presence of a specific comple-
mentary nucleic acid ( Kostrikis et al., 1998a,b; Piatek et al., 1998; Tyagi et al., 1998 ). The
five bases at the two ends of the MB are complementary to each other forming the stem.

Figure 16.11 shows the binding of the target complementary DNA to the biotinylated and
immobilized MB (5 0 -(_TMR) GCA CGT CCA TGC CCA GGA AGG AAC G(Biotin dT)
GC(-DABCYL)-3 0 . TMR is tetramethylrhodmine is the fluorophore, and DABCYL (dim-
ethylaminoazobenzeaminoexal-3-acryinido) is the quencher.

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 16.7 .

It is of interest to note that for a dual-fractal analysis, as the fractal dimension increases by a
factor of 1.49 from a value of D f1 equal to 1.8126 to D f2 equal to 2.7108, the binding rate

40000

30000

20000

10000

0

0 5 10 15 20

Time (min)

Figure 16.11
Binding of complementary ss DNA to a biotinylated molecular beacon immobilized on a biosensor
surface ( Feng et al., 1999 ). 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