Biomedical Engineering Reference
In-Depth Information
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Figure 16.1
(a) Binding of 40 nM FAM-SP-2p
exonuclease in solution to the singly labeled DNA
hairpin smart probe ( Song and Zhao, 2009 ). (b) Binding of 40 nM FAM-SP-2p
þ
10 units of
l
þ
10 units
l
exonuclease
5.6 nM/s T4PNK ( Song and Zhao, 2009 ). 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.
þ
Phillips and Arit, 2007 ), DNA oligonucleotides ( El Atifi et al., 2003; Frauendorf et al.,
2003 ), and in the repair of DNA lesions ( Chappell et al., 2002; Rasouli-Nia et al., 2004 ).
Figure 16.1a shows the binding of FAM (fluorescein)SP-2p
exonuclease in
solution to the singly labeled DNA hairpin smart probe ( Song and Zhao, 2009 ). FAM-SP-2 is
the oligonucleotide sequence (5 0 -3 0 ) GGGCC(AG 10 )GGCCC- FAM, SP: DNA hairpin quenched
solely by the DNA base guanine were introduced as smart probes ( Knemeyer et al., 2000 ).
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 16.1 .
þ
10 units of
l
It is of interest to note that for the dual-fractal analysis, as the fractal dimension increases by
a factor of 1.51 from a value of D f1 equal to 1.9390 to D f2 equal to 2.9296, the binding rate
coefficient increases by a factor of 8.34 from a value of k 1 equal to 640.96 to k 2 equal to
5243.91. The changes in the degree of heterogeneity or the fractal dimension on the biosensor
surface and in the binding rate coefficient are in the same direction.
Figure 16.1b shows the binding of 40 nM FAM-SP-2p
5.6 nM/s
T4 PNK (T4 PNK) in solution to the singly labeled DNA hairpin smart probe ( Song and
Zhao, 2009 ). In this case, a single-fractal analysis is adequate to describe the binding kinetics.
The values of the binding rate coefficient, k , and the fractal dimension, D f , for a single-fractal
analysis are given in Table 16.1 .
þ
10 units
l
exonuclease
þ
Figure 16.2a shows the binding of 40 nM FAM-SP-2
þ
5.6 nM/s 4T PNK
þ
1 mM ATP and
0.5 units of
exonuclease at pH 8.0 to the singly labeled DNA hairpin smart probe ( Song and
Zhao, 2009 ). A dual-fractal analysis is required to adequately describe the binding kinetics.
l
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