Nucleic Acid Based Nanoconstructs for Environmental Analysis …
591
15 20 25 30 35 40 45 50 55 60 65 70 75 80
100
200
300
400
500
Intensity (a.u)
2 Thete (degree)
MNP 3WJ2
220
311
400
511 400
422
15 20 25 30 35 40 45 50 55 60 65 70 75 80
200
300
400
500
Intensity (a.u)
2 Thete (degree)
MNP N3
220
311
400
511 400
422
(a)
(b)
(c)
(d)
Fig. 11 XRD patterns of a MNP, b APTES-MNP, c MNP-Biotinylated 3WJ, d 3WJ with aminofunctionalization immobilized on MNP
3.2 Dye Adsorption and Desorption Studies
We have used SYBR Gold for our current work. SYBR Gold binds with nucleic
acids SYBR Gold binds to the nucleic acid via intercalation mode and displays an
absorption maximum at 485 nm (Zipper et al. 2004). The wavelength maxima is red
shifted upon binding to DNA possibly due to a decrease in π–π
* electron transition.
On increasing concentration of DNA from 1x to 100x, the spectrum shifted toward
higher wavelength which clearly indicates the binding of SYBR Gold to dsDNA
(data not shown).
Various bare and MNP-immobilized nucleic acids were tested for their ability to
adsorb SYBR Gold. Dye adsorption to dsDNA was 20.24% (at 100x of DNA) and
was improved to 26.11% upon attachment of the DNA to MNP (Fig. 12).
We tested our nucleic acid three-way junction-based constructs for dye retention
and retrieval. The nucleic acid samples were incubated with avidin for 2 h at room
temperature. Subsequently, the complexes were incubated with 5x SYBR Gold for
30 min at room temperature at low rpm. This was followed by centrifugation to