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mismatched strands [38,39]. When such subtle discrimination is
amplified, a potential viable DNA detection mechanism is developed.
One way to amplify such molecular recognition events is to use the
size-dependent dielectric properties of gold nanoparticles [28,40].
Another is the utilization of fluorescent properties of either
nanoparticles or organic chromophores and their sensitivity to
distance and size [41]. The focus here is that folding and unfolding
of a hybrid polymer containing alternating biological sequences and
synthetic chromophores with orthogonal fluorescent emissions can
be applied to DNA detection.
To construct foldable polymers with alternating hydrophobic
and hydrophilic structures, we employed solid-phase synthesis
[17,18], which requires that the fluorescent building blocks have
an activated functional group for attachment to the growing end
of the DNA polymer chain and a removable protecting group so
that it can be removed to permit further chain extension [42].
Two fluorescent chromophores are synthesized: one emits in the
yellow with a
l
∼
612 nm and the other emits in the blue with
an emission maximum at 480 nm in organic solvents. In addition
to their orthogonal fluorescent emissions, the absorption maximum
of the yellow chromophore (486 nm) overlaps perfectly with the
fluorescent emission of the blue chromophore. The yellow emitter
is based on the 2,6-diaminostyryl 4-dicyanomethylene-4H-pyran
or DDP structure (Fig. 5.12). Flexible TEG linkers were attached to
both amino groups of DDP, yielding two hydroxyl groups at either
end of the chromophore. One hydroxyl group was protected with a
removable blocker, dimethoxy trityl (DMTr) group, and the other
was activated with a phosphoramidite group. The blue emitter is
1,4-(bis- 4,4
max
′
-(2-(2-(2-(2-hydroxyl ethoxy)ethoxy)ethoxy)ethoxy)
styryl) benzene (HSB) and it is similarly functionalized with a
removable DMTr protection and an active phosphoramidite for
efficient coupling to hydroxyl groups.
∼
In aqueous solutions (pH
5), HSB and DDP in a foldamer
−
−
−
−
construct of HSB
HSB fluoresce at 435 and 545
nm, respectively. The shifts in fluorescence emissions are attributed
to the change of solvent and pH effects on the chromophores. The
purified hybrid foldamer forms predominately folded structures,
in which the two chromophores are in approximately juxtaposed
positions (Fig. 5.12). Since the emission band of HSB overlaps strongly
DNA
DDP
DNA
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