Chemistry Reference
In-Depth Information
develop a highly selective Na
+
indicator. However, applicability of this rotaxane to
design highly stable, water-soluble labels is ambiguous because its stability is
strongly dependent upon presence on Na
+
ions.
An overview of the synthesis, structure, photophysical properties, and applica-
tions of squaraine rotaxanes as fluorescent imaging probes and chemosensors is
provided in a recent review [
67
]. Although a variety of squaraine dyes form
rotaxanes with the molecular cage 25 or with a tetralactam macrocyclic system
introduced by Leigh and co-workers [
16
,
17
], there is no evidence in the literature
that conventional
cyanine
dyes can be embedded in these macrocycles.
5 Dye-Macromolecule Complexes
Embedding of cyanine and squaraine dyes in macromolecules such as
proteins
,
dendrimers,
or
aptamers
also allows fine-tuning of the photophysical properties and
the selectivity of these fluorescent probes and labels.
While the covalent attachment of
cyanine
dyes such as Cy5 or Alexa 647 to
proteins
does not result in noticeable changes in their spectral properties,
squaraine
dyes (oxo-squarines and squaraines with substituted squaraine oxygens) behave
quite the opposite: the absorption and emission maxima of squaraines are in general
red-shifted after binding to proteins and the quantum yields and fluorescence life-
times are manifold increased [
68
-
70
]. In general hydrophobic squaraines exhibit
more pronounced increases compared to hydrophilic dyes. These effects are even
stronger in noncovalent dye-protein complexes. Importantly, the photostability of
squaraines also increases after binding to proteins.
Embedding of pinacyanol in a three-dimensional
polyphenylene dendrimer
results in a red-shift of absorption (from 600 to 620 nm) and emission (from 625
to 648 nm) maxima and in an increase of the quantum yield from 9
10
-4
for free
dye in water to 1.4
10
-2
after insertion in the dendrimeric architecture [
71
]. This
dendrimer was used to develop two FRET systems utilizing cyanine dyes as the
donor (DTCI) and the acceptor (pinacyanol and 26a) molecules [
72
]. The FRET
system allows the time-resolved detection, where energy transfer can be observed at
the single-molecule level.
S
S
DTCI
: n = 1
26a
: n = 2
26b
: n = 3
N
N
N
Et
N
n
Et
Et
Pinacyanol
Et
A dendrimeric system with Cy3 and Cy5 as the reporter dyes was applied to
develop a microarray-based technology for high-throughput functional genomics
research [
73
].
The cyanine dye dimethylindole red (DIR), with significantly reduced affinity
for double-stranded DNA and nonspecific RNA, was used to generate a fluorescent
complex (fluoromodule) with high affinity RNA aptamers (Fig.
12
)[
8
]. DIR has
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