Chemistry Reference
In-Depth Information
positive charges that promotes the aggregate formation. Thus, if the dye molecule
has the structure appropriate for its aggregate to fit to the DNA molecule, the
aggregate can be formed. The above described role of the Coulombic interaction
in the aggregation on DNA explains the fact that unlike aggregation in solution,
increasing of ionic strength leads to the destruction of aggregates formed on DNA.
Unlike the aggregation in solution, there are very few works dealing with the dye
aggregation on DNA, and only in few reports these aggregates are found fluores-
cent. In most of the cases, the aggregates formed on DNA are the non- or weakly
fluorescent H-aggregates, and these aggregates are often supposed to be the dimers.
Particularly, the monomethine cyanine dye thiazole orange (TO, Fig.
7
) was shown
to form dimer aggregates bound to single-stranded synthetic polynucleotides poly
(dC), poly(dT), and poly(dG), while in the presence of dsDNA and poly(dA) no
aggregates were observed [
30
]. The fluorescence of the dimers was not revealed
because of its very low intensity as compared to that of the monomeric TO bound to
polynucleotide. The authors explain the low fluorescence intensity of the bound
aggregate by the peculiarities of the dimer structure, supposing that one of the dye
a
b
S
N
+
S
S
N
O
N
+
N
S
I
-
O
O
-
c
d
S
S
S
N
+
S
N
S
Br
-
N
+
N
I
-
N
+
N
+
Br
-
Br
-
e
f
S
N
+
S
S
N
N
N
+
N
+
N
S
I
-
Fig. 7 Structures of the dyes forming aggregates on DNA: (a) 1-methyl-4-[[3-methyl-2(3
H
)-
benzothiazolylidene]methyl]-quinolinium (Thiazole Orange, TO), (b)3,3
0
-diethylthiadicarbo-
cyanine (DiSC
2
(5)), (c)3,3
0
-trimethylammoniopropylthiadicarbocyanine (DiSC
3+
(5)), (d)
2-[(
Z
)-2-(2,5-dihydro-2-thienyl)-3-[3-methyl-2(3
H
)-benzothiazolylidene]-1-propenyl]-3-methyl-
benzothiazol-3-ium (L-21), (e) 2-[(
E
)-3-[3,7-diethyl-6-[(
E
,2
E
)-3-(1-ethyl-3,3-dimethyl-3
H
-indo-
lium-2-yl)-2-propenylidene]-6,7-dihydrothiazolo[5,4-
f
]benzothiazol-2(3
H
)-ylidene]-1-propenyl]-
1-ethyl-3,3-dimethyl-3
H
-indolium (BCD), (f) 3-methyl-2-[(
E
)-3-methyl-2-[[3-methyl-2(3
H
)-ben-
zothiazolylidene]methyl]-1-butenyl]-benzothiazol-3-ium (Cyan
b
iPr)
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