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undetectable after 4 h at 20 °C or 1 h at 37 °C, that of 9SQFBt was
70% of its initial value after 4 h at 20 °C and was 75% after 1 h at
37 °C. The fluorescence decrease observed at 20 °C was similar to
that obtained with the conjugate 9Cy7mh, while that of 9TO was
unchanged.
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13. 4-[N-(6-iodohexyl)-1,3-benzothiazoliumyl-2-methylene]-2-(N-methyl-2,3-dihydro-
1,3-benzothiazol-2-ylidenemethyl)-3-oxo-1-cyclobutene-1-olate 1: Compound 7a
(380 mg, 1 equiv, 1.20 mmol) was added to a solution of 8a (587 mg, 1 equiv,
1.20 mmol) in a butanol/toluene (1:1, v/v) mixture (15 mL). The mixture was
stirred at 120 °C for 10 h. After removal of the solvent by evaporation, the
residue was purified on a silica gel column using a MeOH gradient (0–5%) in
CH2Cl2, then on preparative silica gel plates using a CH2Cl2/MeOH mixture (96:4,
v/v) as eluent to give a dark blue solid 42 mg. Yield: 12%. TLC: Rf (CH2Cl2/MeOH
8/2) = 0.45. 1H NMR (500 MHz, CDCl3, TMS): d (ppm) = 7.61 (t, 2H, J = 7.8 Hz,
HAr), 7.47 (m, 2H, HAr), 7.32 (m, 4H, HAr), 6.39 (s, 2H, = CH), 4.18 (m, 2H, +N–
CH2–), 3.75 (s, 3H, N–CH3), 3.24 (t, J = 6.9 Hz, 2H, –CH2I), 1.88 (m, 4H, 2 CH2–),
1.56 (m, 4H, 2 CH2–). 13C NMR (126 MHz, CDCl3, TMS): d (ppm) = 6.8, 26.1, 27.4,
30.4, 33.0, 33.4, 46.2, 85.6, 111.4, 111.5, 122.3, 122.4, 124.1, 124.2, 127.2, 127.3,
128.7, 128.9, 141.2, 141.7, 159.9, 160.1. Maldi-Tof-MS: m/z, C27H25O2N2S2I calcd
600.55, found 600 (M+).
The influence of the pH was also tested. The emission spectra of
solutions of conjugates 9SQBt, 9SQFBt, 10SQBt, and 10SQFBt, were re-
corded in aqueous buffer with pH ranging from 5 to 8. The results
indicated nearly equivalent values at any pH for the conjugates
involving the fluorinated squaraine, while the conjugate derived
from the non-fluorinated squaraine was not stable at pH below 7.
The presence of the squaraines induced a weak stability in-
crease of the complexes formed by the conjugates 9SQBt and 9SQFBt
0
0
with their single-stranded 5 GGGAAAAGAAAATTT3 and double-
0
0
0
stranded 5 GCCACTTTTTAAAAGAAAAGGGG3 /3 CGGTGAAAAATTT
0
TCTTTTCCCC5 DNA targets. Upon hybridization at 20 °C, the fluo-
rescence emission of the 9SQBt and 9SQFBt decreased by 28% and
9% in the presence of the single-stranded target and by 8% and
42% in the presence of the double-stranded target.
3. Conclusion
We have reported the synthesis of three squaraine dyes based
on benzothiazole moiety with wavelength emissions beyond
670 nm. Two of them have been successfully used for the labeling
of a series of five oligonucleotides with different sequences,
lengths, and chemistries. The oligonucleotides labeled with the
squaraines exhibited high fluorescent emissions, about 60 and
30-fold those of the corresponding oligonucleotides labeled with
the well-known dyes thiazole orange and Indocyanine Green ana-
logue. As previously reported for thiazole orange, the fluorination
of the benzothiazole heterocycle of the squaraine led to an
improvement in photostability. This photostability increase was
also observed with the labeled oligonucleotides. The presence of
the fluorine atom on the label induced a strong chemical stability
increase, between pH 5 and 8, that reached that of the correspond-
ing thiazole orange labeled oligonucleotide. These properties make
the fluorinated squaraine dyes very promising tools for the labeling
of oligonucleotides.
Acknowledgments
14. 4-[5-Fluoro-N-(6-iodohexyl)-1,3-benzothiazoliumyl-2-methylene]-2-(5-fluoro-
N-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenemethyl)-3-oxo-1- cyclobutene-
We thank the Region Centre for a doctoral fellowship to B.-L.R.,
the «Plateforme de Spectrometrie de masse» of the «Centre de Bio-
physique Moléculaire» for analysis facilities, G. Gabant for running
the mass spectrometers, and H. Meudal for recording the NMR
spectra.
1-olate 2: Compound 7b (440 mg, 1 equiv, 1.32 mmol) was added to
a
solution of 8b (668 mg, 1 equiv, 1.32 mmol) in a butanol/toluene (1:1, v/v)
mixture (15 mL). The mixture was stirred at 120 °C for 10 h. After removal
of the solvent by evaporation, the residue was purified on
a silica gel
column using a MeOH gradient (0–3%) in CH2Cl2, then on preparative silica
gel plates using a CH2Cl2/MeOH mixture (96:4, v/v) as eluent to give a dark
blue solid 91 mg. Yield: 23%. TLC: Rf (CH2Cl2/MeOH 8/2) = 0.45. 1H NMR
(500 MHz, CDCl3, TMS): d (ppm) = 7.47 (m, 2H, HAr), 6.96 (m, 2H, HAr), 6.89
(m, 2H, HAr), 5.91 (s, 2H, @CH), 4.06 (t, 2H, J = 7.8 Hz, +N–CH2–), 3.64 (s, 3H,
N–CH3), 3.23 (t, J = 6.9 Hz, 2H, –CH2I), 1.86 (m, 4H, 2 CH2–), 1.52 (m, 4H, 2
CH2–). 13C NMR (126 MHz, CDCl3, TMS): d (ppm) = 6.7, 26.1, 27.3, 30.4, 33.2,
33.3, 46.6, 86.5 (d, J = 14.7 Hz), 99.4 (d, JC–F = 28.1 Hz), 99.6 (JC–F = 28.1 Hz),
111.7 (t, JC–F = 23.1 Hz), 123.2 (t, JC–F = 10.5 Hz), 161.0, 162.7 (d,
JC–F = 245.7 Hz). Maldi-Tof-MS: m/z, C27H23O2N2S2F2I calcd 636.52, found
637.27 (M+).
Supplementary data
The Supplementary data section includes detailed experimental
conditions and characterization data for compounds 4a, 4b, 6, 7a,
7b, 7c, 8a, 8b and Cy7mh and 9Cy7mh. Supplementary data associ-
ated with this article can be found, in the online version, at
15. 3-Dicyanomethylene-4-[N-(6-iodohexyl)-1,3-benzothiazoliumyl-2-methylene]-2-
(N-methyl-2,3-dihydro-1,3-benzothiazol-2-ylidenemethyl)-1-cyclobutene-1-olate
3: Compound 7c (270 mg, 1 equiv, 0.66 mmol) was added to a solution of 8a
(362 mg, 1.2 equiv, 0.802 mmol) in EtOH (10 mL), and the mixture was heated
to 85 °C for 8 h under stirring. After removal of the solvent by evaporation, the
residue was purified on a silica gel column using a MeOH gradient (0–5%) in
CH2Cl2, then on preparative silica gel plates using a CH2Cl2/MeOH mixture
(98:2, v/v) as eluent to give a turquoise blue solid. Yield: 15%. 1H NMR
(500 MHz, CDCl3, TMS): d (ppm) = 7.57 (t, 2H, J = 7.5 Hz, HAr), 7.41 (d t, 2H,
J = 7.5 Hz, J = 8 Hz, HAr), 7.24 (q, 2H, J = 7 Hz, HAr), 7.17 (m, 2H, HAr), 5.92 (s, 2H,
@CH), 4.12 (t, 2H, J = 7.5 Hz, –+N–CH2–), 3.68 (s, 3H, N–CH3), 3.23 (t, J = 7 Hz,
2H, –CH2I), 1.88 (m, 4H, 2 CH2–), 1.52 (m, 4H, 2 CH2–). 13C NMR (126 MHz,
CDCl3, TMS): d (ppm) = 7.1, 26.0, 27.6, 29.9, 30.3, 33.3, 46.9, 87.3, 112.0, 112.1,
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