Synthesis of solvatofluorochromic 7-arylethynylated 7-deaza-2′- deoxyadenosine derivatives: Application to the design of environmentally sensitive fluorescent probes forming stable DNA duplexes

Article abstract of DOI:10.1016/j.tetlet.2013.02.063

We synthesized environmentally sensitive fluorescent (ESF) 7-deaza-2′-deoxyadenosine derivatives including ethynylanthracene substituted ^atzA (1) and ethynylnaphthalene substituted ^nzA (2a), ^cnzA (2b), ^anzA (2c), and ^dnzA (2d), and investigated their photophysical properties. Among them, only push-pull type cyano- and acetyl-substituted naphthylethynylated 7-deaza-2′-deoxyadenosine, ^cnzA (2b) and ^anzA (2c), exhibited remarkable solvatofluorochromic properties (Δλ = 71 and 63 nm, respectively). We incorporated non-solvatofluorochromic ^atzA (1) and solvatofluorochromic ^cnzA (2b) into oligodeoxynucleotides and found that ^cnzA (2b) forms a stable base pair with both thymine and cytosine, being accompanied by a change of fluorescence intensity. Such ESF nucleosides can be used for studying structures and functions of nucleic acids.

Full text of DOI:10.1016/j.tetlet.2013.02.063

Tetrahedron Letters 54 (2013) 2348–2352
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Tetrahedron Letters
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Synthesis of solvatofluorochromic 7-arylethynylated
7-deaza-20-deoxyadenosine derivatives: application to the design
of environmentally sensitive fluorescent probes forming stable DNA duplexes
Azusa Suzuki a, Kohki Kimura a, Shinya Ishioroshi a, Isao Saito b, , Nobukatsu Nemoto a, Yoshio Saito a,
⇑
⇑
a Department of Chemical Biology and Applied Chemistry, School of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
b NEWCAT Institute, School of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
a r t i c l e i n f o
a b s t r a c t
We synthesized environmentally sensitive fluorescent (ESF) 7-deaza-20-deoxyadenosine derivatives
including ethynylanthracene substituted atzA (1) and ethynylnaphthalene substituted nzA (2a), cnzA
(2b), anzA (2c), and dnzA (2d), and investigated their photophysical properties. Among them, only
push–pull type cyano- and acetyl-substituted naphthylethynylated 7-deaza-20-deoxyadenosine, cnzA
Article history:
Received 1 February 2013
Revised 18 February 2013
Accepted 20 February 2013
Available online 7 March 2013
(2b) and anzA (2c), exhibited remarkable solvatofluorochromic properties (
Dk = 71 and 63 nm, respec-
tively). We incorporated non-solvatofluorochromic atzA (1) and solvatofluorochromic cnzA (2b) into oligo-
deoxynucleotides and found that cnzA (2b) forms a stable base pair with both thymine and cytosine, being
accompanied by a change of fluorescence intensity. Such ESF nucleosides can be used for studying struc-
tures and functions of nucleic acids.
Keywords:
Nucleoside
Fluorescent probe
DNA
Ó 2013 Elsevier Ltd. All rights reserved.
Fluorescent molecules that report the differences in local envi-
ronments such as polarity, viscosity, and pH by a change of fluores-
cence wavelengths and intensities are very attractive for a wide
range of applications in chemistry and chemical biology. In partic-
ular, incorporation of such environmentally sensitive fluorescent
(ESF) molecules into various biomolecules provides powerful tools
for investigating function and interaction of biomolecules such as
proteins and nucleic acids,1 for sensing viscosity or pH,2 for detect-
ing genes,3 for diagnosis,4 drug delivery,5 and bioimaging.6
Although various ESF molecules have been developed, only a lim-
ited number of ESF nucleosides have been reported.7 In particular,
there are only a few reports of DNA probes containing base-modi-
fied ESF nucleosides that can monitor microenvironmental change
by a large shift in emission wavelength.7f,i We recently reported
C8-substituted 20-deoxyadenosine 2,6cnA containing an electron
donor–acceptor system within a molecule as a base-modified ESF
nucleoside.8 Although C8-substituted 2,6cnA exhibited interesting
solvatofluorochromic properties, its incorporation into a DNA du-
plex resulted in a considerable destabilization of the DNA structure
due to the steric bulkiness of the C8-substituent,8 and conse-
quently was not appropriate for the general use as a fluorescent
DNA probe.
modated in the major groove of DNA. Especially, when modifying
purine base, 7-deazapurine derivatives are very attractive because
modifications of the C7-position of 7-deazapurine do not interfere
with the sugar–phosphate backbone and retain the nucleoside in a
favorable anti conformation, and therefore do not cause the
destabilization of DNA duplexes.9 Extensive works of Seela et al.,
on the synthesis and properties of a wide range of 7-deazapurine
nucleoside derivatives are well known.9,10 Seela et al. reported
various 7-deazapurine nucleosides, including C7-hexynylated
7-deaza-20-deoxyadenosine.10c They indicated that 7-substituted
7-deazapurine considerably stabilizes a DNA duplex when incor-
porated in DNA due to the bulky hydrophobic purine base in the
favorable anti conformation required for hybridization. This means
7-deaza-20-deoxyadenosine derivatives containing hydrophobic
substituents at the C7-position may be a good candidate for
DNA-stabilizing ESF nucleosides. In addition, insertion of an intra-
molecular donor–acceptor system into 7-deazaadenine derivatives
seems to be
a suitable approach for attaining remarkable
solvatofluorochromic properties. The electron-donating ability of
7-deazaadenine skeleton is higher than that of natural adenine
base because the oxidation potential of 7-deazaadenine is as low
as that of guanine, which has the lowest oxidation potential among
DNA bases.11 Therefore, in our research program directed toward
the design of base-modified ESF purine nucleosides, we synthe-
sized various substituted C7-arylethynylated 7-deaza-20-deoxyad-
enosines having base-pairing properties with canonical DNA bases
(Fig. 1). Photophysical properties of oligodeoxynucleotides (ODNs)
containing newly synthesized ESF nucleosides are also reported.
When considering base modification of DNA duplexes, C5-posi-
tion of pyrimidines and C7-position of 7-deazapurines are most
appropriate, since the substituents at these positions are accom-
⇑
Corresponding authors.
E-mail address: saitoy@chem.ce.nihon-u.ac.jp (Y. Saito).
0040-4039/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.tetlet.2013.02.063

A. Suzuki et al. / Tetrahedron Letters 54 (2013) 2348–2352
2349
donor-acceptor
system
R
acceptor
major
groove
donor
NH2
N
NH2
N
NH2
CN
N
N
N
N
N
N
HO
stable
basepair
N
HO
N
DNA
HO
O
O
O
OH
atzA (1)
2,6cnA
OH
OH
nzA (2a : R = H)
anzA (2c
cnzA (2b: R = CN)
C8-substituted
2'-deoxyadenosines
R
= COCH3)
:
dnzA (2d: R = NMe2)
C7-substituted 7-deaza-2'-deoxyadenosines
= Ar
Figure 1. Design of C7-arylethynylated 7-deaza-20-deoxyadenosines.
The synthesis of 7-deaza-20-deoxyadenosine derivatives includ-
ing ethynylanthracene substituted atzA (1) and various ethynyl-
naphthalene substituted nzA (2a), cnzA (2b), anzA (2c), and dnzA
(2d) is shown in Scheme 1. 7-Iodo-7-deaza-20-deoxyadenosine 3,
which was prepared according to the protocol reported by Seela
et al.,9,10b was coupled with 9-ethynylanthracene using Pd(PPh3)4
to afford 1.12 According to a similar protocol, 3 was also coupled
with previously reported 2-ethynylnaphthalene derivatives using
Pd(PPh3)4 to afford 2a–d in high yields. All the newly synthesized
compounds were characterized by 1H and 13C NMR as well as
HRESI MS and their photophysical properties were evaluated.13
Initially, we measured the fluorescence spectra of unsubstituted
arylethynylated 7-deaza-20-deoxyadenosine derivatives, anthra-
cene atzA (1) and naphthalene nzA (2a), in solvents of different
polarities. As shown in Figure 2, 9-ethynylanthracene conjugated
7-deaza-20-deoxyadenosine atzA (1) exhibited a strong fluorescence
emission at ca. 440–468 nm in both non-polar and polar solvents.
The fluorescence quantum yields of atzA (1) in non-polar solvents
such as chloroform and ethyl acetate were 0.71 and 0.52, respec-
tively. In polar solvents such as acetonitrile and methanol, the
quantum yields were decreased to 0.40 and 0.41, respectively.
Although the fluorescence quantum yields of atzA (1) were signifi-
cantly large, the red shift of fluorescence emission by increasing
derivative 2,6cnA.8 It is supposed that the high electron-donating
ability of the 7-deazaadenine skeleton gives rise to the formation
of an intramolecular donor–acceptor system between the
7-deazaadenine moiety and the electron-withdrawing cyanonaph-
thalene ring to result in a remarkably large solvatofluorochromic-
ity. A similar solvatofluorochromicity was also observed with
electron-withdrawing acetyl-substituted anzA (2c) (Fig. 3B,
D
k = 63 nm). The photophysical properties of dnzA (2d) bearing
an electron-donating N,N-dimethylamino group were next investi-
gated. As shown in Figure 3C and Table 1, the fluorescence
quantum yields of dnzA (2d) were much more larger than those
of nzA (2a) and cnzA (2b). However, when solvent polarity was
increased, the red shift of the fluorescence emission was not
observed in contrast to electron-withdrawing cyano group substi-
tuted cnzA (2b), and dnzA (2d) did not show any solvatofluorochro-
mic properties (Fig. 3C). In the case of electron-withdrawing
cyano- or acetyl-substituted naphthalenes cnzA (2b) or anzA (2c),
the 7-deazaadenine moiety acted as an electron donor to result
in a formation of an intramolecular donor–acceptor system. In
contrast, the 7-deazaadenine moiety is unable to act as an electron
acceptor in dnzA (2d) containing an electron-donating N,N-
dimethylamino group. It is confirmed that an intramolecular
donor–acceptor system such as those in cnzA (2b) and anzA (2c) is
very important for creating solvatofluorochromic properties.
To study the thermal stability and photophysical properties of
oligodeoxynucleotides (ODN) containing these newly synthesized
fluorescent nucleosides, non-solvatofluorochromic anthracene
solvent polarity was not so large (Dk = 28 nm). On the other hand,
ethynylnaphthalene substituted nzA (2a) exhibited a very weak
fluorescence at ca. 371–400 nm in either polar or non-polar
solvents, and the red shift of fluorescence emission by increasing
solvent polarity was less evident as shown in Figure 2B. These re-
sults clearly indicate that unsubstituted arylethynylated 7-deaza-
20-deoxyadenosines did not show notable solvatofluorochromicity.
In order to know the effect of electron donor and acceptor sub-
stituents on the naphthalene moiety, the photophysical properties
of C7-substituted-7-deaza-20-deoxyadenosines with 2,6-disubsti-
tuted naphthalenes, cyano-substituted cnzA (2b), acetylated aczA
(2c), and N,N-dimethylamino substituted dnzA (2d) were investi-
gated in various solvents. With excitation of 2,6-disubstituted
naphthalene derivative cnzA (2b) containing an electron-withdraw-
ing cyano substituent at 345 nm, a strong fluorescence emission
a)
NH2
N
N
N
NH2
N
HO
I
O
N
N
OH
atzA(1) : 84%
HO
O
3
R
OH
NH2
N
(
Ufl = 0.10) was observed at 423 nm in chloroform as shown in
Figure 3A. Upon excitation of cnzA (2b) in ethyl acetate, we ob-
served a medium emission at 458 nm. In contrast, the fluorescence
emission of cnzA (2b) in more polar solvents like methanol and
acetonitrile was weak and emitted at longer wavelengths of 478
and 493 nm, respectively. As expected, cnzA (2b) showed a high
b)
N
N
HO
R
O
OH
4a :
nzA 2a
( ) : 91%
R = H
R
( = H)
R = CN
cnzA(2b) : 84% (R = CN)
4b :
4c :
4d :
anzA(2c) : 89% (R = COCH3)
sensitivity to solvent polarity, indicating
a remarkably large
R = COCH3
dnzA 2d
R
= NMe2
R
( = NMe2)
(
) : 85%
solvatofluorochromicity ( k = 71 nm). It is noteworthy that the
D
wavelength of the emission is about 20–40 nm longer than that
previously reported for C8-substituted 20-deoxyadenosine
Scheme 1. Reagents and conditions: (a) 9-ethynylanthracene, Pd(PPh3)4, CuI, Et3N,
DMF, 80 °C, 2 h; (b) 4a, 4b, 4c, or 4d, Pd(PPh3)4, CuI, Et3N, DMF, 60 °C, 1 h.

2350
A. Suzuki et al. / Tetrahedron Letters 54 (2013) 2348–2352
A
B
Figure 2. Fluorescence spectra of (A) atzA (1, 10
l
M) and (B) nzA (2a, 10
lM) in various solvents. The slit width was 1.5 nm
A
B
C
Figure 3. Fluorescence spectra of (A) cnzA (2b, 10 M), (B) anzA (2c, 10 M), and (C) dnzA (2d, 10
l l lM) in various solvents. The slit width was 1.5 nm.
substituted atzA (1) and highly solvatofluorochromic cnzA (2b) were
incorporated into ODNs via automated DNA synthesis. The syn-
thetic route of the corresponding phosphoramidites is indicated
in Scheme 2. After protection of the amino group of atzA (1) with
N,N-dimethylformamide diethylacetal, 5 was reacted with DMTrCl
in dry pyridine to give 6. Protected 6 was then converted to phos-
phoramidite 7. The phosphoramidite of atzA (1) was used for ODN
synthesis by employing an automated DNA/RNA synthesizer. The
phosphoramidite of cnzA (2b) was also prepared and incorporated
into ODNs via a similar protocol.
mation of 20-deoxyadenosine (A) due to the steric repulsion to
result in a syn conformation.14 Incorporation of such C8 substituted
adenine nucleoside into ODN resulted in a large decrease of melt-
ing temperatures due to the lack of A/T base pair formation. In con-
trast, it has been reported that 7-deaza-20-deoxyadenosine
derivatives preferred normal anti conformation even when bulky
substituents were introduced at the C7 position.10c To understand
the effect of C7-substituents on the syn and anti conformations of
newly synthesized 7-deaza-20-deoxyadenosine derivatives, their
inherent glycosidic bond conformations were examined by 1H
and 13C NMR spectroscopy. It is well established that an anti-to-
syn conformational change results in a downfield shift of C10, C30,
C40, and H20 signals, as well as an upfield shift of C20 signal.10c As
shown in Table 2, such shifts were not observed for all the C7-
Thermal stability of DNA duplexes containing modified nucleo-
sides is profoundly affected by glycosidic bond conformations of
modified nucleosides. It is known that substituents at the C8 posi-
tion of purine base destabilize the normally preferred anti confor-

A. Suzuki et al. / Tetrahedron Letters 54 (2013) 2348–2352
2351
Table 1
Table 2
13
Photophysical properties of fluorescent 7-deaza-20-deoxyadenosine derivatives
1H and C NMR chemical shifts of 20-deoxyadenosine and 7-deaza-20-deoxyadeno-
sine derivatives in DMSO-d6
abs
fl
Compound
Solvent
Ufl
k
(nm)
k
(nm)
max
max
Compound
H (20)
C (10)
C (20)
C (30)
C (40)
C (50)
atzA (1)
Ethyl acetate
Chloroform
Acetonitrile
Ethanol
405
407
405
405
403
465
443, 462
468
441, 463
440, 462
0.52
A (anti)
2.72
3.25
3.20
2.50
2.60
2.54
2.54
2.50
2.53
84.0
86.4
85.1
83.3
83.2
83.3
83.3
83.3
83.3
38.9
37.0
37.8
b
b
b
b
b
b
71.0
71.1
71.2
71.1
70.9
71.0
71.0
71.0
70.9
88.0
88.3
88.4
87.3
87.6
87.6
87.6
87.6
87.6
61.9
62.1
62.2
62.1
61.9
61.9
61.9
61.9
61.8
0.71
0.40
0.50
0.41
Br-Aa (syn)
2,6cnA8 (syn)
zA10c (anti)
atzA (1)
Methanol
nzA (2a)
cnzA (2b)
anzA (2c)
dnzA (2d)
Ethyl acetate
Chloroform
Acetonitrile
Ethanol
318
319
318
318
315
383
374
400
371
377
<0.01
<0.01
<0.01
<0.01
<0.01
nzA (2a)
cnzA (2b)
anzA (2c)
dnzA (2d)
Methanol
a
8-Bromo-20-deoxyadenosine.
Overlapped with DMSO (39.5 ppm).
Ethyl acetate
Chloroform
Acetonitrile
Ethanol
345
345
345
345
345
458
423
494
469
478
0.08
0.10
0.05
0.04
0.02
b
Methanol
Table 3
Ethyl acetate
Chloroform
Acetonitrile
Ethanol
347
345
344
346
344
461
445
508
475
464
0.08
0.12
0.02
<0.01
<0.01
Thermal melting temperatures (Tm) and photophysical properties of duplexes ODN 1/
ODN 2; ODN 1: 50-CGCAAT X TAACGC-30 (X = cnzA, A or A), ODN 2: 30-GCGTTA N
atz
ATTGCG-50 (N = T or C)
abs
max
fl
Duplex
Tm (°C)
k
(nm)
k
(nm)
Methanol
max
ODN 1 (cnzA)
—
351
350
461
468
446
Ethyl acetate
THF
Acetonitrile
2-Propanol
Ethanol
333
335
336
333
334
336
418
418
432
419
421
424
0.54
0.58
0.51
0.57
0.49
0.39
ODN 1 (cnzA)/ODN 2 (T)
ODN 1 (cnzA)/ODN 2 (C)
ODN 1 (atzA)
52.8
50.1
—
52.2
53.1
52.6
45.4
336, 351
410, 430
410, 435
410, 435
—
447, 469
447, 472
448, 472
—
ODN 1 (atzA)/ODN 2 (T)
ODN 1 (atzA)/ODN 2 (C)
ODN 1 (A)/ODN 2 (T)
ODN 1 (A)/ODN 2 (C)
Methanol
—
—
N
N
Ar
NH2
N
Ar
N
N
nucleosides (A, T, G, C), Seela et al. reported that 7-deaza-20-
deoxyadenosine (zA) can form a strong base pair not only with T
but also with C.10f As shown in Table 3, the melting temperatures
of ODN 1 (X = atzA or cnzA)/ODN 2 (T) and ODN 1 (X = atzA or
a)
b)
N
N
N
HO
O
HO
O
atzA 1
(
)
5
: 87%
5b : 95%
OH
cnzA 2b
OH
(
)
cnzA)/ODN
2 (C) were considerably higher than those of
unmodified mismatched duplex ODN 1 (A)/ODN 2 (C) and other
mismatched duplexes (Supplementary data, Table S2), suggesting
that newly synthesized 7-deazaadenosine derivatives atzA (1) and
cnzA (2b) can form stable base pairs with both T and C. This is
consistent with the previous report that 7-substituted 7-deazapu-
rines generally form a protonated base pair with cytosine.10f In the
CD spectra of ODN 1 (cnzA)/ODN 2 (N = T or C), a negative peak at
250 nm and a positive peak at 280 nm were observed (Supplemen-
tary data, Fig. S4). These spectral data also indicate that cnzA-con-
taining DNA duplexes maintain a normal B-DNA structure.
UV–visible absorption and fluorescence spectra of ODNs con-
taining atzA (1) and cnzA (2b) were then examined. As shown in
Figure 4A, the fluorescence emission of ss ODN 1 (cnzA) was rela-
tively weak and appeared at 461 nm. When complementary
strands were added, the fluorescence intensity of the duplex
ODN was considerably enhanced. When the opposite base of the
complementary strand is thymine (T) in duplex ODN 1 (cnzA)/
ODN 2 (T), a strong emission was observed at a slightly red shifted
wavelength (468 nm). Interestingly, when the opposite base of the
complementary strand is cytosine (C) in duplex ODN 1 (cnzA)/ODN
2 (C), the fluorescence maximum was blue-shifted to 446 nm by
22 nm with a stronger emission intensity (Fig. 4A). The fluores-
cence change caused by the difference in the opposite base of a
complementary strand may be ascribable to the local environmen-
tal change near the solvatofluorochromic cnzA (2b) moiety.15 On
the other hand, non-solvatofluorochromic atzA-labeled ODN 1
showed an environmentally insensitive nature. Even when the
opposite base of complementary strand is changed from thymine
to cytosine, a similar but slightly enhanced fluorescence was
observed in both cases (Fig. 4B). Although ODN containing
N
N
N
N
Ar
N
Ar
N
N
c)
N
N
N
DMTrO
DMTrO
O
O
OH
6
: 87%
: quant
O
O
7
NC
P
6b
N(iPr)2
7b
DNA synthesis ODN 1:
ODN 2:
X
5'-CGCAAT TAACGC-3'
N
N
5'-GCGTTA ATTGCG-3' ( = T or C)
Ar
NH2
N
NC
X =
Ar =
N
N
O
O
2b, 5b - 7b
1, 5 - 7
O
Scheme 2. Reagents and conditions: (a) N,N-dimethylformamide diethylacetal,
DMF, 60–80 °C, 2–5 h; (b) DMTrCl, pyridine, rt, 3–6 h; (c) 2-cya-
noethyldiisopropylphosphoramidite, Et3N, acetonitrile, rt, 30 min.
substituted 7-deaza-20-deoxyadenosine derivatives synthesized as
compared to previously reported 2,6cnA, indicating their preference
of anti conformation.
Single-stranded (ss) ODNs containing atzA (1) and cnzA (2b)
were hybridized with complementary ODNs, and the resulting du-
plexes were examined for thermal stability. As for the base recog-
nition of 7-deazaadenosine derivatives toward four canonical

2352
A. Suzuki et al. / Tetrahedron Letters 54 (2013) 2348–2352
A
B
Figure 4. Fluorescence spectra of ODN 1 [X = cnzA (A) and atzA (B)] hydridized with ODN 2 (N = T or C); ‘ss’ denotes a single-stranded ODN 1 (2.5
lM ODNs, 0.1 M sodium
chloride, 50 mM sodium phosphate buffer, pH 7.0, rt). The slit width was 1.5 nm.
solvatofluorochromic cnzA (2b) showed an environmentally sensi-
tive fluorescence emission when hybridized with complementary
ODNs, such a drastic change in fluorescent intensity and wave-
length was not observed in non-solvatofluorochromic atzA-con-
taining ODN (Fig. 4, Table 3). Thus, it is clear that non-
solvatofluorochromic anthracene-containing atzA (1) can be used
as a fluorescent probe of high intensity but never used as an envi-
ronmentally sensitive fluorescent ODN probe.
In conclusion, we have synthesized various substituted aryleth-
ynylated 7-deaza-20-deoxyadenosine derivatives. Among them,
only push–pull type cyano- and acetyl-substituted naphthylethy-
nylated 7-deaza-20-deoxyadenosines, cnzA (2b), and anzA (2c),
E.; Esposito, I.; Schmid, R. M.; Schneider, G.; Saur, D. Proc. Natl. Acad. Sci. USA
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exhibited remarkable solvatofluorochromic properties (Dk = 71
and 63 nm, respectively). Unsubstituted and N,N-dimethylamino-
substituted derivatives having no intramolecular donor–acceptor
system did not show such solvatofluorochromic properties. Ther-
mal melting data indicated that an ODN probe containing cnzA
(2b) can form a stable base pair either with thymine or cytosine,
and maintain a stable B-DNA structure, similar to that reported
for 7-deaza-20-deoxyadenosine (zA). The microenvironmental
change caused by the change of opposite bases resulted in a con-
siderable change of the fluorescence intensity and emission wave-
length in cnzA-containing ODN probe. Fluorescent DNA probes
containing such a base-modified ESF nucleoside can be used as a
tool for studying structures and functions of nucleic acids and for
studying interactions between nucleic acids and proteins.
8. Suzuki, A.; Takahashi, N.; Okada, Y.; Saito, I.; Nemoto, N.; Saito, Y. Bioorg. Med.
Chem. Lett. 2013, 23, 886.
9. For a review: Seela, F.; Budow, S.; Peng, X. Curr. Org. Chem. 2012, 16, 161.
10. (a) Seela, F.; Thomas, H. Helv. Chim. Acta 1995, 78, 94; (b) Seela, F.; Zulauf, M.
Synthesis 1996, 726; (c) Seela, F.; Zulauf, M. Chem. Eur. J. 1998, 4, 1781; (d)
Seela, F.; Zulauf, M. Helv. Chim. Acta 1878, 1999, 82; (e) Seela, F.; Zulauf, M.;
Sauer, M.; Deimel, K. Helv. Chim. Acta 2000, 83, 910; (f) Peng, X.; Li, H.; Seela, F.
Nucleic Acids Res. 2006, 34, 5987; (g) Vrábel, M.; Pohl, R.; Votruba, I.; Sajadi, M.;
Kovalenko, S. A.; Ernsting, N. P.; Hocek, M. Org. Biomol. Chem. 2008, 6, 2852.
11. Baik, M.-H.; Silverman, S. J.; Yang, V. I.; Ropp, A. P.; Szalai, A. V.; Yang, W.;
Thorp, H. H. J. Phys. Chem. B 2001, 105, 6437.
12. Sonogashira, K.; Tohda, Y.; Hagihara, N. Tetrahedron Lett. 1975, 16, 2267.
13. Spectroscopic data for atzA (1): 1H NMR (DMSO-d6, 400 MHz) d 2.27 (ddd,
J = 2.8, 6.0, 13.2 Hz, 1H), 2.60 (ddd, J = 5.8, 8.0, 13.2 Hz, 1H), 3.54–3.67
(complex, 2H), 3.88 (m, 1H), 4.41 (m, 1H), 5.12 (m, 1H), 5.34 (d, J = 4.1 Hz,
1H), 6.59 (dd, J = 6.0, 8.0 Hz, 1H), 6.84 (br, 2H), 7.63 (m, 2H), 7.70 (m, 2H), 8.17
(s, 1H), 8.19 (d, J = 8.4 Hz, 2H) 8.22 (s, 1H), 8.53 (m, 2H), 8.71 (s, 1H); 13C NMR
(DMSO-d6, 100 MHz) d 61.9, 70.9, 83.2, 87.4, 87.6, 94.3, 94.9, 102.2, 116.3,
125.9 (ꢀ2), 126.1 (ꢀ2), 127.4, 127.4 (ꢀ2), 127.9, 129.0 (ꢀ2), 130.8 (ꢀ2), 131.8
(ꢀ2), 149.6, 152.9, 157.7. C(20) overlapped with DMSO; HRMS (ESI) m/z
473.1590 calcd for C27H22N4O3Na [M+Na]+, found 473.1596. Spectroscopic data
for cnzA (2b): 1H NMR (DMSO-d6, 400 MHz) d 2.24 (ddd, J = 2.8, 6.0, 13.2 Hz,
1H), 2.54 (m, 1H, overlapped with DMSO), 3.55–3.63 (complex, 2H), 3.86 (m,
1H), 4.38 (m, 1H), 5.12 (m, 1H), 5.32 (d, J = 4.1 Hz, 1H), 6.54 (dd, J = 6.0, 7.8 Hz,
1H), 6.88 (br, 2H), 7.82–7.86 (complex, 2H), 7.98 (s, 1H), 8.09–8.14 (complex,
2H) 8.18 (s, 1H), 8.34 (m, 1H), 8.61 (m, 1H); 13C NMR (DMSO-d6, 100 MHz) d
61.9, 71.0, 83.3, 85.6, 87.6, 91.0, 94.4, 102.0, 109.0, 119.1, 123.4, 127.3, 127.7,
128.9, 129.1, 129.7, 130.6, 131.1, 134.0, 134.2, 149.6, 152.9, 157.6. C(20)
overlapped with DMSO; HRMS (ESI) m/z 448.1386 calcd for C24H19N5O3Na
[M+Na]+, found 448.1407.
Supplementary data
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.tetlet.2013.
02.063.
References and notes
1. (a) Weissleder, R.; Tung, C. H.; Mahmood, U.; Bogdanov, A., Jr. Nat. Biotechnol.
1999, 17, 375; (b) Dai, N.; Kool, E. T. Chem. Soc. Rev. 2011, 40, 5756.
2. Gatzogiannis, E.; Chen, Z.; Wei, L.; Wombacher, R.; Kao, Y. T.; Yefremov, G.;
Cornish, V. W.; Min, W. Chem. Commun. 2012, 48, 8694.
3. For reviews, see: (a) Okamoto, A.; Saito, Y.; Saito, I. Photochem. Photobiol. C:
Photochem. Rev. 2005, 6, 108; (b) Ranasinghe, R. T.; Brown, T. Chem. Commun.
2005, 5487; (c) Wilson, J. N.; Kool, E. T. Org. Biomol. Chem. 2006, 4, 4265; (d)
Venkatesan, N.; Seo, Y. J.; Kim, B. H. Chem. Soc. Rev. 2008, 37, 648; (e)
Sinkeldam, R. W.; Greco, N. J.; Tor, Y. Chem. Rev. 2010, 110, 2579; (f) Østergaard,
M. E.; Hrdlicka, P. J. Chem. Soc. Rev. 2011, 40, 5771.
14. Eason, R. G.; Burkhardt, D. M.; Phillips, S. J.; Smith, D. P.; David, S. S. Nucleic
Acids Res. 1996, 24, 890.
15. When ODN probes containing GC rich sequence like –CcnzAC– were used, the
fluorescence emission was strongly quenched by flanking C/G base pairs. This
4. Eser, S.; Messer, M.; Eser, P.; von Werder, A.; Seidler, B.; Bajbouj, M.;
Vogelmann, R.; Meining, A.; von Burstin, J.; Algül, H.; Pagel, P.; Schnieke, A.
indicates that there is
a limitation for the sequence when ODN probe
containing cnzA is used.