Photoisomerization of 2′-deoxyribofuranosyl and ribofuranosyl 2-phenylazoimidazole

Article abstract of DOI:10.1016/S0040-4039(03)01697-6

Novel photo responsive nucleosides, 1-N-(2′-deoxyribofuranosyl) 2-phenylazoimidazole and 1-N-ribofuranosyl 2-phenylazoimidazole have been designed and synthesized. trans-cis Photoisomerizations of the nucleosides with irradiation at a specific wavelength have been observed and the isomerizations are perfectly reversible.

Full text of DOI:10.1016/S0040-4039(03)01697-6

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 44 (2003) 6903–6906
Photoisomerization of 2%-deoxyribofuranosyl and ribofuranosyl
2-phenylazoimidazole
Masayuki Endo, Koji Nakayama, Yuka Kaida and Tetsuro Majima*
Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
Received 2 June 2003; revised 5 July 2003; accepted 8 July 2003
Abstract—Novel photo responsive nucleosides, 1-N-(2%-deoxyribofuranosyl) 2-phenylazoimidazole and 1-N-ribofuranosyl 2-
phenylazoimidazole have been designed and synthesized. trans–cis Photoisomerizations of the nucleosides with irradiation at a
specific wavelength have been observed and the isomerizations are perfectly reversible.
© 2003 Elsevier Ltd. All rights reserved.
Photochemical control of biomolecules both in vitro
and in vivo is of increasing interest in molecular and
cellular biology.1 For application to living systems,
photochemical reactions are advantageous because the
reactions can be controlled from outside without addi-
tion of chemicals for initiation of biomolecular’s func-
tions. Caged compounds which can be removed by
photo irradiation have been attached to DNA, RNA,
and proteins for initiation of biological phenomena.1
Many cellular processes including gene expression and
signal transduction need regulations in both positive
and negative ways. Biomolecules possessing a photo-
chemically controllable residue just like a switch are
required for precise control of target biological pro-
cesses. Azobenzene derivatives are the most commonly
used photochemical switches for functionalization of
the polymers and biomolecules.2–4 For nucleic acids,
azobenzene derivatives have been introduced to DNA
strands using methylene chain units analogous to a
ribose for control of double and triple helix forming
activities.5–8
Unnatural base 2-phenylazoimidazole (1) was prepared
according to the previously reported method.9 We tried
two coupling procedures. The first procedure we used
was the standard coupling method in which the hydro-
gen atom of N1 on 2-phenylazoimidazole (1) was acti-
vated by sodium hydride in acetonitrile and then
2-deoxy-3,5-di-O-(p-toluoyl)-D
-ribofuranosyl chloride10
was added for base–sugar coupling. a- and b-anomers
were separated by a silica gel column chromatography
and stereochemistry of the anomers was determined by
differential nuclear Overhauser enhancement (NOE)
spectroscopy.11 Using this procedure, the isolated yield
of the protected nucleosides was 48% and undesirable
a-anomer was a major product. The ratio of the a- and
b-anomer was 67:33. In the second procedure, 2-phenyl-
azoimidazole was treated with potassium hydroxide in
methylenechloride in the presence of tris[2-(2-
methoxyethoxy)ethyl]amine (TDA-1) and then 2-deoxy-
3,5-di-O-(p-toluoyl)-
D
-ribofuranosyl
chloride
was
added. We successfully obtained the b-anomer (2) in
53% yield and the production of the a-anomer was
almost suppressed. Deprotection of 2 by saturated
Since nucleic acid bases are packed into a double helix
DNA by base stacking to maintain a canonical DNA
backbone structure, an azobenzene derivative attached
to C1% position of a ribose is preferable for fixing a base
to the original position on the ribose. Based on this
notion, we designed and synthesized photo functional-
ized nucleosides 1-N-(2%-deoxyribofuranosyl) 2-phenyla-
zoimidazole (3) and 1-N-ribofuranosyl 2-phenylazo-
imidazole (5) (Fig. 1).
Figure 1. Schematic representation of trans–cis photoisomer-
ization of the photo responsive nucleosides (3 and 5).
* Corresponding author. Tel.: +81-6-6879-8495; fax: +81-6-6879-8499;
e-mail: majima@sanken.osaka-u.ac.jp
0040-4039/$ - see front matter © 2003 Elsevier Ltd. All rights reserved.
doi:10.1016/S0040-4039(03)01697-6

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M. Endo et al. / Tetrahedron Letters 44 (2003) 6903–6906
small amount of trimethylsilyl chloride (TMS-Cl) for
1.5 h for silylation. After concentration, coupling of the
silylated nucleoside and 1-O-acetyl 2,3,5-tri-O-bezoyl-
b-D-ribofuranose was accomplished in acetonitrile with
trimethylsilyl triflate (TMSOTf) at rt for 1 h. Purifica-
tion by a silica gel column chromatography gave
nucleoside 4 in 67% yield. Deprotection of 4 was car-
ried out by sodium methylate at rt for 20 min. The
reaction mixture was purified by a silica gel column
chromatography and nucleoside 5 was isolated in 79%
yield. Stereochemistry of nucleoside 5 was determined
by differential NOE spectroscopy.13,14
Figure 2. Reagents: (a) i. KOH, TDA-1, CH2Cl2, ii. 2-deoxy-
3,5-di-O-(p-toluoyl)-
D-ribofuranosyl chloride. (b) NH3/
CH3OH. (c) i. HMDS, TMS-Cl, ii. 1-O-acetyl
2,3,5-tri-O-benzoyl-D-ribofuranose, TMSOTf. (d) NaOCH3/
CH3OH.
To characterize photochemical behaviors of these syn-
thetic nucleosides, we acquired UV/vis spectra for mon-
itoring their absorption changes by photo irradiation.
A spectrum of untreated 3 showed the two major peaks
at 360 and 437 nm which are identified as characteristic
p–p* and n–p* absorption bands of trans isomer of
azobenzene derivatives, respectively.15 By photo irradia-
tion to a methanoic solution of 3 at 360 nm using a
high-pressure mercury lamp, the peak at 360 nm
rapidly decreased and largely shifted to 325 nm, while
the peak at 437 nm increased and shifted to 455 nm16
(Fig. 3(A)). The reaction completed within 2 min (Fig.
4(A)). When irradiation to this product (cis-3) was
Figure 3. UV–vis spectra of photoisomerization of nucleoside
3. (A) trans to cis isomerization with irradiation at 360 nm for
0, 5, 10, 20, 30, 40, 60, and 120 s. (B) cis to trans isomeriza-
tion with irradiation at 455 nm for 0, 10, 20, 30, 40, 60, 120,
and 300 s. Arrows indicate increase and decrease of absorp-
tion peaks.
methanoic ammonia at rt for 8 h gave nucleoside 3 in
78% yield (Fig. 2).12
Figure 4. The ratios of trans isomers in trans–cis photoiso-
merization of nucleoside 3 (A) and 5 (B) under the experimen-
tal conditions in the text. The ratio was calculated from the
absorption spectra.
For synthesis of ribonucleoside 4, 2-phenylazoimidazole
was refluxed in hexamethyldisilazane (HMDS) and

M. Endo et al. / Tetrahedron Letters 44 (2003) 6903–6906
6905
NMR spectroscopy (Fig. 5). The ratio of trans and cis
isomers of 3 was also quantified. After irradiation at
365 nm for 20 min at 0°C,20 the peaks identical to the
cis isomer appeared and the ratio of cis and trans
isomers of 3 was 96:4 based on the integration of the
identical trans and cis peaks in the NMR spectrum
(Fig. 5(C)). To investigate the behavior of cis–trans
isomerization, the cis isomer of nucleoside 3 was
exposed to visible light.21 UV/vis spectra taken at sev-
eral intervals showed slower spectral change than that
of trans to cis isomerization. The cis to trans isomeriza-
tion of 3 was observed and the ratio of the trans and cis
isomers in the spectrum for 20 min irradiation was 92:8
under this experimental condition (Fig. 5(E)). No trace
of degraded products was observed in the NMR spec-
tra, indicating the cis–trans photoisomerization of
nucleoside 3 is perfectly reversible.
In conclusion, we have synthesized the photo respon-
sive 2%-deoxyribonucleoside and ribonucleoside possess-
ing 2-phenylazoimidazole. These nucleosides show
photoisomerization functionality similar to commonly
used azobenzene derivatives and work as reversible
photochemical switches.
Figure 5. cis to trans photoisomerization of nucleoside 3
monitored by NMR spectroscopy. (A) Without irradiation.
(B)(C) Irradiation at 365 nm for 1 and 20 min, respectively.
(D)(E) Photo irradiation to the sample C using visible light
for 5 and 20 min, respectively.
Acknowledgements
This work has been partly supported by a Grant-in-Aid
for Scientific Research on Priority Area (417) and oth-
ers from Ministry of Education, Culture, Sport, Sci-
ence, and Technology (MEXT) of Japanese
Government.
carried out using 455 nm light, the increasing peak at
325 nm shifted to 360 and the decreasing one at 455 nm
shifted to 437 nm (Fig. 3(B)). The reaction completed
within 5 min (Fig. 4(A)). This behavior is also charac-
teristic for cis to trans isomerization of azobenzene
derivatives, indicating reversible trans–cis photoisomer-
ization of nucleoside 3 occurred under this condition.15
The half-lives for trans to cis and cis to trans isomeriza-
tions of 3 are 7.1 and 35 s, respectively, under the
present experimental conditions.
References
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In the case of nucleoside 5, a similar photoisomeriza-
tion was observed by photo irradiation. The half-lives
for trans to cis and cis to trans isomerizations of 5 are
9.4 and 40 s, respectively, under the present experimen-
tal conditions (Fig. 4(B)). The efficiencies of the pho-
toisomerization were characterized by measuring
quantum yields of these nucleosides. The quantum
yields for trans to cis isomerizations of 3 and 5 in
isopropanol were b=0.08 and 0.06, respectively.17,18
Also the quantum yields for cis to trans isomerizations
of 3 and 5 in isopropanol were b=0.41 and 0.34,
respectively. These results indicate higher efficiency of
the trans–cis isomerizations of 3 than those of 5.17,18
The photoisomerization efficiencies of 3 and 5 are lower
than those of azobenzene, however, these nucleosides
still maintain substantial potentials for photochemical
switches.19
9. Chattopadhyay, P.; Dolui, B. K.; Sinha, C. Ind. J. Chem.
1997, 36, 429–432.
10. Takeshita, M.; Chang, C.-N.; Johnson, F.; Will, S.;
Grollman, A. P. J. Biol. Chem. 1987, 262, 10171–10179.
11. In the differential NOE spectrum of the product 2 irradi-
ated at C1% proton, 2¦H, 4%H and 5H were enhanced,
which is identical to a b-anomer. On the other hand, 2%H,
3%H and 5H were enhanced for the counterpart
diastereomer of 2, which is identical to an a-anomer.
Further monitoring of cis and trans isomers of
nucleoside 3 by photo irradiation was performed on an

6906
M. Endo et al. / Tetrahedron Letters 44 (2003) 6903–6906
12. 1H NMR of 3 [CD3OD (TMS)]; l 7.98 (m, 2H, Ph), 7.80
(d, J=1.4 Hz, 1H, 5), 7.57 (m, 3H, Ph), 7.25 (d, J=1.4
Hz, 1H, 4), 6.96 (t, J=6.5 Hz, 1H, 1%), 4.52 (m, 1H, 3%),
4.03 (m, 1H, 4%), 3.76 (ddd, J=4.1, 11.9, 16.5 Hz, 2H, 5%),
2.52 (m, 2H, 2%). ESI-MS (positive) m/z calcd for
C14H16N4O3Na=311.1; obsd 311.1 [M+Na]+.
13. In the differential NOE spectrum of nucleoside 5 irradi-
ated at C1% proton, 2%H, 4%H, 5H and aromatic protons
were enhanced, which is identical for a b-anomer.
14. 1H NMR of 5 [CD3OD (TMS)]; l 8.00 (m, 2H, Ph), 7.85
(d, J=1.4 Hz, 1H, 5), 7.54 (m, 3H, Ph), 7.27 (d, J=1.4
Hz, 1H, 4), 6.57 (d, J=5.0 Hz, 1H, 1%), 4.40 (t, J=5.0 Hz,
1H, 2%), 4.30 (t, J=4.3 Hz, 1H, 3%), 4.12 (m, 1H, 4%), 3.82
(ddd, J=3.0, 12.2, 27.8 Hz, 1H, 5%). ESI-MS (positive)
m/z calcd for C14H16N4O4Na=327.1; obsd 327.0 [M+
Na]+.
equipped with a circular temperature controller. UV/vis
spectra were obtained at 0°C.
17. The quantum yields for trans to cis isomerization of
nucleoside 3 and 5 were measured at rt referring to the
quantum yields of trans to cis and cis to trans photoiso-
merizations of azobenzene (b=0.14 and 0.42, respec-
tively) as standard.
18. Ronayette, J.; Arnaud, R.; Lebourgeois, P.; Lemaire, J.
Can. J. Chem. 1974, 52, 1848–1857.
19. Thermal isomerizations from cis to trans isomer were
observed. When cis isomers of nucleoside 3 and 5 were
left at 20°C in methanol, the cis isomers slowly went back
to the trans isomers. The rate constants for 3 and 5 are
0.18 h−1 (~1/2=4.0 h) and 0.13 h−1 (~1/2=5.4 h), respec-
tively.
20. Photo irradiation to observe trans to cis isomerization
was performed in a 0.6 mL of CD3OD solution contain-
ing 20 mM of 3 in an NMR tube using a UV transillumi-
nator (UVP LMS-20E; 40 W) at 365 nm on ice.
21. Conversion from the cis to trans isomer was carried out
in the same NMR sample by irradiation using the same
ultra high-pressure mercury lamp with a UV cut-off filter
below 430 nm wavelength (Sigma Koki UTF-50-43Y
cut-off filter).
15. Anzai, J.; Osa, T. Tetrahedron 1994, 50, 4039–4070.
16. Photo irradiation was carried out in a 1.0 mL of
methanoic solution containing 20 mM of nucleoside 3 or
5 by using a 500 W ultra high pressure mercury lamp
(Ushio USH-500D; 500 W) equipped with
a
monochrometor (Ritsuoyo Kogaku MC-10N) which can
control specific wavelength within 4 nm full-width at half
maximum. A quartz cell with 1 cm path length was used
and the sample was cooled to 0°C in a cell holder