Conformational changes of DNA by photoirradiation of DNA-bis(Zn II-cyclen)-azobenzene complex

Article abstract of DOI:10.1080/15257770600684142

Bis(Zn^II-cyclen)-azobenzene derivative, which has two Zn ^II-macrocyclic tetraamine complexes connected through azobenzene spacer, has been synthesized as a cross-linking agent for double stranded DNA in aqueous solution. The Zn^I

Full text of DOI:10.1080/15257770600684142

Nucleosides, Nucleotides, and Nucleic Acids, 25:453–462, 2006
Copyright ꢀC Taylor & Francis Group, LLC
ISSN: 1525-7770 print / 1532-2335 online
DOI: 10.1080/15257770600684142
CONFORMATIONAL CHANGES OF DNA BY PHOTOIRRADIATION
II
OF DNA-BIS(Zn -CYCLEN)-AZOBENZENE COMPLEX
Kenji Maie, Mitsunobu Nakamura, and Kazushige Yamana
2
Department of
Materials Science and Chemistry, University of Hyogo, Hyogo, Japan
II
II
2
Bis(Zn -cyclen)-azobenzene derivative, which has two Zn -macrocyclic tetraamine complexes
connected through azobenzene spacer, has been synthesized as a cross-linking agent for double stranded
II
DNA in aqueous solution. The Zn -cyclen derivative selectively binds to A-T base pairs producing
II
complexes between the Zn -cyclen moiety and the imide-deprotonated thymine with breaking A-T
base pairs. The azobenzene spacer undergoes cis/trans photoisomerization in the complex between
II
the Zn -cyclen derivative and the DNA duplex. The conformation of the DNA remarkably changed
II
by photoisomerization of the azobenzene linker, when the Zn -cyclen derivative binds to the DNA
duplex with an interstrand cross-linking manner.
II
Keywords Zn -cyclen; Azobenzene; Photoisomerization; Conformational change
INTRODUCTION
There is current interest in applications of DNA to the development of
novel functional nano-materials.[1−4] The regulation of DNA structures or
conformation by an external stimulus such as light is an important approach
to extend the scope of the applications.[
5−9]
One such example is the changes
[
6−9]
of DNA hybridization by the covalently attached azo-dyes.
An attractive
alternative approach to generate a photoregulation system involving DNA is
the use of a photoresponsive receptor that can physically bind to DNA.
We have been interested in tetraaza-cyclododecane Zn(II) complexes
II
II
(
Zn -cyclen) and their derivatives, because the Zn -cyclen can strongly bind
to DNA via the coordination of the Zn atom with the thymine base nitrogen
and the hydrogen bonds between the carbonyl group of thymine and the
II
[10−14]
NH groups of Zn -cyclen.
It is therefore anticipated that a designed
Received 28 December 2005; accepted 31 January 2006.
We thank Professor Yoshihisa Inoue, Professor Takehiko Wada, and Dr. Hideo Nishino for technical
advice in CD analyses.
This article is dedicated to Professor Eiko Ohtsuka on the occasion of her 70th birthday.
Address correspondence to Mitsunobu Nakamura and Kazushige Yamana, Department of Materi-
als Science and Chemistry, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2201, Japan. E-mail:
mitunobu@eng.u-hyogo.ac.jp, yamana@eng.u-hyogo.ac.jp
4
53

454
K. Maie et al.
SCHEME 1 Reagents and conditions: (i) 4-nitorobenzyl alcohol, Zn powder, NaOH aq, ethanol, reflux 2h;
◦
◦
(
ii) Br2, triphenyl phosphine, dry acetonitrile, 60 C, 1h; (iii) cyclen, chloroform, 40 C, 12h, HBr; (iv)
Zn(ClO4)2 • 6H2O, ethanol.
II
molecule such as two Zn -cyclens connected with an azobenzene moiety may
act as a photoresponsible cross-linking agent for a DNA. In this report, we
II
describe the synthesis of the (Zn -cyclen)-azobenzene derivatives and their
II
binding to DNA. The conformational changes of the DNA-(bis-Zn -cyclen)-
azobenzene complexes were observed by photo-irradiation.
RESULTS AND DISCUSSION
II
Synthesis of (Zn -Cyclen)-Azobenzene Derivatives
II
II
According to Scheme 1, bis(Zn -cyclen)-azobenzene 1, mono-(Zn -
II
cyclen)-azobenzene 2, and Zn -cyclen 3, whose chemical structures are
shown in Chart I, were prepared. The reductive coupling of 4-nitrobenzyl
ꢁ
alcohol under the basic conditions afforded the 4,4 -hydroxymethyl azoben-
zene 4. After the conversion of the hydroxyl group to the bromine func-
tion, the reaction of 6 with excess amount of cyclen yielded the bis-cyclen
8
. The mono-cyclen 9 was obtained in a similar procedure by using 4-
hydroxymethyl azobenzene 5 that was obtained from the coupling reaction
between 4-nitrobenzyl alcohol and 4-nitrobenzene. The zinc complexes 1
and 2 were obtained as orange crystals from an ethanol solution of 8 and 9
II
treated with an equimolecular amount of Zn(ClO ) • 6H O. Zn -cyclen 3
4
2
2
was prepared from acid free cyclen by treating with Zn(ClO ) • 6H O.
4
2
2
II
Binding of (Zn -Cyclen)-Azobenzene Derivatives
to Double-Helical DNA
II
We first examined the binding of (Zn -cyclen)-azobenzene derivatives
II
1
,2, and Zn -cyclen 3 to the DNA duplexes (I–III), where I and II have
thymine bases at the defined positions, while III has no thymine base
II
(
Chart I). Therefore, with bis(Zn -cyclen)-azobenzene 1, the duplexes I and

II
Photoirradiation of DNA-Bis(Zn -Cyclen)-Azobenzene Complex
455
II may be expected to form interstrand and intrastrand cross-links, respec-
tively. Figure 1 shows the duplex melting curve for I and II in the presence
and absence of 1. The Tm values obtained from the melting studies are
◦
summarized in Table 1. The duplex I melted at 33 C in the absence of 1,
while the addition of an equimolecular amount of 1 to the duplex I low-
◦
◦
ered the T to 28 C. Similar destabilization took place for II in the presence
m
◦
of 1. The T (35 C) of the native DNA II decreased to 24 C upon addi-
m
II
tion of an equimolecular amount of 1. In contrast, the mono(Zn -cyclen)-
azobenzene 2 and Zn -cyclen 3 barely affected the T s of I and II under
II
m
similar conditions. Since it is known that the binding of Zn-cyclen derivatives
to thymine-containing DNA duplexes results in the breakage of A-T base
[
11−13]
pair,
our observations that the significant destabilization of the DNA
duplexes occurred only with the bis-Zn-cyclen 1, not with the mono-cyclen
derivatives, appeared to be consistent with the efficient breakage of at least

456
K. Maie et al.
TABLE 1 Tm of Double Helical DNA (7.16 × 10−6 mol dm ) in the Presence of Cyclen Derivativesa
−3
1
2
3
DNA
duplex Tm/ C [1]/10 mol dm
◦
−6
−3
◦
−6
−3
◦
−6
−3
◦
Tm/ C [2]/10 mol dm
Tm/ C [3]/10 mol dm
Tm/ C
I
II
III
33
35
42
7.16
7.16
7.16
5.80
28
24
42
41
7.16
7.16
30
31
7.16
7.16
31
32
3
a
◦
UV-melting curves monitored at 260 nm were measured with increasing temperature from 0 to 80 C
◦
at a rate of 0.5 C/min.
two A-T base pairs in the duplex DNA. The thermal denaturation studies
thus strongly suggested the cross-linking of our bis-cyclen compound with
multi-thymine-containing DNAs. In the case of intrastrand cross-link of 1 on
DNA, the observed destabilization of DNA is reasonable. Although the in-
terstrand cross-link generally acts as a stabilizer of duplex DNA, the duplex
destabilization observed for DNA I may be due to the significant energy loss
from the base pair breakage and the structural constraint owing to the rigid
aromatic linker.
Since it has been reported that Zn-cyclen derivatives could coordinate
phosphate anions such as the 4-nitorophenyl phosphate dianion in aqueous
[
14]
solution,
bound only to the thymine base without coordinating with the phosphate
the binding of 1 to III was also examined in order to clarify that
1
anion in a DNA main chain. The duplex III exhibited typical transition with
◦
the T at 42 C, and the even addition of excess amounts of 1 did not reduce
m
the T . Therefore, little or no coordination of 1 occurs to the phosphate
m
anion of the DNA main chain in our experimental conditions.
−
6
−3
−6
−3
FIGURE 1 UV melting curves of I (7.16 × 10 mol dm ) (a) and II (7.16 × 10 mol dm ) (b) in
−6
the presence (7.16 × 10 mol dm-3) and absence of compound 1–3 monitored at 260 nm in 0.1 mol
−
3
−3
dm NaNO3 and 0.01 mol dm HEPES, adjusted to pH 7.4.

II
Photoirradiation of DNA-Bis(Zn -Cyclen)-Azobenzene Complex
457
−
6
−3
FIGURE 2 Absorption spectral change of 1 (7.16 × 10 mol dm ) in the complex with I (7.16 ×
−
6
−3
−3
−3
1
0
mol dm ) during UV-irradiation in 0.1 mol dm NaNO3 and 0.01 mol dm HEPES, adjusted to
pH 7.4.
II
Photoisomerization of Bis(Zn -Cyclen)-Azobenzene Bound
to Double-Helical DNA
We next measured the changes in absorption spectra for the complex
of 1 with double-helical DNA under the UV-illumination conditions. The
results are shown in Figure 2. The decrease in the absorption intensity at
3
30 nm and the increase of the intensity at 425 nm were observed with
the isosbestic point at 386 nm. These spectral changes are well consistent
with the trans →cis photoisomerization of an azobenzene derivative. Under
the photo-stationary state that was reached within the short period (1 min)
of the irradiation, the trans to cis isomer ratio was estimated in ca. 20:80.
By the visible light irradiation, the absorption spectrum went back to the
original spectrum obtained before the UV-irradiation. These results prove
that the reversible photoisomerization of 1 occurs in the complex with a DNA
duplex. The photoisomerization of 1 and 2 in the complexes were found to
be similarly effective compared to those of 1 and 2 in the absence of DNAs.
We could not evaluate the stability of the complexes possessing the cis-form
of 1 and 2 by thermal denaturing studies, because of the rapid cis →trans
thermal isomerization.
II
Conformational Changes in DNA-Bis(Zn -Cyclen)-Azobenzene
Complex by Photo Irradiation
The DNA I and II forms a B-form duplex that shows typical CD signal
−
3
−3
in pH 7.4, 0.1 mol dm NaNO and 0.01 mol dm HEPES aqueous solu-
3
tion with positive CDs at 275 and 266 nm, respectively (Figures 3a and 3b).
Unfortunately, the CD signal below 250 nm was perturbed by the HEPES
buffer under the conditions. Upon the addition of 1 to I, the CD signal at

458
K. Maie et al.
−
6
−3
FIGURE 3 Circular dichroism spectra of (a) I (7.16 × 10 mol dm ) in the absence and the presence
−
6
−3
−6
−3
(
7.16 × 10 mol dm ) of 1, (b) I (7.16 × 10 mol dm ) in the absence and the presence (7.16 ×
−
6
−3
−6
−3
1
0
mol dm ) of 2, and (c) II (7.16 × 10 mol dm ) in the absence and the presence of 1, in 0.1
3
−
−3
mol dm NaNO3 and 0.01 mol dm HEPES, adjusted to pH 7.4.
2
75 nm slightly decreased in intensity accompanied with a negative induced
CD around 450 nm due to azobenzene chromophore. With the trans →cis
photoisomerization of 1 in 1-I complex, remarkable changes in CD spec-
trum were induced. The positive CD signal at 275 nm decreased from
2
−1
2
−1
[
σ] = 13, 700 deg cm dmol to 9,900 deg cm dmol , and the negative-
induced CD signal around 451 nm disappeared with appearance of posi-
tive induced CD signal around 420 nm, indicating 1 is capable of modu-
lating the duplex helicity upon photoirradiation (Figure 3a). Similar CD
profiles were observed for II in the presence of 1. The negative induced
peak around 450 nm due to azobenzene chromophore was inverted to posi-
tive peak around 420 nm by photoirradiation; however, the decrease of the
intensity for the positive peak at 266 nm was not as large as those observed in
1
-I (Figure 3b). On the other hand, upon addition of 2 to I, the positive peak
at 275 barely changed and no induced peak appeared around 450 nm. Pho-
toisomerization of 2 in 2-I reduced the positive peak at 275 nm slightly and
induced the weak positive peak around 420 nm (Figure 3c). These results
II
provide that the Zn -cyclen-azobenzene derivatives bind to I and II produc-
ing a complex, and that the photoisomerization of the derivatives in the
complex changes the conformation of the complex. Especially, 1 is capable
of modulating the duplex structure effectively with photoirradiation in 1-I
system. The reverse of the induced CD signal in the region of 450 nm for 1-I
upon photoirradiation would be caused by the changes of the transition mo-
ment of the azobenzene backbone in trans → cis isomerization, and by the
conformational change of the complex; i.e., the cis-azobenzene backbone,
which is not planer structure, would be located out of duplex.
SUMMARY
II
The Zn -cyclen-azobenzene derivatives are capable of binding to the
DNA duplex–containing thymine bases at appropriate positions. The

II
Photoirradiation of DNA-Bis(Zn -Cyclen)-Azobenzene Complex
459
II
reversible isomerization of the Zn -cyclen-azobenzene occurs in the com-
plex with change in the global conformation by photoirradiation. When
II
the bis (Zn -cyclen) derivative binds to a DNA duplex in interstrand
manner, remarkable conformational changes take place with the cis/trans-
photoisomerization of the azobenzene chromophore.
EXPERIMENTAL
General Methods
Melting points were measured with a Yanaco micro melting point appa-
1
ratus and were uncorrected. Furthermore, H NMR spectra were recorded
on a JEOL JNM-EX270 (270 MHz) spectrometer, in which chemical shifts
were determined on the basis of a residual peak of solvent (2.49 for DMSO-
d , or 7.26 for CDCl ). Absorption spectra were recorded on a Hitachi U-
6
3
3
500 spectrophotometer, and CD spectra were obtained on a JASCO 720WI
spectrophotometer.
Preparation of Materials
[
4-(4-Hydroxymethyl-phenylazo)-phenyl]-methanol 4. Zinc powder (4.2 g,
0
0
.064 mol) was slowly added to a mixture of 4-nitrobenzyl alcohol (5.0 g,
.032 mol) and sodium hydroxide (6.4 g) in ethanol (100 mL) with stirring.
The mixture was refluxed for 2 h and then filtered while hot. The precip-
itate was washed with ethanol and the filtrate was evaporated. The residue
was suspended into 6M hydrochloric acid to remove excess zinc powder and
Na ZnO . Crude 4 was then obtained by filtration from the suspension. Re-
2
2
1
crystallization with methanol gave 1.5 g of pure 4 with 39% yield. H NMR
(
(
DMSO) δ = 4.70 (d, J = 5.61 Hz, 4H), 5.49 (t, J = 5.61 Hz, 2H), 7.62
HH
HH
◦
d, J = 8.58 Hz, 4H), 7.95 (d, J = 8.58 Hz, 4H). Mp: 230–231 C.
HH
HH
(
4-Phenylazo-phenyl)-methanol 5. The title compound was prepared by re-
action of 4-nitorobenzyl alcohol (2.0 g, 0.014 mol) and nitrobenzene (1.6 g,
.014 mol) according to the same procedure as 4. Silica gel column chro-
0
1
matography with ethyl acetate (R = 0.6) gave 0.8 g (27%) of pure 5. H NMR
f
(CDCl , Me Si) δ = 1.93 (broad, 1H), 4.89 (s, 2H), 6.83 (d, 8.0 Hz, 2H), 7.19
(
2
3
4
d, J = 8.0 Hz, 2H), 7.24 (dd, J = 8.0, 7.5 Hz, 1H), 7.56 (d, J = 8.0 Hz,
HH
HH
HH
H), 7.97 (d, J = 7.5 Hz, 2H).
HH
Bis-(4-bromomethyl-phenyl)-diazene 6. Bromine (0.33 g, 0.004 mol) was
added to a solution of triphenyl phosphine (1.05 g, 0.004 mol) in dry ace-
tonitrile (30 ml), and to this solution was added the solution of 4 (0.5 g, 0.002
mol) in acetonitrile (10 ml) while vigorously stirring. The reaction mixture
◦
was heated at 60 C for 1 h while stirring. The precipitate was subsequently
1
filtered and recrystallized with ethyl acetate (0.59 g, 80%). H NMR (CDCl ,
3

460
K. Maie et al.
Me Si) δ = 4.56 (s, 4H), 7.55 (d, J = 8.2 Hz, 4H), 7.89 (d, JHH = 8.2 Hz,
4
HH
◦
4
H). Mp: 228–230 C.
4-Bromomethyl-phenyl)-phenyl-diazene 7. The title compound was pre-
(
pared from 0.5 g of 5 according to the same procedure as 6. Recrystallization
1
with ethyl acetate gave 0.48 g of pure 7 (75%). H NMR (CDCl , Me Si)
3
4
δ = 4.79 (s, 2H), 7.06 (d, 8.5 Hz, 2H), 7.72 (d, J = 7.0 Hz, 2H), 7.77 (dd,
HH
J
2
= 7.0, 7.5 Hz, 1H), 8.13 (d, J = 8.5 Hz, 2H), 8.14 (d, J = 7.5 Hz,
HH
HH
HH
◦
H). Mp: 103–105 C.
Bis-[4-(1,4,7,10-tetraaza-cyclododec-1-ylmethylzinc)-phenyl]-diazene octahydro-
bromic acid salt ([8] • 8HBr). To a solution of cyclen (1.8 g 0.011 mol)
in chloroform (40 ml) was added a solution of 6 (0.5 g 0.0014 mol) in
chloroform (15 ml) with stirring at room temperature. The reaction mixture
◦
was heated for 12 h at 40 C, and then washed with two portions of water to
remove excess cyclen. Chloroform was removed under reduced pressure.
The residue was dissolved in ethanol, after which 40% hydrobromic acid was
added to the ethanol solution followed by filtration to remove unreacted
6
6
3
. The title compound was purified by recrystallization with ethanol (1.1 g,
1
8%). H NMR (D O) δ = 2.86 (t, J = 5.50 Hz, 8H), 2.92 (broad, 6H),
2
HH
.06 (t, J = 5.5 Hz, 8H), 3.08 (m, 16H), 3.85 (s, 4H), 7.50 (d, J = 10.0
HH
HH
Hz, 4H), 7.82 (d, J = 10.0 Hz, 4H).
HH
Phenyl-[4-(1,4,7,10-tetraaza-cyclododec-1-ylmethyl)-phenyl]-diazene tetrahydro-
bromic acid salt ([9] • 4HBr). The title compound was prepared from 7
(
0.4 g, 0.0015 mol) according to the same procedure as 8. Crude [9] • 4HBr
1
was recrystallized with ethanol (0.76 g, 73%). H NMR (D O) δ = 2.83 (t,
2
J
8
= 5.50 Hz, 4H), 2.92 (broad, 3H), 3.18 (t, J = 5.50 Hz, 4H), 3.25 (m,
HH
HH
H), 3.97 (s, 2H), 7.02 (d, 8.4 Hz, 2H), 7.34 (d, JHH = 7.0 Hz, 2H), 7.59 (dd,
JHH = 7.0, 7.5 Hz, 1H), 7.64 (d, JHH = 8.4 Hz, 2H), 7.93 (d, J = 7.5 Hz,
HH
2
H).
Bis-[4-(1,4,7,10-tetraaza-cyclododec-1-ylmethylzinc)-phenyl]-diazene
1. An
aqueous solution of the hydrobromic acid salt of 8 (1.1 g) was passed
through anion exchange resin. Acid free 8 (0.47 g) was given after evapora-
tion. Zn(ClO ) • 6H O in ethanol was added to a solution of 8 (0.47 g) in
4
2
2
ethanol. The precipitate was filtered and recrystalized with 0.1 M NaClO4
1
aqueous solution (0.62 g, 67%). H NMR (D O) δ = 2.81 (m, 32H), 3.16
2
(
broad, 6H), 4.02 (s, 4H), 7.51 (d, J = 8.50 Hz, 4H), 7.83 (d, J = 8.50
HH
HH
Hz, 4H).
Phenyl-[4-(1,4,7,10-tetraaza-cyclododec-1-ylmethylzinc)-phenyl]-diazene 2. An
aqueous solution of the hydrobromic salt of 9 (0.76 g) was passed through
anion exchange resin. Acid free 9 (0.39 g) was given after evaporation.
Zn(ClO ) • 6H O in ethanol was added to a solution of 9 (0.39 g) in ethanol.
4
2
2
The precipitate was filtered and recrystallized with 0.1 M NaClO aqueous
4
1
solution (0.46 g, 73%). H NMR (DMSO) δ = 2.62 (t, J = 8.0 Hz, 4H), 2.67
HH
(
t, J = 8.0 Hz, 4H), 2.72 (m, 8H), 3.00 (broad, 3H), 3.95 (s, 2H), 7.45 (d,
HH

II
Photoirradiation of DNA-Bis(Zn -Cyclen)-Azobenzene Complex
461
7
7
.5 Hz, 2H), 7.58 (d, JHH = 9.0 Hz, 2H), 7.61 (dd, J = 9.0, 7.5 Hz, 1H),
HH
.87 (d, JHH = 7.5 Hz, 2H), 7.90 (d, J = 7.5 Hz, 2H).
HH
Preparation of Oligonucleotide Solution for UV Melting
Measurements
Oligonucleotide solutions were prepared using a buffer containing 0.1 M
NaNO and 0.01 M HEPES, adjusted to pH 7.4. Oligonucleotide concentra-
3
tions were determined by absorbance at 260 nm and the calculated single-
[
24]
strand extinction coefficients based on a nearest neighbour model.
Prior
◦
to conducting the melting experiments, the solutions were heated to 80 C,
kept there for 5 min, then gradually cooled down to room temperature. All
duplex melting curves by UV spectra were measured with increasing temper-
◦
◦
ature from 0 to 80 C at a rate of 0.5 C/min.
Photoirradiation Procedure
An aerated sample solution charged in a quartz cell (10 mm × 10 mm)
connected to a Pyrex tube was irradiated using a 300-W, water-cooled
◦
(
20–25 C) high-pressure mercury lamp. For the UV irradiation process, a
Ni(NO ) /Co(NO ) solution in a 10-mm-thick doughnut-type Pyrex cell
3
2
3 2
was used as a band-pass filter (band-pass region; 330–390 nm). For the visible
light irradiation, a K CrO /CuSO solution in a 10-mm-thick doughnut-type
2
4
4
[
25]
Pyrex cell was used as a cut off filter (cut off below 400 nm).
yields were measured as follows. A 3-cm buffer solution of 1 saturated with
The quantum
3
argon gas in a quartz cell was irradiated within 10% conversion. Actinom-
[
25]
etry was carried out using benzophenone and benzhydrol solution.
product yield was determined by absorption spectra.
The
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