Regulation of one-electron oxidation rate of guanine and hole transfer rate in DNA through hydrogen bonding

Article abstract of DOI:10.1016/S0040-4039(02)01949-4

The effects of methyl and bromo groups at C5 of C on the one-electron oxidation rate of G, and on the hole transfer rate in DNA have been investigated. The rates of one-electron oxidation of G and hole transfer from Py^·+ to 8-oxo-7,8-dihydrogua

Full text of DOI:10.1016/S0040-4039(02)01949-4

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 43 (2002) 8083–8085
Regulation of one-electron oxidation rate of guanine and hole
transfer rate in DNA through hydrogen bonding
Kiyohiko Kawai,* Tadao Takada, Sachiko Tojo and Tetsuro Majima*
The Institute of Scientific and Industrial Research (SANKEN), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047,
Japan
Received 17 June 2002; revised 7 August 2002; accepted 10 September 2002
Abstract—The effects of methyl and bromo groups at C5 of C on the one-electron oxidation rate of G, and on the hole transfer
+
’
rate in DNA have been investigated. The rates of one-electron oxidation of G and hole transfer from Py to 8-oxo-7,8-dihy-
droguanine were suppressed and enhanced by introducing bromo and methyl groups, respectively, on the C at the complementary
strand. © 2002 Elsevier Science Ltd. All rights reserved.
One-electron oxidation of DNA leads to formation of
the radical cation of G (G ), the nucleobase with the
strated to be useful in making an ionization potential
gradient in DNA.5 Since ionization potential of G is
highly dependent on the flanking sequences, it is also
possible to design a DNA sequence in which hole flows
in one direction.6–9 Recently, from the experiment in
dichloromethane, we have demonstrated that the oxida-
tion potential of G can be controlled by introducing a
substituent on base pairing cytosine (C).10,11 When a
methyl group was introduced as an electron donating
group at C5 of cytosine (mC), the one-electron oxida-
tion rate of G in G:mC base pair was accelerated. On
the other hand, bromo substituent on C as an electron
withdrawing group (brC) lead to the suppression of the
one-electron oxidation rate of G in G:brC base pair.
Here, in order to regulate the hole transfer rate and
ultimate oxidation site in DNA, the effects of methyl
and bromo groups at C5 of C on the one-electron
oxidation rate of G, and the hole transfer rate in DNA
have been investigated.
+
’
lowest ionization potential, which migrates via a multi-
step hopping in DNA. In the last 5 years, occurrence of
,
the long range hole transfer through DNA up to 200 A
has been demonstrated by Giese,1 Schuster2 and Bar-
ton.3 If the hole flow in DNA could be artificially
controlled to deposit at the desired site in DNA, it may
enable site-selective oxidation and strand scission of
DNA which is desired from a therapeutical point of
view. Furthermore, the regulation of the transfer rate
and direction of the hole generated in DNA is of
interest from the perspective of using DNA as a build-
ing block for electronic devices.4 Several G derivatives
with different ionization potential have been demon-
13-Mer oligodeoxynucleotides (ODNs) containing C
(ODN-C), mC (ODN-mC), or brC (ODN-brC) as com-
plementary base for G were synthesized. For the one-
electron oxidation of G, naphthalimide (NI) was
selected as a photosensitizer (Scheme 1).9,12–14 In the
presence of NI, ODN was photo-irradiated with a
high-pressure Hg lamp. A 330 nm cutoff filter was used
so that all the light was absorbed by the sensitizer but
not by the ODN. After photo-irradiation, photooxi-
dized ODNs were digested with sv P. D. E./P1 nucle-
ase/AP and the consumption of G was quantified by
HPLC (Table 1).15 Interestingly, lower consumption of
G was observed for ODN-brC compared with those of
ODN-C and ODN-mC. The one-electron oxidation of
Scheme 1. Chemical structure of NI and mechanistic scheme
for photosensitized one-electron oxidation of ODN.
Keywords: DNA; hydrogen bonding; one-electron oxidation; hole
transfer.
* Corresponding authors. Tel.: +81-6-6879-8496; fax: +81-6-6879-
8499; e-mail: kiyohiko@sanken.osaka-u.ac.jp; majima@sanken.
osaka-u.ac.jp
0040-4039/02/$ - see front matter © 2002 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(02)01949-4

8084
K. Kawai et al. / Tetrahedron Letters 43 (2002) 8083–8085
Table 1. Consumption of G in the photosensitized one-
electron oxidation of ODNsa
ODN
Sequence
−G (%)
4.7
ODN-mC
ODN-C
ODN-brC
5%-TGTGTGTGTGTGT
3%-AmCAmCAmCAmCAmCAmCA
5%-TGTGTGTGTGTGT
3%-ACACACACACACA
5%-TGTGTGTGTGTGT
5.2
1.4
3%-AbrCAbrCAbrCAbrCAbrCAbrCA
a Each of the reaction mixtures containing ODN (0.04 mM strand
conc.) and NI (0.1 mM) in pH 7.0 sodium cacodylate buffer (20
mM) was photo-irradiated with a high-pressure Hg lamp fitted with
a 330 nm cutoff filter for 20 min. The reaction mixture was directly
subjected to enzymatic digestion with snake venom P. D. E., P1
nuclease and alkaline phosphatase and the consumption of G was
quantified by reverse phase HPLC.
Scheme 2. Mechanistic scheme for generation of oxidizing
reagent SO4 during pulse radiolysis, hole generation and
transfer in Py and oxG containing ODN.
−
’
versus NHE in CH3CN), hole transfer occurs from
+
16
+
’
’
pyrene radical cation (Py ) to oxG. Py was gener-
ated from one-electron oxidation during the pulse radi-
olysis in the presence of K2S2O8, and the hole transfer
G can occur either with NI in the singlet excited state
(1NI*) or with NI in the triplet excited state (3NI*).13,14
One-electron oxidation process via NI* was studied by
+
’
from Py to oxG in DNA was monitored by the
+
1
’
time-resolved transient absorption of Py as has been
+
’
previously reported (Scheme 2).16,17 Decays of Py ,
steady-state fluorescence quenching experiment (Fig.
1A). G selectively quenched the fluorescence intensity
of NI, while moderate quenching was observed for C,
mC, and brC with a similar extent. Triplet quenching
experiments clearly show the selective quenching of
3NI* by G as shown in Fig. 1B. These results preclude
which correspond to the hole transfer from Py + to oxG
’
(Scheme 2 path b), were single exponential and the rate
constants (kobs) were listed in Table 2. Slightly faster
and slower hole transfer rates were observed for
PyODN-mC and PyODN-brC, respectively, compared
to PyODN-C. It is demonstrated that the hole transfer
rate in DNA can be regulated by introducing methyl
and bromo groups at the C5 of C.
1
3
the efficient quenching of either NI* or NI* by brC
compared to those of C. Thus, it is clearly demon-
strated that the oxidation potential of G is higher in
G:brC base pair than in G:C base pair in DNA.
Slightly lower consumption of G in the case of ODN-
mC compared to that of ODN-C may be explained by
the alteration of the interaction between NI and ODN
due to the methyl group at cytosine C5. Since methyl
and bromo groups are similar in size, such a mechanism
may also contribute to the lower consumption of G
observed in the case of ODN-brC to some extent.
Differences between the oxidation potentials of G:C
base pair and G:mC or G:brC were estimated to be
+
0.01–0.03 V.10 In the case of the hole transfer from Py
’
to oxG studied here, the high driving force (ca. −0.4 V)
lead to the moderate effect of methyl and bromo
groups on the hole transfer rate. However, these sub-
stituents may exert significant effects on the equilibrium
+
+
’
+
’
’
between G :C and G :mC, and G :brC in DNA
(Scheme 3).18–20
Next, in order to regulate the hole transfer in DNA,
pulse radiolyses of pyrene (Py) and 8-oxo-7,8-dihy-
droguanine (oxG) containing ODNs with C (PyODN-
C), mC (PyODN-mC), or brC (PyODN-brC) as the
complementary base for oxG were performed. Since the
oxidation potential of pyrene (E°=1.40 V versus NHE
in CH3CN) is higher than that of oxG (E°=1.09 V
In the present study, suppression of the one-electron
oxidation rate of G in the G:brC base pair, and the
acceleration and suppression of hole transfer rate from
+
’
Py to 8-oxo-7,8-dihydroguanine was demonstrated by
introducing methyl and bromo groups on C, respec-
Figure 1. (A) Fluorescence quenching (uex=360 nm) of NI (5 mM) by C, mC, brC and G (8 mM). (B) Time profiles of transient
absorption monitored at 475 nm upon 355 nm excitation of Ar-saturated aqueous solution of NI (40 mM) in the presence of C,
mC, brC and G (5 mM), respectively. (C) Time profiles of transient absorption monitored at 470 nm for PyODN-C during pulse
radiolysis. The measurements conditions were shown in Table 2.

K. Kawai et al. / Tetrahedron Letters 43 (2002) 8083–8085
Table 2. Observed rate constant of the hole transfer (kobs
8085
)
1999, 6, 85.
+
from Py to oxG for Py and oxG containing ODNsa
’
4. Porath, D.; Bezryadin, A.; de Vries, S.; Dekker, C.
Nature 2000, 403, 635.
5. Nakatani, K.; Dohno, C.; Saito, I. J. Am. Chem. Soc.
2000, 122, 5893.
6. Nakatani, K.; Dohno, C.; Saito, I. J. Am. Chem. Soc.
1999, 121, 10854.
7. Meggers, E.; Michel-Beyerle, M. E.; Giese, B. J. Am.
Chem. Soc. 1998, 120, 12950.
ODN
Sequence
kobs (104 s−1
)
PyODN-mC
PyODN-C
PyODN-brC
5%-Py-AAmCACACACAAAA 13
3%-TToxGTGTGTGTTTT
5%-Py-AACACACACAAAA
3%-TToxGTGTGTGTTTT
5%-Py-AAbrCACACACAAAA
3%-TToxGTGTGTGTTTT
11
9.7
8. Sugiyama, H.; Saito, I. J. Am. Chem. Soc. 1996, 118,
7063.
a Pulse radiolysis was carried out in an Ar-saturated aqueous solution
containing 10 mM K2S2O8, 100 mM t-BuOH, 50 mM pH 7.0 Na
phosphate buffer, and 0.2 mM (strand conc.) ODN.
9. Saito, I.; Takayama, M.; Sugiyama, H.; Nakatani, K.;
Tsuchida, A.; Yamamoto, M. J. Am. Chem. Soc. 1995,
117, 6406.
10. Kawai, K.; Wata, Y.; Hara, M.; Tojo, S.; Majima, T. J.
Am. Chem. Soc. 2002, 124, 3586.
11. Kawai, K.; Wata, Y.; Ichinose, N.; Majima, T. Angew.
Chem., Int. Ed. 2000, 39, 4327.
12. Rogers, J. E.; Abraham, B.; Rostkowski, A.; Kelly, L. A.
Photochem. Photobiol. 2001, 74, 521.
13. Rogers, J. E.; Weiss, S. J.; Kelly, L. A. J. Am. Chem. Soc.
2000, 122, 427.
14. Rogers, J. E.; Kelly, L. A. J. Am. Chem. Soc. 1999, 121,
3854.
Scheme 3. Schematic representation of hole transfer, site
selective oxidation, and strand scission.
15. When enzymatic digestion was performed at 4°C, 2-
aminoimidazolone was identified as a guanine oxidation
product. See: Kino, K.; Saito, I.; Sugiyama, H. J. Am.
Chem. Soc. 1998, 120, 7373.
16. Kawai, K.; Takada, T.; Tojo, S.; Ichinose, N.; Majima,
T. J. Am. Chem. Soc. 2001, 123, 12688.
tively. Our results suggest that the direction of the hole
transfer and ultimate oxidation site in DNA may be
controlled by introducing a substituent on cytosine.
17. Kawai, K.; Takada, T.; Tojo, S.; Majima, T. Tetrahedron
Lett. 2002, 43, 89.
Acknowledgements
18. For comparison, differences between the oxidation poten-
tials of G in the G and GG sequences is about 0.05 V.
See: Lewis, F. D.; Liu, X. Y.; Liu, J. Q.; Hayes, R. T.;
Wasielewski, M. R. J. Am. Chem. Soc. 2000, 122, 12037.
19. Not only the hole transfer rate but also the hole trapping
rate determines the oxidation site of DNA. Nakatani, K.;
Dohno, C.; Saito, I. J. Am. Chem. Soc. 2001, 123, 9681
(however, there is no direct measurement of the hole
trapping rate of G or G in the GG, and GGG sequences
in DNA).
We thank the members of the Radiation Laboratory of
SANKEN, Osaka University for running the linear
accelerator. This work has been partly supported by a
Grant-in-Aid for Scientific Research from Ministry of
Education, Science, Sport and Culture of Japan.
References
20. Regulation of the hole transfer rate by hydrogen bonding
to protein was recently reported. See: Nakatani, K.;
Dohno, C.; Ogawa, A.; Saito, I. Chem. Biol. 2002, 9, 361.
1. Giese, B. Acc. Chem. Res. 2000, 33, 631.
2. Schuster, G. B. Acc. Chem. Res. 2000, 33, 253.
3. Nunez, M. E.; Hall, D. B.; Barton, J. K. Chem. Biol.