observed in the MS/MS for the 54.9-min fractions gives the
same product-ion spectra (MS3, Figure 4e,f). In this regard,
we observed facile losses of NH3 and HNCO from the
modified nucleobase component. These two neutral losses
have been previously found for the fragmentation of proto-
nated uracil.14 The most abundant fragment ion observed in
MS3 is, however, due to the loss of a 71-Da neutral fragment,
which can be attributed to the elimination of both CO and
HNCO. This type of neutral loss was shown to be a very
minor pathway for protonated uracil,14 and this loss from
the cyclic product can be explained from its unique structure
(Scheme S1, Supporting Information).
It is worth noting that similar photochemistry was observed
previously for diphenyl thioether, which, upon UV irradiation
in I2-containing cyclohexane solution under N2 atmosphere,
results in the efficient production of dibenzothiophene.15
Following the mechanism proposed for the formation of
dibenzothiophene,15 we proposed a mechanism for the
formation of the cyclic product (Scheme 3). In this respect,
MS of the two intermediates with that of d(PhSUG) revealed
a markedly decreased formation of the ion of m/z 219, which
is the deprotonated ion of the modified uracil component,
for the two intermediates (Figure S10, Supporting Informa-
tion). These results are in accordance with the saturation of
the uracil moiety in the two intermediates thereby supporting
that the these two intermediates are the two isomeric
dihydrouracil derivatives. As the irradiation time increases,
we observed a gradual increase of d(PhSU*G) with the
concomitant decrease of the two dihydrouracil derivatives
(Figure S9, Supporting Information). This, together with the
fact that 254 nm irradiation of both intermediates can lead
to the formation of d(PhSU*G) (data not shown), supports
that d(PhSU*G) is the secondary product formed from the
two dihydrouracil derivatives (Scheme 3).
To summarize, we synthesized 5-phenylthio-2′-deoxyuri-
dine, incorporated it into ODNs, and showed that the
irradiation of dPhSU-bearing dinucleoside monophosphates
and double-stranded ODNs with 254 nm light can result in
the facile formation of a product with benzothiophene being
fused to the uracil ring. Recent work by Kool and co-
workers16-22 showed that duplex DNA containing a thymine
analogue with increased base-pair size can lead to more stable
duplexes. When compared with the previous synthesis of the
thymidine analogues, the chemistry reported here offered a
more convenient preparation of another class of duplex DNA
with an enlarged π system. In this respect, the improved π
stacking offered by the modified nucleoside may lead to the
formation of more stable duplexes than natural double-
stranded DNA, which may be employed for the sensitive
detection of nucleic acids in vivo.
Scheme 3
photoirradiation can result in the covalent coupling of the
C2 carbon of the phenyl component to the C6 of the uracil
moiety. The resulting coupling product may undergo pho-
tooxidation to give the benzothiophene analogue of the
nucleobase component (Scheme 3).
Acknowledgment. The authors thank the National Insti-
In support of our proposed mechanism, we were able to
isolate two intermediates from the mixture emanating from
shorter periods of irradiation (HPLC traces for the time-
course study are shown in Figure S9, Supporting Informa-
tion). These two intermediates are very likely the dihydro-
uracil derivatives of the dinucleoside monophosphate based
on ESI-MS and MS/MS results (Figure S10, Supporting
Information). In this respect, ESI-MS showed that the
two intermediates shared the same molecular weights as
d(PhSUG) (Figure S10, Supporting Information). Product-ion
spectra of the [M - H]- ions of these two products showed
the facile cleavage of the glycosidic bond of the 5′ nucleoside
to give an ion of m/z 444. Moreover, comparison of the MS/
tutes of Health for supporting this research (R01 CA96906).
Supporting Information Available: NMR spectra of
synthetic compounds, LC traces, MS data, and LC-MS/MS
results. This material is available free of charge via the
OL060659V
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Org. Lett., Vol. 8, No. 12, 2006