close

Вход

Забыли?

вход по аккаунту

?

c7cp06452g

код для вставкиСкачать
PCCP
View Article Online
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
PAPER
Cite this: DOI: 10.1039/c7cp06452g
View Journal
Formation of pyrimidine–pyrimidine type DNA
intrastrand cross-links: a theoretical verification†
Shoushan Wang,
Lishi Wang *b
ab
Min Zhang,a Peng Liu,
a
Shilei Xie,
a
Faliang Cheng*a and
Pyrimidine-type radicals have been demonstrated to be able to attack their 3 0 or 5 0 neighboring purine
nucleotides forming diverse DNA intrastrand cross-links, but whether or not these radicals can attack
their surrounding pyrimidine nucleotides forming pyrimidine–pyrimidine type DNA intrastrand cross-links
remains unclear. To resolve this question, probable additions of the uracil-5-methyl ( UCH2) radical to
the C5QC6 double bond of its 3 0 /5 0 neighboring pyrimidine nucleotides in the four models, 5 0 -T( UCH2)3 0 , 5 0 -C( UCH2)-3 0 , 5 0 -( UCH2)T-3 0 , and 5 0 -( UCH2)C-3 0 , are explored in the present work employing
density functional theory (DFT) methods. The C6 site of its 5 0 neighboring thymidine is the preferred
target for UCH2 radical addition, while additions of the UCH2 radical to the C6 and C5 sites of its 5 0
neighboring deoxycytidine are found to be competitive reactions. The UCH2 radical can react with both
the C6 and C5 sites of its 3 0 neighboring pyrimidine nucleotides, but the efficiencies of these reactions
are predicted to be much lower than those of the corresponding addition reactions to its 5 0 neighboring
pyrimidine nucleotides, indicating the existence of an obvious sequence effect. All the addition products
could be finally transformed into closed-shell intrastrand cross-links, the molecular masses of which are
Received 20th September 2017,
Accepted 29th September 2017
found to be exactly the same as certain MS values determined in a recent study of an X-irradiated
DOI: 10.1039/c7cp06452g
corroborates the fact that the reactive
rsc.li/pccp
nucleotides forming several pyrimidine–pyrimidine type DNA intrastrand cross-links, but also provides a
plausible explanation for the identities of these structurally unknown intrastrand cross-links.
deoxygenated aqueous solution of calf thymus DNA. The present study thus not only definitely
Introduction
Both endogenous Fenton-type reactions and exogenous ionizing
radiation can cause a great deal of DNA damage,1–3 which is
considered to be associated with aging and a variety of human
diseases, including cancer.4–7 Among these lesions, DNA intrastrand cross-links, in which two neighboring nucleobases in the
same strand are tethered together by a single covalent bond,
have attracted great interest due to their important biological
significance. Replication studies in vitro employing numerous
types of replicative and translesional synthesis polymerases
showed that DNA intrastrand cross-links can markedly interrupt
DNA replication or considerably decrease the efficiency and
fidelity of nucleotide incorporation.8–12 Mutational studies in
a
Guangdong Engineering and Technology Research Center for Advanced
Nanomaterials, School of Environment and Civil Engineering,
Dongguan University of Technology, Dongguan 523808,
People’s Republic of China. E-mail: chengfl@dgut.edu.cn
b
School of Chemistry and Chemical Engineering, South China University of
Technology, Guangzhou 510641, People’s Republic of China.
E-mail: wanglsh@scut.edu.cn
† Electronic supplementary information (ESI) available. See DOI: 10.1039/c7cp06452g
This journal is © the Owner Societies 2017
UCH2 radical can attack its 3 0 /5 0 neighboring pyrimidine
mammalian cells and Escherichia coli further confirmed that
DNA intrastrand cross-links can significantly block DNA replication
and induce substantial base transition and transversion
mutations.12–14 On the other hand, UvrABC nuclease (a multienzyme complex in Escherichia coli consisting of the excision
repair proteins UvrA, UvrB, and UvrC) studies demonstrated
that DNA intrastrand cross-links are able to resist, to some
extent, the excision repair of the DNA nucleotide excision repair
system,15–17 and the low repair efficiency was putatively attributed
to the small structural distortion of the DNA double helix
containing an intrastrand cross-link.18–21 Thus, DNA intrastrand cross-links that are not repaired in time are mutagenic
and cytotoxic, which can further lead to apoptotic cell death,
and were proposed to be associated with the pathophysiology of
many human genetic diseases, such as hemochromatosis,
Wilson’s disease, and xeroderma pigmentosa.11,16 But conversely,
in cancer radiotherapy, enhancing the formation of DNA intrastrand
cross-links is greatly helpful for inhibiting cancer cell division and
proliferation, preventing cancer from spreading, and eventually
achieving the goal of cancer cure.
Since the seminal study of Box et al. on the X-irradiated
oxygen-free aqueous solution of d(CpGpTpA) oligomer finding
Phys. Chem. Chem. Phys.
View Article Online
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
Paper
Scheme 1
PCCP
Molecular structures and partial atomic numberings of the uracil-5-methyl radical, thymine, and cytosine.
the G(8-5m)T intrastrand cross-link,22 where the C8 atom of
guanine is covalently linked with the 5-methyl carbon atom of
its 3 0 neighboring thymine, more than 15 tandem lesions have
been identified in the past two decades in aqueous solutions of
DNA fragments with different sizes and in mammalian cells
exposed to ionizing radiation or Fenton-type reagents.3,8,11–14,23–31
Formation of all these DNA intrastrand cross-links was proposed
as a single-radical event. Hydroxyl radicals from Fenton-type
reactions32 or water radiolysis33 can either add to the C5QC6
double bond (related atomic numberings are depicted in
Scheme 1) or abstract a hydrogen atom from the 5-methyl
group of pyrimidine nucleotides forming the corresponding
base-centered secondary radicals, which can then attack their
surrounding purine nucleotides producing diverse DNA intrastrand cross-links.34 This reaction mechanism was definitely
confirmed by UV irradiation experiments of DNA fragments
modified by related photolabile precursors, and many other
DNA intrastrand cross-links were further isolated.10,35–45 However,
one point to be noted is that the type of all these DNA intrastrand
cross-links is either the 50 -purine–pyrimidine-30 or 50 -pyrimidine–
purine-3 0 cross-link, and whether or not the pyrimidine basecentered secondary radicals can attack their surrounding
pyrimidine nucleotides forming pyrimidine–pyrimidine type
DNA intrastrand cross-links remains unclear. The UCH2 radical
was shown to be able to attack the C6 site of thymidine forming
the Tdi adduct in g-irradiated frozen aqueous solutions of
thymidine monophosphate and 5-chloromethyluracil.46 Recently,
several new DNA intrastrand cross-links with their mass spectrometry (MS) values lying in a range 529–543 Da (in comparison,
the molecular masses of the four sequences, 5 0 -TT-3 0 , 5 0 -CC-30 ,
5 0 -TC-3 0 , and 5 0 -CT-3 0 , lie in the range of 515–545 Da) were
detected in X-irradiated oxygen-free aqueous solutions of calf
thymus DNA,31 but as of now, their identities are still unknown.
Solid tumor cells are always in a hypoxic environment,47 and
hypoxic cells were shown to be 2.5–3.0 times less radiosensitive to
ionizing radiation than oxic ones,48 which makes the introduction
of radiosensitizers indispensable in cancer radiotherapy. Although
in vitro studies demonstrated that 5-bromouracil (5-BrU, a
precursor of the uracil-5-yl radical) was a potential radiosensitizer,43,44,49–52 its radiosensitization effects in vivo were
proved to be considerably suppressed.53,54 Furthermore, evident
improvement was not observed in cancer clinical trials employing
5-BrU.55–57 Searching for novel and efficient radiosensitizers is
Phys. Chem. Chem. Phys.
thus justified and urgent. On the grounds of the fact that the
efficiency of the UCH2 radical reacting with its surrounding
purine nucleotides forming the cytotoxic DNA intrastrand crosslinks is greatly higher than that of the uracil-5-yl radical,43,58
radiolabile precursors of the UCH2 radical may be a class of
potentially efficient radiosensitizers. By this token, investigating
the probable formation of the pyrimidine–pyrimidine type DNA
intrastrand cross-links is not only helpful for better understanding of the radiosensitizing action of such precursors, but
also can provide additional materials for the design of novel and
efficient radiosensitizers.
In the present study, probable addition reactions between
the reactive UCH2 radical and the C5 and C6 sites of its 3 0 and 5 0
neighboring pyrimidine nucleotides are investigated. It is
found that the UCH2 radical can add to either site of its 3 0 or
5 0 neighboring pyrimidine nucleotide, and an obvious sequence
effect is predicted, namely the efficiencies of UCH2 radical
addition to its 5 0 neighboring pyrimidine nucleotides are much
higher than those of UCH2 radical addition to its corresponding
3 0 neighboring pyrimidine nucleotides. Detailed results are
presented below.
Computational details
Formation of DNA intrastrand cross-links in simple dinucleoside
monophosphates can be extrapolated to complex systems, such
as oligomers, duplexes, and even cells.8,11–14,23,26–29,31,35–38,40,42–45
In addition, aqueous phase dinucleoside monophosphates were
proved to be relevant models for investigations of DNA intrastrand cross-links.59 Herein, dinucleoside monophosphates were
therefore selected as model compounds to investigate the
possible addition reactions between the UCH2 radical and its
3 0 /5 0 neighboring pyrimidine nucleotides. Initial structures of
the four models, 5 0 -T( UCH2)-3 0 , 5 0 -C( UCH2)-3 0 , 5 0 -( UCH2)T-3 0 ,
and 5 0 -( UCH2)C-3 0 , were constructed on the basis of the three
canonical sequences, 5 0 -TT-3 0 , 5 0 -CT-3 0 , and 5 0 -TC-3 0 , extracted
from an experimental X-ray crystal structure of a B-DNA (PDB
code: 5FMP), by eliminating a hydrogen from the 5-methyl
group of the corresponding thymine moiety, capping the two
phosphodiester bonds with methyl groups,60 and inserting a
sodium ion between the two phosphate oxygens to mimic
physiological conditions.61 The M06-2X functional62 in combination
This journal is © the Owner Societies 2017
View Article Online
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
PCCP
with the standard 6-31G(d,p) basis set was employed for all
geometry optimizations and free energy calculations. The M062X/6-31G(d,p) level of theory was recommended to explore the
structure and/or reactivity of a dinucleoside monophosphate,61
and has been shown to be reliable for studies of DNA intrastrand cross-links.19,63 Frequency analyses were performed to
characterize all structures obtained as minimum points or
first-order saddle points on potential energy surfaces. Intrinsic
reaction coordinate calculations confirmed that each transition
state is connected with its corresponding reactant and product.
The IEF-PCM formalism64 with a dielectric constant e = 78.4 was
used to approximate the solvated environment.59,61 Related
kinetic and thermodynamic characteristics for each reaction
process were estimated on the basis of Gibbs free energies
calculated in the rigid-rotor harmonic oscillator approximation
at T = 298 K and p = 1 atm. Geometry optimizations and free
energy calculations were carried out using the Gaussian 09
package,65 and structures of all stationary points were analysed
employing the X3DNA suite of programs.66
Results and discussion
Addition reactions between the uracil-5-methyl radical and
its 5 0 neighboring thymidine
The proper distances (3.65–3.98 Å, Fig. 1 and 2) from the UCH2
radical center (the C7 atom, related spin density distributions
are depicted in Fig. S2–S9 in the ESI†) separately to the C5 and
Paper
C6 sites of its 5 0 neighboring thymidine make the two sites both
possible targets for UCH2 radical addition. The complete reaction
path for the UCH2 radical addition to the C6 site of its 5 0
neighboring thymidine is depicted in Fig. 1. The distance
(dT/C6–U/C7) between the UCH2/C7 atom and the T/C6 site is
3.65 Å in the optimized 5 0 -T( UCH2)-3 0 canonical sequence,
which is shortened to 2.17 Å in the located transition state
(denoted as TSC6/TU), and eventually reduced to 1.57 Å forming a
standard C–C single bond in the addition product (denoted
as 5 0 - T6H(6-5m)T-3 0 ). Meanwhile, due to the hybridization
transition of both T/C6 and UCH2/C7 atoms from sp2 to sp3,
the C6–C5 and C6–N1 bonds in the 5 0 T moiety and the C7–C5
bond in the 3 0 UCH2 moiety are gradually elongated to 1.49,
1.46, and 1.50 Å in the 5 0 - T6H(6-5m)T-3 0 adduct from values of
1.35, 1.38, and 1.39 Å in the 5 0 -T( UCH2)-30 sequence, respectively.
The other bonds in the 5 0 T/C6 addition process remain relatively
stable with their bond length changes no more than 0.04 Å. In
particular, the stacked base–base arrangement is, to a large
extent, maintained along the reaction path, as illuminated by
the small increase of the angle f (defined as the dihedral angle
between the planes of the two bases in a dinucleotide monophosphate 5 0 -XY-3 0 ) from 141 in the 5 0 -T( UCH2)-3 0 sequence to
401 in the 5 0 - T6H(6-5m)T-3 0 adduct via a value of 211 in the
TSC6/TU state (Fig. 1). Thus, in double stranded DNA, taking
the stabilizing weak interactions (such as hydrogen bonds and
base stacking interactions) into account, formation of the
50 - T6H(6-5m)T-30 adduct is predicted to have only minor influences
on the DNA double helical structure. In fact, a similar behaviour
Fig. 1 Optimized structures and partial structural parameters for stationary points charactering the reaction path of UCH2 radical addition to the C6 site
of its 5 0 neighboring thymidine.
Fig. 2 Optimized structures and partial structural parameters for stationary points characterizing the reaction path of UCH2 radical addition to the C5 site
of its 5 0 neighboring thymidine.
This journal is © the Owner Societies 2017
Phys. Chem. Chem. Phys.
View Article Online
Paper
PCCP
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
Table 1 Related activation free energies (DG*) and reaction free energies
(DG1, DG2, DGt) for the eight possible reactions of UCH2 radical addition to
the C5 and C6 sites of its 3 0 and 5 0 neighboring pyrimidine nucleotides.
Energies are in kcal mol1
Addition
DG1a
DG*
DG2b
DGtc
50
50
30
30
50
50
30
30
—
0.09
0.32
13.97
—
1.29
1.24
10.18
14.24
19.75
23.93
16.10
17.76
18.52
24.50
19.88
2.05
3.55
12.29
3.26
4.94
3.22
13.85
4.61
—
3.46
12.61
10.70
—
4.51
12.61
14.80
a
T/C6
T/C5
T/C5
T/C6
C/C6
C/C5
C/C5
C/C6
DG1 = GIntermediate GCanonical sequence. b DG2 = GAddition product GInc
DGt = GAddition product GCanonical sequence.
termediate.
has already been observed in the reaction path of UCH2 radical
addition to the C8 site of its 5 0 neighboring guanine forming the
5 0 - G8H(8-5m)T-3 0 cross-link.18,58
Related kinetic and thermodynamic characteristics for the
eight possible reactions of UCH2 radical addition to the C5 and
C6 sites of its 3 0 /5 0 neighboring pyrimidine nucleotides are
collectively listed in Table 1. An activation free energy of
14.24 kcal mol1 and a reaction free energy of 2.05 kcal mol1
are calculated for addition of the UCH2 radical to the C6 site of
its 5 0 neighboring thymidine, which indicate that this one-step
5 0 T/C6 addition is kinetically efficient and thermodynamically
slightly favourable. Starting from the 5 0 - T6H(6-5m)T-3 0 adduct,
the hydrogen bonded to the C6 site of the 5 0 T moiety may be
released by direct hydrogen abstraction or via an oxime
intermediate63 producing the final closed-shell 5 0 -T(6-5m)T-3 0
intrastrand cross-link (Fig. S1 and S11 in the ESI,† the reaction
free energy for which is estimated to be 71.29 kcal mol1).
Recently, a structurally unknown tandem lesion with a MS
value of 543 Da was isolated in an X-irradiated deoxygenated
aqueous solution of calf thymus DNA.31 On the basis of the
above discussions and the fact that the molecular mass of
the 5 0 -T(6-5m)T-3 0 cross-link is 543 Da, the MS signal at the
543 Da may thus be partly attributed to the formation of the
5 0 -T(6-5m)T-3 0 intrastrand cross-link.
Apart from the C6 site, the C5 site of the 5 0 T moiety is also a
candidate for UCH2 radical addition, the complete reaction path
is depicted in Fig. 2. Before the 5 0 T/C5 addition step proceeds,
the initial canonical 5 0 -T( UCH2)-3 0 sequence must be firstly
adjusted into an intermediate (denoted as INTC5/TU), where the
distance between the T/C5 site and the UCH2/C7 atom (dT/C5–U/C7)
is shortened to 3.61 Å from 3.98 Å. At the located transition state
(denoted as TSC5/TU) for the 5 0 T/C5 addition step, the distance
dT/C5–U/C7 is decreased to 2.14 Å, and ultimately reduced to 1.58 Å
forming a standard C–C single bond in the addition product
(denoted as 5 0 - U5m(5-5m)T-3 0 ). Similar to the case of 5 0 T/C6
addition, the 5 0 T/C5 addition also makes the hybridization of
both T/C5 and UCH2/C7 atoms evolve from sp2 to sp3. As a
consequence, the C5–C6 and C5–C4 bonds in the 5 0 T moiety and
the C7–C5 bond in the 3 0 UCH2 moiety are elongated to 1.49,
1.52, and 1.50 Å in the 5 0 - U5m(5-5m)T-3 0 adduct from values of
1.35, 1.46, and 1.39 Å in the INTC5/TU intermediate, respectively.
Phys. Chem. Chem. Phys.
The bond length changes of the other bonds are found to be
insignificant (o0.04 Å). Along the 5 0 T/C5 addition path, the
increment of the angle f (16–181, Fig. 2) is relatively small,
indicating that the stacked base–base arrangement remains
nearly complete. Thus, in double stranded DNA, formation of
the 5 0 - U5m(5-5m)T-3 0 adduct has only minor effects on the DNA
double helical structure.
As listed in Table 1, the conformational adjustment from the
canonical 5 0 -T( UCH2)-3 0 sequence to the intermediate INTC5/TU
is thermodynamically slightly favourable (0.09 kcal mol1
reaction free energy). The 5 0 T/C5 addition step needs to overcome an activation free energy of 19.75 kcal mol1, which is ca.
5.5 kcal mol1 higher than that for the 5 0 T/C6 addition. On the
other hand, different from the exothermicity of the 5 0 T/C6
addition, formation of the 5 0 - U5m(5-5m)T-3 0 adduct absorbs a
reaction free energy of ca. 3.5 kcal mol1. Positive reaction free
energies were also reported for reactions of UCH2 radical addition
to the C8 site of its 5 0 neighboring purine nucleotides.18,58,59,67,68
When taking the very negative reaction free energy for the
preceding step of formation of the canonical 5 0 -T( UCH2)-3 0
sequence (27.24 kcal mol1, Fig. S10 in the ESI†) into account,
the driving force for formation of the 5 0 - U5m(5-5m)T-3 0 adduct
is thermodynamically favourable (23.78 kcal mol1). Hence,
based on the above energetics, it is suggested that the UCH2
radical is preferred to attack the C6 site of its 5 0 neighboring
thymidine forming the 5 0 - T6H(6-5m)T-3 0 adduct, with the
attack on the C5 site forming the 5 0 - U5m(5-5m)T-3 0 adduct only
secondary. The adduct 5 0 - U5m(5-5m)T-3 0 may eliminate the
methyl group bonded to the C5 site of the 5 0 T moiety producing
the final closed-shell 5 0 -U(5-5m)T-30 intrastrand cross-link (Fig. S1
and S11 in the ESI,† a reaction free energy of 64.91 kcal mol1 is
estimated). The molecular mass of the 50 -U(5-5m)T-30 intrastrand
cross-link is 529 Da, which is exactly the same as the MS value of a
structurally unknown tandem lesion detected in a recent study of
an X-irradiated deoxygenated aqueous solution of calf thymus
DNA,31 indicating that the MS signal at the 529 Da may be partly
derived from the formation of the 5 0 -U(5-5m)T-3 0 intrastrand
cross-link.
Addition reactions between the uracil-5-methyl radical and its
3 0 neighboring thymidine
Fig. 3 depicts the reaction path of UCH2 radical addition to the
C5 site of its 3 0 neighboring thymidine. A conformational
adjustment from the 5 0 -( UCH2)T-3 0 sequence to an intermediate
(denoted as INTC5/UT) is firstly required before the addition step
proceeds, which makes the distance dT/C5–U/C7 lower to 4.17 Å
from a value of 5.40 Å. The distance dT/C5–U/C7 is further reduced
to 2.13 Å in the located transition state (denoted as TSC5/UT) for
the 3 0 T/C5 addition step, and ultimately decreased to 1.61 Å
forming a C–C single bond in the addition product (denoted as
5 0 -T(5m-5)( U5m)-3 0 ). Transition of the T/C5 and UCH2/C7 atom
hybridizations from sp2 in the INTC5/UT intermediate to sp3 in
the 5 0 -T(5m-5)( U5m)-3 0 adduct elongates the related C5–C6 and
C5–C4 bonds in the 3 0 T moiety and the C7–C5 bond in the 5 0
UCH2 moiety to 1.50, 1.52, and 1.49 Å from 1.35, 1.46, and 1.39
Å, respectively. Insignificant changes (no more than 0.04 Å) are
This journal is © the Owner Societies 2017
View Article Online
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
PCCP
Paper
Fig. 3 Optimized structures and partial structural parameters for stationary points characterizing the reaction path of UCH2 radical addition to the C5 site
of its 3 0 neighboring thymidine.
found for the other bond lengths. Along the 3 0 T/C5 addition
path, the deviation degree of the angle f (Fig. 3) is within the
scope of thermal fluctuation (201),58 indicating that formation
of the 5 0 -T(5m-5)( U5m)-3 0 adduct has nearly negligible effects
on the DNA double helical structure.
Only 0.32 kcal mol1 reaction free energy (Table 1) is required for
the conformational adjustment from the 50 -( UCH2)T-30 canonical
sequence to the INTC5/UT intermediate, which is readily overcome
by the thermal molecular motion. An activation free energy
of 23.93 kcal mol1 is calculated for the 3 0 T/C5 addition step,
4.18 kcal mol1 higher than that for the 5 0 T/C5 addition. On
the other hand, the reaction free energy for formation of the
5 0 -T(5m-5)( U5m)-3 0 adduct is estimated to be ca. 12 kcal mol1
(or ca. 15 kcal mol1 when taking into account the preceding
step of formation of the canonical 5 0 -( UCH2)T-3 0 sequence,
Fig. S10 in the ESI†), which is ca. 9 kcal mol1 larger than that
for formation of the 5 0 - U5m(5-5m)T-3 0 adduct. From the points
of view of these kinetic and thermodynamic characteristics,
addition of the UCH2 radical to the C5 site of its 3 0 neighboring
thymidine is inefficient, and a sequence effect is predicted,
namely addition of the UCH2 radical to the C5 site of its 5 0
neighboring thymidine is much more efficient than that to the C5
site of its 3 0 neighboring thymidine. A similar behaviour has
already been observed in the formation of pyrimidine-type radicals
induced purine–pyrimidine intrastrand cross-links.8,27–29,37,38,42,43
Just like its sequence isomer 5 0 - U5m(5-5m)T-3 0 , the 5 0 -T(5m-5)( U5m)-3 0 adduct may eliminate the methyl group bonded to the
C5 site of the 3 0 T moiety producing the final closed-shell
5 0 -T(5m-5)U-3 0 intrastrand cross-link (Fig. S1 and S11 in the
ESI,† 74.46 kcal mol1 reaction free energy is calculated), the
molecular mass of which is 529 Da. Thus, the formation of
the 5 0 -T(5m-5)U-3 0 intrastrand cross-link may also partly contribute to the MS signal at the 529 Da determined in a recent
study of an X-irradiated deoxygenated aqueous solution of calf
thymus DNA.31
Different from the one-step 5 0 T/C6 addition, as depicted in
Fig. 4, the reaction path of UCH2 radical addition to the C6 site
of its 30 neighboring thymidine is relatively complex. The canonical
5 0 -( UCH2)T-3 0 sequence needs to be firstly transformed into an
intermediate (denoted as INTC6/UT), in which the two base
This journal is © the Owner Societies 2017
moieties are parallel and both adopt a near T-shaped orientation
making the distance dT/C6–U/C7 lower to 4.66 Å. Since this conformational transformation involves, at the same time, rotation
of the two base moieties about their corresponding glycosidic
bonds and twists of DNA backbone around the C30 –O30 , O30 –P,
and P–O50 bonds, efforts on determining the related possible
transition states ultimately failed. Starting from the INTC6/UT
intermediate, the 3 0 T/C6 addition step proceeds. The distance
dT/C6–U/C7 is continuously shortened to 2.19 Å in the located
transition state (denoted as TSC6/UT), and further reduced to
1.56 Å forming a standard C–C single bond in the addition
product (denoted as 5 0 -T(5m-6)( T6H)-3 0 ). Evolution of the T/C6
and UCH2/C7 atom hybridizations and alterations of the C6–C5
and C6–N1 bonds in the 3 0 T moiety and the C7–C5 bond in the 5 0
UCH2 moiety are found to be very analogous to those observed in
the case of 5 0 T/C6 addition. Although the angle f only fluctuates
in a range of 61–461 along the reaction path (Fig. 4), the
prerequisite of a large conformational transformation implies
that, in double stranded DNA, formation of the 5 0 -T(5m-6)( T6H)3 0 adduct may greatly influence the DNA double helical structure.
A reaction free energy of 13.97 kcal mol1 (Table 1) is
calculated for the conformational transformation from the
initial 5 0 -( UCH2)T-3 0 sequence to the INTC6/UT intermediate.
Such a positive reaction free energy requirement is, however,
unsurprising. The thermodynamic characteristic for a similar
structural transformation in the reaction path of UCH2 radical
addition to the C8 site of its 3 0 neighboring deoxyguanosine was
estimated to be 15.11 kcal mol1, yet the final closed-shell T(5m-8)G
intrastrand cross-link has already been isolated.12,24,27,35,36 For
the 3 0 T/C6 addition step, the activation free energy and reaction
free energy are calculated to be 16.10 and 3.26 kcal mol1,
respectively. Though starting from the 5 0 -( UCH2)T-3 0 sequence,
the prerequisite conformational transformation makes the reaction
free energy for formation of the 50 -T(5m-6)( T6H)-30 adduct increase
to 10.70 kcal mol1, taking the preceding step of formation of
the 5 0 -( UCH2)T-3 0 sequence into account (Fig. S10 in the ESI†),
the total driving force for formation of the 5 0 -T(5m-6)( T6H)-3 0
adduct is still thermodynamically favourable (16.76 kcal mol1).
Comparing these energetics with those estimated in the one-step
5 0 T/C6 addition, an obvious sequence effect is predicted,
Phys. Chem. Chem. Phys.
View Article Online
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
Paper
PCCP
Fig. 4 Optimized structures and partial structural parameters for stationary points charactering the reaction path of UCH2 radical addition to the C6 site
of its 3 0 neighboring thymidine.
namely the yield of the 5 0 -T(5m-6)( T6H)-3 0 adduct is much
lower than that of its sequence isomer 5 0 - T6H(6-5m)T-3 0 . The
5 0 -T(5m-6)( T6H)-3 0 adduct may release the hydrogen bonded to
the C6 site of the 3 0 T moiety producing the final closed-shell
5 0 -T(5m-6)T-3 0 intrastrand cross-link (Fig. S1 and S11 in the
ESI,† the reaction free energy for which is calculated to be
74.24 kcal mol1),63 a sequence isomer of the 5 0 -T(6-5m)T-3 0
intrastrand cross-link. Hence, the MS signal at the 543 Da
determined in a recent study of an X-irradiated deoxygenated
aqueous solution of calf thymus DNA31 may also partly stem
from the formation of the 5 0 -T(5m-6)T-3 0 intrastrand cross-link.
Addition reactions between the uracil-5-methyl radical and its
5 0 neighboring deoxycytidine
As depicted in Fig. 5, similar to the 5 0 T/C6 addition, starting
from the canonical 5 0 -C( UCH2)-3 0 sequence, addition of the
UCH2 radical to the C6 site of its 5 0 neighboring deoxycytidine is
also a one-step reaction. The distance (dC/C6–U/C7) between the
UCH2/C7 atom and the C/C6 site is shortened to 2.12 Å in the
located transition state (denoted as TSC6/CU), and ultimately
reduced to 1.57 Å forming a standard C–C single bond in the
addition product (denoted as 5 0 - C6H(6-5m)T-3 0 ). The 5 0 C/C6
addition makes the hybridization of the UCH2/C7 and C/C6
atoms evolve from sp2 to sp3, which induces the C6–C5 and
C6–N1 bonds in the 5 0 C moiety and the C7–C5 bond in the 3 0
UCH2 moiety to gradually elongate to 1.48, 1.46, and 1.50 Å in
the 5 0 - C6H(6-5m)T-3 0 adduct from values of 1.35, 1.36, and
1.39 Å in the canonical 50 -C( UCH2)-3 0 sequence, respectively. The
other bonds are found to remain relatively stable with their
bond length changes no more than 0.04 Å. Due to the small
increase of the angle f from 171 to 381, in double stranded
DNA, formation of the 5 0 - C6H(6-5m)T-3 0 adduct is predicted to
give rise to only minor influences on the DNA double helical
structure.
An activation free energy of 17.76 kcal mol1 and a reaction
free energy of 4.94 kcal mol1 (Table 1) are calculated for this
one-step 5 0 C/C6 addition, and the reaction free energy is
decreased to 21.33 kcal mol1 when considering the preceding
step of formation of the canonical 5 0 -C( UCH2)-3 0 sequence
(Fig. S10 in the ESI†), indicating that formation of the
5 0 - C6H(6-5m)T-3 0 adduct is kinetically feasible and thermodynamically favourable. The 5 0 - C6H(6-5m)T-3 0 adduct may bind
a dissociative hydrogen produced from water radiolysis33 forming
a closed-shell intermediate (denoted as 5 0 -C5,6H(6-5m)T-3 0 ), which
could then be transformed into the final 5 0 -U5,6H(6-5m)T-3 0
intrastrand cross-link via a deamination reaction of the saturated
cytosine moiety (Fig. S1 and S12 in the ESI,† with the driving
force estimated to be 95.47 kcal mol1).24,69 The molecular
mass of the 5 0 -U5,6H(6-5m)T-3 0 intrastrand cross-link is 531 Da,
which is exactly the same as the MS value of a structurally
unidentified tandem lesion determined in a recent study of an
X-irradiated oxygen-free aqueous solution of calf thymus DNA.31
Fig. 5 Optimized structures and partial structural parameters for stationary points charactering the reaction path of UCH2 radical addition to the C6 site
of its 5 0 neighboring deoxycytidine.
Phys. Chem. Chem. Phys.
This journal is © the Owner Societies 2017
View Article Online
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
PCCP
Paper
Fig. 6 Optimized structures and partial structural parameters for stationary points charactering the reaction path of UCH2 radical addition to the C5 site
of its 5 0 neighboring deoxycytidine.
Accordingly, the MS signal at the 531 Da may be partly attributed
to the formation of the 5 0 -U5,6H(6-5m)T-3 0 intrastrand cross-link.
Fig. 6 depicts the reaction path of UCH2 radical addition to
the C5 site of its 5 0 neighboring deoxycytidine. As in the case of
5 0 T/C5 addition, a conformational adjustment of the initial
5 0 -C( UCH2)-3 0 sequence to an intermediate (denoted as INTC5/CU)
is firstly required. The distance (dC/C5–U/C7) between the UCH2/C7
atom and the C/C5 site that is 3.46 Å in the INTC5/CU intermediate
is lowered to 2.11 Å in the located transition state (denoted as
TSC5/CU) for the 5 0 C/C5 addition step, and finally reduced to
1.57 Å forming a standard C–C single bond in the addition
product (denoted as 5 0 - C5H(5-5m)T-30 ). Hybridization transition
of the UCH2/C7 and C/C5 atoms from sp2 in the INTC5/CU intermediate to sp3 in the 5 0 - C5H(5-5m)T-30 adduct makes the related
C5–C6 and C5–C4 bonds in the 5 0 C moiety and the C7–C5 bond in
the 3 0 UCH2 moiety increase to 1.48, 1.51, and 1.50 Å from values
of 1.35, 1.43, and 1.39 Å, respectively. Changes of the other bond
lengths are found to be less than 0.04 Å. The relatively small
deviation (161–281) of the angle f along the 5 0 C/C5 reaction path
implies that formation of the 5 0 - C5H(5-5m)T-3 0 adduct has only
minor effects on the DNA double helical structure.
As listed in Table 1, an activation free energy of 18.52 kcal mol1
is calculated for the 5 0 C/C5 addition step, which is comparable to that for the 5 0 C/C6 addition. On the other hand,
the reaction free energies estimated for formation of the
50 - C5H(5-5m)T-30 adduct (4.51 kcal mol1, and 21.76 kcal mol1
when taking the preceding step of formation of the canonical
5 0 -C( UCH2)-3 0 sequence into account, Fig. S10 in the ESI†) are
also comparable to those (4.94 kcal mol1 and 21.33 kcal
mol1) for formation of the 5 0 - C6H(6-5m)T-3 0 adduct. Thus,
additions of the UCH2 radical to the C5 and C6 sites of its
50 neighboring deoxycytidine are competitive. Just like 50 - C6H(6-5m)T-30 , the 50 - C5H(5-5m)T-30 adduct may finally be transformed
into the closed-shell 50 -U5,6H(5-5m)T-30 intrastrand cross-link via
reactions of hydrogen addition followed by deamination of the
saturated cytosine moiety (Fig. S1 and S12 in the ESI,† a reaction
free energy of 92.60 kcal mol1 is estimated),24,69 the molecular
mass of which is the same as that of the 5 0 -U5,6H(6-5m)T-3 0 crosslink, implying that the MS signal at the 531 Da observed in a
recent study of an X-irradiated oxygen-free aqueous solution of
calf thymus DNA31 may also partly result from the formation of
the 5 0 -U5,6H(5-5m)T-3 0 intrastrand cross-link.
Addition reactions between the uracil-5-methyl radical and its
3 0 neighboring deoxycytidine
The reaction path of UCH2 radical addition to the C5 site of its 3 0
neighboring deoxycytidine is depicted in Fig. 7. A conformational
adjustment from the initial canonical 5 0 -( UCH2)C-3 0 sequence to
an intermediate (denoted as INTC5/UC) making the distance
dC/C5–U/C7 lower to 4.89 Å from a value of 5.39 Å is firstly
required, after which the 3 0 C/C5 addition step proceeds. In
the located transition state (denoted as TSC5/UC), the distance
Fig. 7 Optimized structures and partial structural parameters for stationary points charactering the reaction path of UCH2 radical addition to the C5 site
of its 3 0 neighboring deoxycytidine.
This journal is © the Owner Societies 2017
Phys. Chem. Chem. Phys.
View Article Online
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
Paper
dC/C5–U/C7 is further reduced to 2.11 Å, and eventually shortened
to 1.60 Å forming a C–C single bond in the addition product
(denoted as 5 0 -T(5m-5)( C5H)-3 0 ). The transition of both C/C5
and UCH2/C7 atom hybridizations from sp2 to sp3 makes the
bond length changes of the related C5–C6 and C5–C4 bonds in
the 3 0 C moiety and the C7–C5 bond in the 5 0 UCH2 moiety very
analogous to those observed in the reaction path of 5 0 C/C5
addition. As in the case of 3 0 T/C5 addition, the deviation degree
of the angle f along the reaction path is within the scope of
thermal fluctuation. Formation of the 5 0 -T(5m-5)( C5H)-3 0
adduct in double stranded DNA is thus suggested to have nearly
negligible influences on the DNA double helical structure.
As listed in Table 1, the conformational adjustment from the
canonical 50 -( UCH2)C-3 0 sequence to the intermediate INTC5/UC is
thermodynamically slightly favourable (1.24 kcal mol1 reaction
free energy). An activation free energy of 24.50 kcal mol1 and a
reaction free energy of 12.61 kcal mol1 (or 13.67 kcal mol1
when taking the preceding step of formation of the canonical
5 0 -( UCH2)C-3 0 sequence into account, Fig. S10 in the ESI†) are
estimated for formation of the 5 0 -T(5m-5)( C5H)-3 0 adduct,
which are separately 5.98 and 8.10 (or 8.09) kcal mol1 larger
than those for the case of the 5 0 C/C5 addition. Based on these
energetics, it is predicted that addition of the UCH2 radical to
the C5 site of its 3 0 neighboring deoxycytidine is feasible but
inefficient, and further the efficiency of this reaction is much
lower than that of UCH2 radical addition to the C5 site of its 5 0
neighboring deoxycytidine. The 5 0 -T(5m-5)( C5H)-3 0 adduct
may also capture a dissociative hydrogen forming a closedshell intermediate, which could then be transformed into the
final 5 0 -T(5m-5)U5,6H-3 0 intrastrand cross-link via a deamination
reaction of the saturated cytosine moiety (Fig. S1 and S12 in
the ESI,† with the reaction free energy calculated to be
94.95 kcal mol1).24,69 Therefore, besides its sequence isomer
5 0 -U5,6H(5-5m)T-3 0 , the formation of the 5 0 -T(5m-5)U5,6H-3 0
intrastrand cross-link may also partly contribute to the MS
signal at the 531 Da determined in a recent study of an
X-irradiated oxygen-free aqueous solution of calf thymus DNA.31
A reaction path similar to that of the 3 0 T/C6 addition is
suggested for addition of the UCH2 radical to the C6 site of its 3 0
neighboring deoxycytidine, as depicted in Fig. 8. Before the 3 0
C/C6 addition step, the initial canonical sequence 5 0 -( UCH2)C-3 0
PCCP
must be firstly transformed into an intermediate (denoted as
INTC6/UC), the configuration of which is very analogous to
that of the INTC6/UT intermediate (Fig. 4 and 8). The distance
dC/C6–U/C7, which is reduced to 4.60 Å in the INTC6/UC intermediate, is decreased to 2.13 Å in the located transition state
(denoted as TSC6/UC) for the 3 0 C/C6 addition step, and ultimately lowered to 1.56 Å forming a standard C–C single bond in
the addition product (denoted as 5 0 -T(5m-6)( C6H)-3 0 ). Changes
of the hybridization of both C/C6 and UCH2/C7 atoms and the
bond lengths of the C6–C5 and C6–N1 bonds in the 3 0 C moiety
and the C7–C5 bond in the 5 0 UCH2 moiety are found to be
nearly the same as those observed in the 5 0 C/C6 addition. Along
the reaction path, the angle f fluctuates only in a scope of
7–481, but the prerequisite conformational transformation
involving rotation of the two base moieties about their corresponding glycosidic bonds and twists of DNA backbone around
the C3 0 –O3 0 , O3 0 –P, and P–O5 0 bonds indicates that, in double
stranded DNA, formation of the 5 0 -T(5m-6)( C6H)-3 0 adduct may
give rise to great effects on the DNA double helical structure.
The activation free energy for the 3 0 C/C6 addition step is
calculated to be 19.88 kcal mol1 (Tables 1), 2.12 kcal mol1
higher than that for the 5 0 C/C6 addition. Starting from the
canonical 50 -( UCH2)C-30 sequence, the prerequisite conformational
transformation makes the reaction free energy for formation of the
50 -T(5m-6)( C6H)-30 adduct increase to 14.80 kcal mol1. But when
taking the preceding step of formation of the 50 -( UCH2)C-30
sequence (Fig. S10 in the ESI†) into account, the total driving force
for formation of the 5 0 -T(5m-6)( C6H)-3 0 adduct is thermodynamically favourable, with the total reaction free energy
lower to 11.48 kcal mol1, a value that is 9.85 kcal mol1
larger than that for formation of the 5 0 - C6H(6-5m)T-3 0 adduct.
These structural changes and free energy characteristics manifest
the fact that addition of the UCH2 radical to the C6 site of its 3 0
neighboring deoxycytidine is feasible, but the reaction efficiency
is much lower than that of the UCH2 radical addition to the C6
site of its 5 0 neighboring deoxycytidine, namely an obvious
sequence effect is predicted. The 5 0 -T(5m-6)( C6H)-3 0 adduct
may also be eventually transformed into the 5 0 -T(5m-6)U5,6H-3 0
intrastrand cross-link (a sequence isomer of the 50 -U5,6H(6-5m)T-30
intrastrand cross-link) via reactions of hydrogen addition
followed by deamination of the saturated cytosine moiety
Fig. 8 Optimized structures and partial structural parameters for stationary points charactering the reaction path of UCH2 radical addition to the C6 site
of its 3 0 neighboring deoxycytidine.
Phys. Chem. Chem. Phys.
This journal is © the Owner Societies 2017
View Article Online
PCCP
(Fig. S1 and S12 in the ESI,† 94.38 kcal mol1 reaction free
energy is estimated).24,69 Thus, the MS signal at the 531 Da
detected in a recent study of an X-irradiated oxygen-free aqueous
solution of calf thymus DNA31 may also partly stem from the
formation of the 50 -T(5m-6)U5,6H-30 intrastrand cross-link.
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
Conclusions
At the DFT level of theory, probable addition reactions between
the UCH2 radical and its 3 0 /50 neighboring pyrimidine nucleotides
are explored in the present work. For its 5 0 neighboring thymidine,
the one-step addition to the C6 site is primary, while the addition
to the C5 site is only secondary due to the relatively unfavourable
kinetic and thermodynamic requirements. Additions of the UCH2
radical to the C5 and C6 sites of its 30 neighboring thymidine are
feasible but inefficient, and the efficiencies of both reactions are
predicted to be much lower than those of the corresponding
addition reactions to its 50 neighboring thymidine, indicating
the existence of an obvious sequence effect. Additions of the UCH2
radical to the C5 and C6 sites of its 50 neighboring deoxycytidine
are competitive reactions, and a sequence effect is also predicted,
namely the reaction efficiencies of the UCH2 radical addition to the
C5 and C6 sites of its 50 neighboring deoxycytidine are much higher
than those of the UCH2 radical addition to the C5 and C6 sites of its
30 neighboring deoxycytidine. The above addition products could
be eventually transformed into closed-shell intrastrand cross-links,
the molecular masses of which are found to be well consistent with
certain MS values of several structurally unknown tandem lesions
detected in a recent study of an X-irradiated deoxygenated aqueous
solution of calf thymus DNA.31 All current results definitely verify
that the uracil-5-methyl radical can attack its 30 /5 0 neighboring
pyrimidine nucleotides forming the pyrimidine–pyrimidine type
DNA intrastrand cross-links, and further can offer some valuable
insights into the identities of these experimentally unidentified
tandem lesions. The present study thus broadens our knowledge
about the possible types of DNA intrastrand cross-links, provides
additional materials for the design of novel and efficient radiosensitizers, and may be helpful for better understanding of the
pathophysiology of human genetic diseases.
Conflicts of interest
There are no conflicts to declare.
Acknowledgements
This work was supported by the China Postdoctoral Science
Foundation (No. 2016M602455), the National Natural Science
Foundation of China (No. 21375016, 21475022, and 21505019),
the Natural Science Foundation of Guangdong Province (No.
2015A030310272), the Technology Planning Project of Guangdong
Province (No. 2015B090927007), the Guangdong Provincial
Key Platform and Major Scientific Research Projects for
Colleges and Universities (No. 2014KZDXM073, 2015KCXTD029,
2016KTSCX136).
This journal is © the Owner Societies 2017
Paper
Notes and references
1 S. Steenken, Chem. Rev., 1989, 89, 503.
2 M. D. Evans, M. Dizdaroglu and M. S. Cooke, Mutat. Res.,
2004, 567, 1.
3 Y. Wang, Chem. Res. Toxicol., 2008, 21, 276.
4 M. A. Lovell, S. Soman and M. A. Bradley, Mech. Ageing Dev.,
2011, 132, 443.
5 K. Satoh, B. C. Berk and H. Shimokawa, Nitric Oxide, 2011,
25, 211.
6 T. B. Kryston, A. B. Georgiev, P. Pissis and A. G. Georgakilas,
Mutat. Res., 2011, 711, 193.
7 A. Kotsinas, V. Aggarwal, E. J. Tan, B. Levy and V. G. Gorgoulis,
Cancer Lett., 2012, 327, 97.
8 C. Gu and Y. Wang, Biochemistry, 2004, 43, 6745.
9 C. Gu and Y. Wang, Biochemistry, 2005, 44, 8883.
10 S. Bellon, D. Gasparutto, C. Saint-Pierre and J. Cadet, Org.
Biomol. Chem., 2006, 4, 3831.
11 Y. Jiang, H. Hong, H. Cao and Y. Wang, Biochemistry, 2007,
46, 12757.
12 L. C. Colis, P. Raychaudhury and A. K. Basu, Biochemistry,
2008, 47, 8070.
13 H. Hong, H. Cao and Y. Wang, Nucleic Acids Res., 2007,
35, 7118.
14 P. Raychaudhury and A. K. Basu, Biochemistry, 2011,
50, 2330.
15 Z. Yang, L. C. Colis, A. K. Basu and Y. Zou, Chem. Res.
Toxicol., 2005, 18, 1339.
16 C. Gu, Q. Zhang, Z. Yang, Y. Wang, Y. Zou and Y. Wang,
Biochemistry, 2006, 45, 10739.
17 I. Talhaoui, V. Shafirovich, Z. Liu, C. Saint-Pierre, Z. Akishev,
B. T. Matkarimov, D. Gasparutto, N. E. Geacintov and
M. Saparbaev, J. Biol. Chem., 2015, 290, 14610.
18 J. Garrec, C. Patel, U. Rothlisberger and E. Dumont, J. Am.
Chem. Soc., 2012, 134, 2111.
19 C. D. M. Churchill, L. A. Eriksson and S. D. Wetmore, Chem.
Res. Toxicol., 2011, 24, 2189.
20 E. Dumont, T. Dršata, C. F. Guerra and F. Lankaš, Biochemistry, 2015, 54, 1259.
21 C. D. M. Churchill, L. A. Eriksson and S. D. Wetmore,
J. Phys. Chem. B, 2016, 120, 1195.
22 H. C. Box, E. E. Budzinski, J. D. Dawidzik, J. C. Wallace,
M. S. Evans and J. S. Gobey, Radiat. Res., 1996, 145, 641.
23 H. C. Box, E. E. Budzinski, J. B. Dawidzik, J. S. Gobey and
H. G. Freund, Free Radical Biol. Med., 1997, 23, 1021.
24 H. C. Box, E. E. Budzinski, J. B. Dawidzik, J. C. Wallace and
H. Iijima, Radiat. Res., 1998, 149, 433.
25 H. C. Box, H. B. Patrzyc, J. B. Dawidzik, J. C. Wallace,
H. G. Freund, H. Iijima and E. E. Budzinski, Radiat. Res.,
2000, 153, 442.
26 H. C. Box, J. B. Dawidzik and E. E. Budzinski, Free Radical
Biol. Med., 2001, 31, 856.
27 S. Bellon, J. L. Ravanat, D. Gasparutto and J. Cadet, Chem.
Res. Toxicol., 2002, 15, 598.
28 H. Hong, H. Cao, Y. Wang and Y. Wang, Chem. Res. Toxicol.,
2006, 19, 614.
Phys. Chem. Chem. Phys.
View Article Online
Published on 03 October 2017. Downloaded by Griffith University on 26/10/2017 04:39:57.
Paper
29 H. Cao and Y. Wang, Nucleic Acids Res., 2007, 35, 4833.
30 J. Wang, H. Cao, C. You, B. Yuan, R. Bahde, S. Gupta,
C. Nishigori, L. J. Niedernhofer, P. J. Brooks and Y. Wang,
Nucleic Acids Res., 2012, 40, 7368.
31 H. B. Patrzyc, J. B. Dawidzik, E. E. Budzinski, H. G. Freund,
J. H. Wilton and H. C. Box, Radiat. Res., 2012, 178, 538.
32 E. S. Henle and S. Linn, J. Biol. Chem., 1997, 272, 19095.
33 B. G. Ershov and A. V. Gordeev, Radiat. Phys. Chem., 2008,
77, 928.
34 M. Dizdaroglu and P. Jaruga, Free Radical Res., 2012, 46, 382.
35 A. Romieu, S. Bellon, D. Gasparutto and J. Cadet, Org. Lett.,
2000, 2, 1085.
36 S. Bellon, D. Gasparutto, A. Romieu and J. Cadet, Nucleosides,
Nucleotides Nucleic Acids, 2001, 20, 967.
37 Q. Zhang and Y. Wang, J. Am. Chem. Soc., 2003, 125, 12795.
38 Y. Zeng and Y. Wang, J. Am. Chem. Soc., 2004, 126, 6552.
39 Q. Zhang and Y. Wang, J. Am. Chem. Soc., 2004, 126, 13287.
40 H. Hong and Y. Wang, J. Am. Chem. Soc., 2005, 127, 13969.
41 Q. Zhang and Y. Wang, Chem. Res. Toxicol., 2005, 18, 1897.
42 Q. Zhang and Y. Wang, Nucleic Acids Res., 2005, 33, 1593.
43 Y. Zeng and Y. Wang, Nucleic Acids Res., 2006, 34, 6521.
44 Y. Zeng and Y. Wang, Biochemistry, 2007, 46, 8189.
45 G. Lin, J. Zhang, Y. Zeng, H. Luo and Y. Wang, Biochemistry,
2010, 49, 2346.
46 Y. R. Wang and W. M. D. Sevilla, Int. J. Radiat. Biol., 1997,
71, 387.
47 B. T. Oronsky, S. J. Knox and J. Scicinski, Transl. Oncol.,
2011, 4, 189.
48 A. Das- u and J. Denekamp, Radiother. Oncol., 1998, 46, 269.
49 L. Chomicz, J. Rak and P. Storoniak, J. Phys. Chem. B, 2012,
116, 5612.
50 S. Wang, P. Zhao, C. Zhang and Y. Bu, J. Phys. Chem. B, 2016,
120, 2649.
51 Y. Park, K. Polska, J. Rak, J. R. Wagner and L. Sanche,
J. Phys. Chem. B, 2012, 116, 9676.
52 K. Westphal, J. Wiczk, J. Miloch, G. Kciuk, K. Bobrowski and
J. Rak, Org. Biomol. Chem., 2015, 13, 10362.
53 S. Cecchini, S. Girouard, M. A. Huels, L. Sanche and
D. J. Hunting, Radiat. Res., 2004, 162, 604.
54 S. Cecchini, S. Girouard, M. A. Huels, L. Sanche and
D. J. Hunting, Biochemistry, 2005, 44, 1932.
55 M. D. Groves, M. H. Maor, C. Meyers, A. P. Kyritsis, K. A. Jaeckle,
W. K. A. Yung, R. E. Sawaya, K. Hess, J. M. Bruner, P. Peterson
and V. A. Levin, Int. J. Radiat. Oncol., Biol., Phys., 1999, 45, 127.
Phys. Chem. Chem. Phys.
PCCP
56 M. D. Prados, C. Scott, H. Sandler, J. C. Buckner, T. Phillips,
C. Schultz, R. Urtasun, R. Davis, P. Gutin, T. L. Cascino,
H. S. Greenberg and W. J. Curran Jr, Int. J. Radiat. Oncol.,
Biol., Phys., 1999, 45, 1109.
57 M. D. Prados, W. Seiferheld, H. M. Sandler, J. C. Buckner,
T. Phillips, C. Schultz, R. Urtasun, R. Davis, P. Gutin,
T. L. Cascino, H. S. Greenberg and W. J. Curran Jr, Int.
J. Radiat. Oncol., Biol., Phys., 2004, 58, 1147.
58 C. Patel, J. Garrec, C. Dupont and E. Dumont, Biochemistry,
2013, 52, 425.
59 J. Garrec and E. Dumont, Chem. Res. Toxicol., 2014, 27, 1133.
60 C. Dupont, C. Patel and E. Dumont, J. Phys. Chem. B, 2011,
115, 15138.
61 C. D. M. Churchill and S. D. Wetmore, Phys. Chem. Chem.
Phys., 2011, 13, 16373.
62 Y. Zhao and D. G. Truhlar, Theor. Chem. Acc., 2008, 120, 215.
63 J. P. Cerón-Carrasco, D. Jacquemin and E. Dumont, J. Phys.
Chem. B, 2013, 117, 16397.
64 G. Scalmania and M. J. Frisch, J. Chem. Phys., 2010, 132, 114110.
65 M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria,
M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone,
B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato,
X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng,
J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda,
J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao,
H. Nakai, T. Vreven, J. A. Montgomery, Jr, J. E. Peralta, F. Ogliaro,
M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov,
T. Keith, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell,
J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega,
J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken,
C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann,
O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L.
Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador,
J. J. Dannenberg, S. Dapprich, A. D. Daniels, O. Farkas,
J. B. Foresman, J. V. Ortiz, J. Cioslowski and D. J. Fox, Gaussian
09, Revision E.01, Gaussian, Inc., Wallingford CT, 2013.
66 X. J. Lu, H. J. Bussemaker and W. K. Olson, Nucleic Acids
Res., 2015, 43, e142.
67 B. Xerri, C. Morell, A. Grand, J. Cadet, P. Cimino and
V. Barone, Org. Biomol. Chem., 2006, 4, 3986.
68 V. Labet, C. Morell, A. Grand, J. Cadet, P. Cimino and
V. Barone, Org. Biomol. Chem., 2008, 6, 3300.
69 M. Polverelli and R. Teoule, Z. Naturforsch., C: J. Biosci.,
1974, 29, 16.
This journal is © the Owner Societies 2017
Документ
Категория
Без категории
Просмотров
2
Размер файла
2 772 Кб
Теги
c7cp06452g
1/--страниц
Пожаловаться на содержимое документа