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Calculated strand breaks from 125I in coiled DNA
TIM GOORLEY1, MICHEL TERRISSOL2, & HOOSHANG NIKJOO3
1Department of Nuclear Engineering, Massachusetts Institute of Technology, USA, 2Laplace, Universite Paul Sabatier,
Toulouse, France, and 3Radiation Biophysics Group, Medical Radiation Physics, Karolinska Institute, Stockholm, Sweden
(Received 2 February 2008; revised 9 September 2008; accepted 15 September 2008)
AbstractPurpose: DNA single strand breaks (SSB) and double-strand breaks (DSB) induced by Auger electrons from incorporated125I decay were calculated using a B-DNA model to assess contributions from direct and OH damage and effects of higher-order structure. Three decay sites, linker DNA, nucleosome, and two adjacent nucleosomes, were assessed and compared toexperimental data.Method: A Monte Carlo track structure code for electron was used to track electrons, OH and H radicals through linear anda higher-order model of B-DNA. Direct and indirect DNA hits were scored and used to determine SSB and DSB.Results: The three different 125I decay locations produced different number of DSBs and fraction of radical damage. Theaverage number of DSB per 125I decay was 0.83, 0.86 and 1.33, respectively, for the three sites. OH radicalattack contributed to or exclusively caused 70%, 57%, and 50%, of the DSBs located in the entire model. When only10 base pairs on either side of the incorporation site were considered, radical damage contributions were 40%, 25% and67%, respectively. Locations distant from the site of incorporation, however, consistently yielded 70–80% of the DSB fromradical attack.Conclusions: Coiling of DNA can greatly change both the absolute number of DSB per incorporated 125I decay and therelative contributions of radical damage to the local site of decay and, to a lesser extent, the average over all DNA. Higherorder structure only slightly affects the number and quality of DNA damage to distant locations, which is mostly from radicalattack.
Keywords: Auger electron, Monte Carlo, track structure, 125I, DNA damage, direct and indirect damage
Introduction
Experimental research in radiation biology, particu-
larly DNA damage, has used 125I extensively. With
its short range and high-LET emissions, the 125I
Auger cascade electrons have been used to probe the
radiosensitivity of specific sub-cellular targets. Early
experiments were focused on targeting the nucleus
and DNA, but now specific genes can be targeted,
and 125I anti-gene radiotherapy investigations for
breast cancer (Nakamoto and Saga 2000), and
thyroid carcinoma (Haberkorn and Henze 2001)
are underway. Even though 125I and other Auger
cascade emitting radioisotopes are being investigated
for advanced therapies, several fundamental ques-
tions remain concerning their effects on mammalian
DNA. The absolute number of SSB and DSB in
mammalian DNA per 125I decay, and the contribu-
tion of radical attack to these breaks, are of concern
in this paper.
A study by Walicka and colleagues measured
CHV79 cell survival (Walicka et al. 1998a) and the
number of double-strand breaks (Walicka et al.
1998b), and deduced contributions of radical and
direct damage to mammalian DNA. Their conclu-
sion that on average, more than one DSB resulted
from each 125I decay, is in contrast to earlier work
with plasmid or linear DNA indicating 0.8–1.0 DSB
per decay. They hypothesized additional damage is
from coiling of DNA in nucleosomes, whereby
regions of DNA *80 base pairs distant are physically
located near the decay site, or from tertiary structure
coiling, involving hundreds or thousands of inter-
mediate base pairs. They also assert that damage to
Correspondence: Dr Hooshang Nikjoo, Radiation Biophysics Group, Medical Radiation Physics, Karolinska Institute, SE17176 Stockholm. Tel:þ46 8 5177 5190.
E-mail: [email protected]
Int. J. Radiat. Biol., Vol. 84, No. 12, December 2008, pp. 1050–1056
ISSN 0955-3002 print/ISSN 1362-3095 online � 2008 Informa Healthcare USA, Inc.
DOI: 10.1080/09553000802478109
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these nearby locations is mostly from radical attack.
This increase in DNA damage from nearby DNA
may be offset, however, by the reaction of the histone
support proteins with free radicals, thereby
protecting the DNA against radical attack (Sak
et al. 2000).
Computer simulated radiation transport of the 125I
Auger electron spectra and associated radical diffu-
sion, coupled with atomistic representation of DNA,
is complementary to these experiments, and is used
to investigate these difficult to measure processes.
Earlier simulation efforts for 125I have focused on
linear fragments of DNA (Nikjoo et al. 1996, 1997),
circular plasmid DNA (Pomplun and Terrissol
1994), single nucleosomes (Terrissol 1994), triplex
DNA (Nikjoo et al. 2000, 2006), or quadruplex
DNA (Laughton et al. 2004). Their results agree well
with plasmid DNA experiments. While researchers
have investigated the effects of higher-order structure
on DNA damage from external X-ray (Friedland
et al. 1998, Fulford et al. 2001), gamma, alpha
(Newman et al. 2000) and heavy charged particles
(Holley and Chatterjee 1996), the effects of 125I have
not been investigated until now. These other efforts,
which use solenoid and/or zigzag chromatin struc-
tures, have been used to predict chromosome
aberrations, small fragment production and fragment
size distributions (Holley and Chatterjee 1996). This
paper presents the calculated DNA breaks from 125I
decays in coiled DNA. Both the absolute number of
strand breaks, and the relative contribution of
radicals were calculated.
Materials and methods
DNA model
This paper presents computer simulations of 125I
Auger electron transport, subsequent radical pro-
duction and diffusion, and resulting single and
double strand breaks to coiled DNA. The linear
model of B-DNA including the first hydration shell
was described by Umrania et al. (1995) and used in
the Study by Watanabe and Nikjoo (2002). The
coiled model of a nucleosome and the chromatin
segment were created based on published data and
models of nucleosome by Friedland et al. (1998),
Felsenfeld (1996), van Holde and Zlatanova (1995),
Terrissol and Pomplun (1994), Widom (1989) and
Finch and Klug (1976). Full details of structure
simulation will be reported in a separate commu-
nication. An important aspect of the simulation of
the small or large macromolecular structures is that
the structure should be tested using Molecular
Dynamic techniques. To our knowledge no such
test has yet been reported to large simulated
structures such as nucleosome and chromatin.
To elucidate the effect of DNA coiling, three decay
sites were chosen for the incorporated 125I, which
replaced a methyl group in the base tyrosine. Site A
is a region of linker DNA, with no other DNA in
range of the emitted Auger electrons, and represents
the maximum potential for radical attack. Site B is in
a nucleosome, with an adjacent loop of DNA and a
histone region core, shown in Figure 1. Site C is in
between two adjacent nucleosomes, with both having
histone cores, and represents a minimum of radical
attack. All the sites are identified in the same 40 nm
long solenoid DNA model, shown in Figure 2. The
size of the model exceeds the range of most Auger
electrons and most of the free radicals they create.
Strictly speaking K and L shell electrons and
Figure 1. Atomistic model of nucleosome. The histone core region
shown, as well as a region of linker DNA.
Figure 2. Two orthogonal size view sections of the chromatin
model. The small black dots are where the 125I decays are located.
Site A is a region of linker DNA, site B is in a nucleosome, but is
relatively distant from other nucleosomes. Site C is where two
nucleosomes are adjacent. The 125I atom replaced a methyl group
in tyrosine.
DNA damage by 125I 1051
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conversion electrons have ranges which could exceed
40 nm.
Electron track simulation and radical transport
For each of these sites, sampled 125I decay electron
spectra were used to specify the number and energies
of the electrons. These electrons were subsequently
transported through liquid water with a Monte Carlo
track structure program. The tracks from the emitted
electrons were randomly superimposed over the
atomistic model and direct hits were scored. Energy
deposition events in the volume of sugar-phosphate
backbone greater than 17.5 eV were scored as single
strand breaks (Charlton and Humm 1988, Nikjoo
et al. 1996, Pomplun et al. 1996). OH and H
radicals, and aqueous electrons, were created and
then transported using random-walk diffusion in
time steps of 1610712s. Radicals were terminated
when they reacted with each other, diffuse 4 nm
away from the model, or after 961079 seconds
following 125I decay. Only reactions of OH radicals
with the sugar-phosphate moiety were considered to
have the probability of causing strand breakage. In
brief, probability of an OH radical causing a strand
break was set at 0.13 (Milligan et al. 1993). Full
detail of the model of damage including the
energetics of DNA damage and probability of OH
radicals causing strand breaks have been published
elsewhere (Nikjoo et al. 1997, 1999, 2001, Nikjoo
and Uehara 2004).
DSB scoring
Strand breaks within 10 base pairs and on opposite
DNA strands were scored as a double strand break.
When one or both of the SSB in a DSB resulted
exclusively from a radical attack, the DSB was scored
as a ‘scavengable’ DSB. The SSB of the same DSB
which resulted from both direct and indirect action
were categorized but not included in the scavengable
contribution.
Results
Double-strand breaks per 125I decay
The average number of single and double-strand
breaks, per 125I decay is shown in Table I. For both
the linker site, site A, and the single nucleosome site,
site B, there were almost equal probabilities that
either one or no DSB occurred. Both also had about
a 15% chance of two DSB, which increased the
average number of DSB per decay to 0.85 for both
cases. Site C, where the 125I was incorporated at a
location where two nucleosomes were adjacent, had
significantly fewer instances of decays with no DSB,
and significantly higher number of average number
of DSBs, 1.33. Three or four DSBs sometimes
resulted from a single decay of 125I for this case with
much higher frequencies than the case A or B. While
the number of 125I decays used in each simulation
varied, the average number of SSB and DSB per
decay is well converged for each case.
Contribution of radical and direct damage
These three decay sites were also evaluated for
contribution of radical damage to the incorporated
and adjacent strands of DNA. The results, shown in
Table II, dramatically varied for each site and also
varied when individual regions of the DNA were
considered. When all DSBs were considered for each
site, the ‘scavengable’ contribution was 70%, 57% and
50%, respectively, for the three cases. When only the
closest 15 base pairs to the incorporated 125I were
considered, the scavengable contribution was 59%,
43% and 28%. For cases B and C, scavengable
contributions to DNA regions adjacent to the incor-
porated strand were 71% and 52%. For all decay sites,
distant DNA DSBs were 80–85% scavengable.
Discussion
This analysis of 125I decays in a coiled DNA model
had several interesting results. Site A, the linker
DNA site, should be comparable to previous linear
DNA simulations. The total number of DSB
remained the same as previous calculations. There
was a large decrease in the number of DSB at the
local site, within 10 base pairs, however, which was
offset by a large number of radical induced DSB at
other locations in the model. For site B, the total
number of induced DSB also agreed with Terrissol’s
nucleosome model calculations of 0.8 DSBs per 125I
decay (Terrissol 1994). Again, these calculations
show significantly fewer DSB at the local site, but an
increased number of radical induced DSB were
Table I. Average number of DSBs per 125I decay.
Per 125I Decay NO DSBs 1 DSB 2 DSBs 3 DSBs 4 DSBs or more Avg # DSBs Avg # SSBs # of decays
Site A 0.42 0.38 0.15 0.03 0.01 0.83 6.5 1000
Site B 0.37 0.45 0.13 0.04 0.00 0.86 5.8 5000
Site C 0.25 0.37 0.22 0.12 0.04 1.33 9.4 1000
1052 T. Goorley et al.
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located further away. Site C, which had a total
number of DSB of 1.3, also had a large fraction of
DSB located not in the immediate vicinity of the
decay site and the immediate associated region on
adjacent DNA strands. This effect, which appeared
for all three decay sites, is probably due to the
interaction of radicals with nearby DNA, which has
not been modeled in previous calculations. A
question that could be asked is whether the yield of
DSB for the unscavengable effect should be the same
for all three sites. This is a reasonable question but
the geometry of the three sites as discussed above is
sufficiently different to account for the differences
seen in the calculations.
While the number of DSB per 125I decay, 1.3 for
site C, agrees with Walicka et al. (1998a, 2000)
experimental evidence of more than 1 DSB per
decay, it conflicts with their deduced fraction of
radical induced DSB of 80% or more. The calcu-
lated value of 50% for site C indicates much greater
amounts of direct damage. Assuming the 125I decays
in uniform distributions over the three sites this
would raise the radical damage contribution to as
much as 70%, but it would lower the average number
of DSB per 125I decay. This provides a closer
agreement with Walicka et al. (1998b, 2000) experi-
mental results, but still representing less than a
quarter of total DNA double strand breaks. Such
averaging would also lower the average number of
DSB per decay to 0.61+ 0.13 (20% variance with a
95% confidence), approaching less of an agreement
with the more than 1 DSB per decay determined
experimentally.
To understand the reasons for the differences
between the experimental data and the calculated
values we need to seek the explanation in model
parameters and model of damage on the one hand,
and the need to understand the way experimental
data can be interpreted. The model of damage used
in the present calculations has been bench marked
and is similar to the one used in previous work. To
what extent the coiled model of DNA and the
cellular conditions determine the outcome has to be
investigated by alternative methods.
The difference in calculated DSB yields resulting
from the addition of secondary and tertiary structure
in DNA is significantly smaller than those observed
for other radiations. Warters and Lyons (1992) have
shown the DSB yield from X-ray radiation of
CHO cell deprotenized DNA was 8.3 and 4.5 times
larger than the yield from DNA nucleosomes and
chromatin fibres, respectively. Other researchers
have found an additional 3- to 5-fold increase in
the DSB yield for deprotenized DNA over DNA
in chromatin fibre form (Elia and Bradley 1992,
Oleinick et al. 1992).
The model of DNA damage assumes a DSB is
formed when two SSB on opposite strands are
separated by no more than 10 base-pairs (Charlton
et al. 1989, Nikjoo et al. 2001, 1999). Changing the
separation of two SSB, for the formation of a DSB,
to 15, 20 or 25 base pairs does not make appreciable
change to the fraction of radical damage or the
absolute number of double strand breaks occurring
in the different regions. This would cause damage
reported in the ‘other’ column of Table II to be
reported in the ‘Incorporated Strand’ or ‘Adjacent
Strand’ columns. Most of the direct and radical
damage to adjacent DNA strands occurs within
10–15 base pairs.
To estimate the statistical uncertainties in the
calculations, we investigated the effects of various
parameters within the code on the induction of SSB
and DSB yields. Each of these parameters has
experimental uncertainty associated with them,
which propagates to uncertainty in the calculated
results. Another source of uncertainty in the calcula-
tions is the result of the random numbers used in the
Table II. Scavengable contributions to DSBs for three sites with incorporated 125I.
Site A Incorp. Strand Other Total
DSBs/decay 0.46 0.37 0.83
Unscavengable 41% 16% 30%
Scavengable 59% 84% 70%
Site B Incorp. Strand Adjacent Strand Other Total
DSBs/decay 0.53 0.10 0.23 0.86
Unscavengable 57% 29% 16% 43%
Scavengable 43% 71% 84% 57%
Site C Incorp. Strand Adjacent Strands Other Total
DSBs/decay 0.45 0.59 0.29 1.33
Unscavengable 72% 48% 21% 50%
Scavengable 28% 52% 79% 50%
DNA damage by 125I 1053
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simulations. Random numbers are used to determine
the number and energy of the electron spectra, the
direction they are emitted, the location and quantity
of energy they deposit, the formation of radicals, the
diffusion of the radicals, and the determination of
damage the radicals create in DNA. In order to
understand whether the resulting calculations were
statistically well converged, 5000 decays of 125I were
sampled and the average number of SSB and DSB
were incrementally averaged in groups of 500 decays
to determine the influence of running additional
histories. The plots of the single and double strand
breaks as a function of these progressive averages are
shown in Figures 3 and 4, respectively. This
simulation used an OH activation probability of
0.13, and a 125I decay located in a nucleosome.
These statistical convergence graphs illustrate that
the average number of DSB and SSBs are within 5%
of their ultimate values after 500 decays, and within
3% after 1000 decays.
Conclusions
The results show that increasing the amount of DNA
near a decay site due to coiling may not necessarily
increase the total number of DSB, as in case B, but
can significantly increase the total number of DSB in
certain situations, such as case C. For case B, the
increased direct damage to DNA from nearby coils
of DNA is apparently balanced by the decreased
radical attack, which is caused by the removal of
radicals from the histone core. For case C, the decay
site is virtually surrounded by DNA, and the direct
mechanism has a much greater role. The result from
Figure 3. Average number of SSBs as a function of 125I decays sampled. The % difference from the converged value, the combined average
over the 5000 sampled decays, is also plotted.
Figure 4. Average number of DSBs as a function of number of sampled 125I decays. The % difference from the converged value, the
combined average over the 5000 sampled decays, is also plotted.
1054 T. Goorley et al.
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this work for the contribution of OH radicals to
induction of DSB per decay is lower than that
deduced by Walicka et al. (1998, 2000) from their
experiment. Although the modelling parameters are
well benchmarked against DNA damage data for
plasmid DNA, we still need to search the differences
in modelling of cellular environment and to what
extent these differ between plasmid and cells.
Acknowledgements
This research was partially supported by DOE grant
to the Harvard/MIT BNCT Program #DE-FG02-
97ER62193 and the Los Alamos National Lab
subcontract H1962-0019-2G.
Declaration of interest: The authors report no
conflicts of interest. The authors alone are respon-
sible for the content and writing of the paper.
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