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J Biol Chem, Vol. 275, Issue 14, 9924-9929, April 7, 2000
From the Groupe "Réparation des Lésions Radio- et Chimio- Induites," UMR 8532 Centre National de la Recherche Scientifique, Institut Gustave Roussy, 39, Rue Camille Desmoulins, 94805 Villejuif Cédex, France
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ABSTRACT |
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The Escherichia coli Fpg protein is a
DNA glycosylase/AP lyase. It removes, in DNA, oxidized purine residues,
including the highly mutagenic C8-oxo-guanine (8-oxoG). The catalytic
mechanism is believed to involve the formation of a transient Schiff
base intermediate formed between DNA containing an oxidized residue and
the N-terminal proline of the Fpg protein. The importance and the role
of this proline upon the various catalytic activities of the Fpg
protein was examined by targeted mutagenesis, resulting in the
construction of three mutant Fpg proteins: Pro-2 7,8-Dihydro-8-oxoguanine
(8-oxoG)1 is the major
mutagenic base lesion generated in DNA by active oxygen during normal
metabolism (1). Because 8-oxoG pairs preferentially with adenine rather than cytosine, it generates transversion mutations after replication (2). To maintain the genetic integrity, this oxydized base is repaired,
in Escherichia coli, by the Fpg protein (2, 3) coded for by
the fpg gene (4). The physical and enzymatic properties of
the protein have been established (5). It is a globular monomer of 30.2 kDa (269 amino acids), pI = 8.6, that contains one zinc
atom/protein molecule present in a zinc finger motif (5). In
vitro, the Fpg protein exhibits three catalytic activities: (i) it
is a DNA glycosylase that liberates modified residues such as
2,6-diamino-4-hydroxy-5-N-methyl-formamido pyrimidine (Fapy) (6), 8-oxoG (3, 7), 8-oxoA, the imidazole ring-opened forms of adenine
and guanine (7), and modified pyrimidines, such as 5-hydroxycytosine,
5-hydroxyuracil, The N-terminal formylmethionine of the cloned wild-type Fpg protein is
post-translationally cleaved in E. coli (4). However, because in some mutant Fpg proteins, the formylmethionine could not be
cleaved, the amino acid sequence of the Fpg protein was numbered Met-1,
Pro-2, etc. (21, 22).
To further understand the role of the N-terminal proline, in the
various catalytic activities of the Fpg protein, Pro-2 was mutated to
three different amino acids: Gly, Thr, or Glu generating the FpgP2G,
FpgP2T, and FpgP2E mutant proteins, respectively. These proteins were
purified, and their catalytic properties toward several substrates as
well as their binding constants were established. Finally, we have
determined the in vivo properties of the mutant Fpg
proteins. Our results show that Pro-2 is involved in the various enzymatic activities of the Fpg protein, although at different extent,
and that one can observe the formation of a robust Schiff base
intermediate with an oligonucleotide containing an abasic site despite
the lack of a detectable AP lyase activity.
Bacterial Strains, Enzymes, and Chemicals--
The following
strains, derived from the E. coli K12 strain, were used: CC
104 (ara
Restriction endonucleases, DNA polymerase, DNA ligase, bovine serum
albumin (molecular biology grade), and other DNA modifying enzymes were
obtained from F. Hoffmann-La Roche (Switzerland), Taq and
Pfu DNA polymerases were obtained from Amersham Pharmacia Biotech and Stratagene (La Jolla, CA), respectively, and used as
recommended by the manufacturers.
[3H]Dimethylsulfate (3.9 Ci/mmol) was purchased from NEN
Life Science Products. [3H]Thymidine (48 Ci/mmol),
[ Site-directed Mutagenesis--
The plasmid pFPG60 was used for
the construction of mutated fpg genes. The site-directed
mutagenesis was achieved by polymerase chain reaction using
Taq and Pfu DNA polymerases. The primers used to
generate amino acid modifications of the Fpg protein are listed in
Table I and were obtained from Genset
(Paris, France). To obtain an unique restriction site
HindIII close to the N terminus of the coding fpg
sequence, the plasmid pFPG7 was constructed by producing a 156-base
pair polymerase chain reaction product (primers 5'-FPG
(HindIII site), reverse (Table I), that was restricted with
BglII and HindIII, and then cloned into the
BglII/HindIII-cut pFPG60. pFPG7 was used to
produce the mutant Fpg proteins with amino acid changed Pro-2 In Vitro Repair Assay--
The procedures used to purify the Fpg
mutant proteins, assay of Fapy- or 8-oxoG-DNA glycosylase activities,
nicking activity of DNA at AP sites, and formation of enzyme-DNA
covalent complexes in the presence of NaBH4, have been
described (21). For DNA binding determination, the gel mobility schift
assays, using radiolabeled duplex oligomer containing a single
synthetic abasic site analog (tetrahydrofuran) (23F:23C; Table I) were
performed as described (28).
In Vivo Repair Assay--
The mutator strain BH990 (fpg
mutY) was transformed by pFPG7P2T, pFPG7P2G, or pFPG7 using
electroporation. The transformation mixture was plated onto LB medium
containing ampicillin (100 µg/ml). Individual colonies (4-6) were
selected, grown overnight at 37 °C in 2 ml of LB broth medium
containing ampicillin and then plated onto M9 minimal medium containing
lactose (0.4%) and ampicillin (100 µg/ml) at a density of 200-500
colonies/plate. The spontaneous mutation rate in the cultures was
monitored for the generation of Lac+
revertants (21, 24).
We have constructed various E. coli mutant Fpg proteins
to ascertain the involvement of the N-terminal proline in the various enzymatic activities of this protein. Proline 2 was mutated to Gly,
Thr, or Glu. Gly and Thr were chosen for substitution because they are
amino acids with uncharged polar R-group and minimal differences (29,
30). Because in the wild-type Fpg protein, the primary structure of
N-terminal side is PELPVET ... , we examined the effect of an
additional negative charge when Pro-2 is changed to Glu and constructed FpgP2E.
The mutant proteins were expressed in E. coli BH20
(fpg
Gly (FpgP2G),
Pro-2
Thr (FpgP2T), and Pro-2
Glu (FpgP2E). The formamidopyrimidine DNA glycosylase activities of FpgP2G and FpgP2T were comparable and accounted for 10% of the wild-type activity. FpgP2G and FpgP2T had barely detectable 8-oxoG-DNA glycosylase activity
and produced minute Schiff base complex with 8-oxoG/C DNA. FpgP2G and
FpgP2T mutants did not cleave a DNA containing preformed AP site but
readily produced Schiff base complex with this substrate. FpgP2E was
completely inactive in all the assays. The binding constants of the
different mutants when challenged with a duplex DNA containing a
tetrahydrofuran residue were comparable. The mutant Fpg proteins barely
or did not complement in vivo the spontaneous transitions
G/C
T/A in E. coli BH990 (fpg mutY) cells.
These results show the mandatory role of N-terminal proline in the
8-oxoG-DNA glycosylase activity of the Fpg protein in vitro and in vivo as well as in its AP lyase activity upon
preformed AP site but less in the
2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine-DNA glycosylase activity.
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INTRODUCTION
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
-ureidoisobutiric acid,
-R-hydroxy-
-ureidoisobutiric acid (8) (for review, see
Ref. 9), (ii) it is an AP lyase that incises DNA at abasic sites by a
-
-elimination mechanism (10, 11), and (iii) it is a
deoxyribophosphodiesterase that removes 5'-terminal deoxyribose phosphate residues (12). Therefore the Fpg protein belongs to the class
of DNA glycosylases endowed with a
-lyase activity (9). It was
hypothesized that the glycosylase and lyase functions of DNA
glycosylases/AP lyases are mechanistically coupled (13-15). A
mechanism involving the nucleophilic attack on C1' of the modified deoxynucleoside targeted for excision has been proposed (13-15) to
explain the catalytic action of this class of enzymes. In this mechanism, the catalytic nucleophile attacks the glycosidic bond, displacing the aberrant base and forming a transient intermediate (Schiff base) with the C1'-deoxyribose moiety. The isomerization of
this transient complex leads to cleavage of the AP site through a
conjugate elimination mechanism. It has been proposed that most DNA
glycosylases/AP lyases use the
- NH2 group of a lysine
as the catalytic nucleophile (16). For the Nth, hOgg1, and hNth proteins, the lysine residues at positions 120, 249, and 212, respectively, are believed to be the catalytic nucleophiles (16-18). However, the NH2 group of the N-terminal amino acid can be
the catalytic amine, as shown in the case of the bacteriophage T4 endonuclease V (19). For the Fpg protein, the N-terminal proline residue was shown to be linked, in a Schiff base complex, with DNA
containing 8-oxoG residues. It was suggested that this proline was the
nucleophile that initiates the catalytic excision of 8-oxoG (20).
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EXPERIMENTAL PROCEDURES
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
(gpt-lac)5, rpsL/F'
(lacI378,lacZ461, proA+B+] (23), BH 990 (as CC 104 but
fpg::kanR,mutY::kanR) (24),
BH 20 (as AB 1157 but fpg::kanR) (25), and DH5
(26). The plasmids containing the cloned fpg-gene pFPG60
(4), pFPG220 (27), and pUC19 were from laboratory stock.
-32P]dATP (3000 Ci/mmol) were from Amersham Pharmacia
Biotech. [
-32P]ATP (3000 Ci/mmol) and [
-35S]dATP (1000 Ci/mmol) were from ICN (Paris, France).
The substrates [3H]Fapy-poly(dG-dC) and
[3H]thymine E. coli DNA containing abasic
sites were prepared as described (4, 10). The preparation of plasmids,
restriction enzyme digestion, agarose gel electrophoresis, DNA
ligation, and bacterial transformation were performed using standard
methods as described by Sambrook et al. (26) or by the manufacturers.
Gly,
Pro-2
Glu, and Pro-2
Thr. The corresponding plasmids are
pFPG7P2G, pFPG7P2E, and pFPG7P2T. The DNA sequence was verified by the
dideoxy chain termination method with T7 DNA polymerase (Sequenase). To
further characterize the mutant proteins, the sequence of the six
N-terminal amino acids of each protein was determined (data not
shown).
Sequences of oligodeoxynucleotides used
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RESULTS
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
) cells to avoid any contamination by the
wild-type enzyme. The amount of overproduced mutant enzymes was
comparable with that of wild type, as evaluated by the abundance of the
30.2-kDa protein in PAGE gels (data not shown). In crude extracts of
BH20 E. coli cells expressing the mutant FpgP2G and FpgP2T,
a Fapy-DNA glycosylase activity was easily detected, but to a lower
level than in cells expressing the wild-type protein. No Fapy-DNA
glycosylase activity could be detected in crude extracts of BH20
E. coli cells expressing the Fpg P2E mutant (Table
II). In contrast, when apurinic
[3H]thymine-labeled DNA was used as substrate, a barely
detectable AP nicking activity was observed in all the extracts (Table
II) in the same order of magnitude as the control and was presumably due to Xth, Nth, or Nei proteins present in the extracts.
Fapy-DNA glycosylase activity and AP lyase activity in crude extracts
of E. coli BH20 (fpg) cells harboring pFPG7 coding for wild-type and
mutant Fpg proteins
Fapy- and 8-oxoG-DNA Glycosylase Activities of Wild-type and Mutant Purified Fpg Proteins-- After purification of the wild-type and mutant Fpg, the fractions obtained after MonoS chromatographic purification step were better than 95% of homogeneity (data not shown) and were used to determine the various enzymatic properties of the mutant Fpg proteins. To further characterize these enzymes, the N-terminal amino acids were microsequenced.
Because the efficacy of the post-translational cleavage of the formylmethionine within the cell is determined largely by the amino acid next to the formylmethionine in the protein (31), it was possible that such cleavage does not occur in cells expressing the mutant enzymes. In fact, the N-terminal methionine was absent, as shown by microsequencing, in the FpgP2G and FpgP2T purified proteins. However in the FpgP2E, the formylmethionine was present (data not shown). None of the various enzymatic properties of the Fpg protein measured below were detectable using the FpgP2E mutant protein (data not shown).
The ability of FpgP2G and P2T to excise Fapy residues was analyzed. The
comparison of the activity of the Fpg wild-type and mutant proteins
showed that FpgP2G and FpgP2T had a comparable but low (about 10% of
wild type) Fapy-DNA glycosylase activity (Fig.
1A).
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The efficiency of Fpg mutant proteins to repair 8-oxoG was investigated using as substrate a double-stranded oligonucleotide containing a single 8-oxoG (Table I). As shown in Fig. 1B, the rate of incision of the duplex was dramatically reduced for the P2G or P2T mutants as compared with the wild-type Fpg protein (about 3%). It was verified that the excision of 8-oxoG residues was not underestimated, because, following the action of the enzyme, in the presence or absence of 10% piperidine (which nicks DNA at AP sites), the same level of incision of the substrate was observed (data not shown). These data indicate that the N-terminal proline is mandatory for 8-oxoG but less for Fapy residues excision.
Nicking Activity of Wild-type and Mutant Fpg Proteins at Abasic
Site--
The ability of P2G and P2T mutant proteins to cleave abasic
sites was evaluated using two different substrates. In the first assay,
E. coli [3H]thymine-labeled DNA containing AP
sites was used as substrate. In this assay, the Fpg protein nicks at AP
sites and liberates acid-soluble [3H]thymine-labeled
short oligonucleotides. Using the purified mutant Fpg proteins, no
detectable AP nicking activity was observed for any of the mutant
proteins (Fig. 2A). In the
second assay, a 50-mer oligonucleotide with an unique preformed abasic
site at a defined position was used as substrate (Table I). The P2G
mutant had less than 1% of the wild-type activity (Fig.
2B), generating only
-elimination pruducts (data not
shown). All together, these experiments suggest that the N-terminal
proline is mandatory for the AP lyase activity when measured upon
preformed AP site.
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Formation of Schiff Base Intermediate--
The Fpg protein forms a
transient Schiff base intermediate with 8-oxoG/C containing DNA in a
stoichiometry 1:1 (32). This intermediate, after reduction with sodium
cyanoborohydride or sodium borohydride, is converted to a covalently
linked Fpg protein-DNA complex (32, 33). We have tested the ability of
the mutant FpgP2G and FpgP2T proteins to trap 8-oxoG/C DNA in the
presence of NaBH4. The trapping efficiency of FpgP2G and
FpgP2T was dramatically reduced (Fig.
3A). This result is in
agreement with the barely detectable 8-oxoG-DNA glycosylase activity
(Fig. 1B).
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In contrast, when the AP site containing DNA is used as substrate, the mutant P2G produces a Schiff base intermediate with an even better efficiency than that of the wild-type protein (Fig. 3B). However, FpgP2G has an almost indetectable AP lyase activity upon preformed AP site (Fig. 2). These results show that it is possible to produce a robust Schiff base intermediate using an enzyme having an impaired DNA repaired activity, i.e. no AP lyase activity.
DNA Binding of Mutant Fpg Proteins-- The purified mutant FpgP2G and P2E proteins were tested for their ability to bind a duplex DNA containing a single tetrahydrofuran residue, a noncatalytically competent substrate (33, 34). The apparent dissociation constants of mutant FpgP2G and P2E were 39 and 60 nM, respectively, comparable with that observed for purified wild-type Fpg protein (45 nM) (Table III). These results suggest that the substitution of the N-terminal proline for glycine or glutamic acid does not interfere with DNA binding.
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G/C
T/A Spontaneous Mutagenesis in fpg, mutY-deficient E. coli
Strain BH990 Expressing Mutant fpg Genes--
E. coli
possesses two DNA glycosylase activities that prevent spontaneous
mutagenesis by 8-oxoG: the Fpg protein, which excises 8-oxoG residues
in DNA (3, 7), and the MutY protein, which excises the adenine residues
incorporated opposite 8-oxoG (35-37). Inactivation of both
fpg and mutY genes of E. coli (BH990
fpg mutY) results in a strong G/C
T/A spontaneous
mutator phenotype (24, 36). To study the repair capacity of the
partially active FpgP2G and FpgP2T proteins in vivo, we have
measured the spontaneous mutagenesis in the BH990(fpg mutY)
cells hosting plasmids coding for the wild-type or mutant Fpg proteins
(Table IV). The strain BH990 (fpg
mutY) hosting pUC19 shows a 800-fold increase in G/C
T/A
transversion compared with the parental CC104 strain. The spontaneous
mutator phenotype because of fpg and mutY
mutations is completely suppressed by expression of the plasmid coding
for the wild-type Fpg protein. In contrast, the plasmids coding for FpgP2G protein barely modify, and the FpgP2T protein does not modify
the spontaneous mutagenesis of the E. coli double mutant (Table IV). This experiment points out the crucial role of N-terminal proline for the biological activity of this protein, presumably via the
removal of the mutagenic 8-oxoG residues.
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DISCUSSION |
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It has been proposed that the N-terminal proline of the Fpg protein could be the nucleophile involved in the Schiff base formation with 8-oxoG residues (20). To investigate, in detail, the implications of this amino acid upon the various activities of the Fpg protein, we have constructed three mutated proteins at this position by site-directed mutagenesis: FpgP2G, FpgP2T, and FpgP2E. These mutated proteins were purified to near homogeneity and characterized for their various enzymatic activities.
The results reveal that the substitution of the N-terminal proline barely affects the DNA binding function of the mutated proteins as compared with the wild type. These data are in agreement with the results of Tchou and Grollman (32), showing that the presence of a maltose-binding protein at the N terminus of Fpg protein does not change DNA binding.
When using as substrate a DNA containing Fapy residues, the FpgP2G and FpgP2T proteins were partially active (about 10% of the activity of the wild-type protein). The evaluation of the 8-oxoG-DNA glycosylase activity of the mutated proteins shows that the activity of the FpgP2G and FpgP2T mutants is dramatically reduced and that these mutants barely produce Schiff base with oligonucleotides containing 8-oxoG residues. Taken together, these results suggest that the N-terminal proline is critical for the catalysis of the 8-oxoG residue excision.
It has been proposed that 8-oxoG is the primary damage recognized by
the Fpg protein in vivo leading, if unrepaired, to G/C
T/A transversion (1, 2, 9, 21). The results show that the FpgP2G
barely, if at all, prevents and that the FpgP2T mutant does not prevent
the spontaneous G/C
T/A mutagenesis in vivo. These
in vivo results are in good agreement with the minute
8-oxoG-DNA glycosylase activity of the respective proteins, measured
in vitro. Therefore the recognition and excision of 8-oxoG residues are complex mechanisms because at least two other amino acids,
Lys-57 and Lys-155, are also involved in these processes (21, 22).
The N-terminal proline is also critical for the
-lyase activity of
the Fpg protein at preformed AP site: two different substrates containing preformed AP site were used, none of the mutant proteins had
detectable activity upon these substrates. The mechanism of action of
the N-glycosylase/AP-lyase has been proposed to occur via a
covalent Schiff base intermediate that can be trapped by treatment of
the enzyme-substrate complex with a reducing agent (13-15). In fact,
an efficient borohydride-dependent trapping of a number of
DNA N-glycosylases possessing AP-lyase activity with their
substrates has been observed (Refs. 15, 20-22, 32, 33, 38, and 39 and
this paper). The results presented above using 8-oxoG containing
oligonucleotide confirm this trapping by the wild-type Fpg protein. It
efficiently excises 8-oxoG residues and readily produces Schiff base
intermediate, whereas the FpgP2G or FpgP2T proteins having a poor
8-oxoG-DNA glycosylase activity barely produce Schiff base with
8-oxoG/C DNA. At variance, when using the oligonucleotide containing a
preformed abasic site and FpgP2G, a mutant protein devoid of AP-lyase
activity (see above), the formation and the amount of the covalent
complex in the presence of NaBH4 was comparable with the
amount of complex obtained with the wild-type Fpg protein. This
unexpected result shows that it is possible to dissociate the formation
of the complex from the incision of the DNA at abasic sites. The
mutagenesis of the N-terminal proline residue reveals an interesting
example of a N-glycosylase readily effective to trap its
substrate without its excision: the Fpg P2G mutant efficiently produced
the covalent Schiff base intermediate with preformed AP site but did
not excise AP site.
The E. coli Mut Y protein is a DNA glycosylase excising
adenine residues in a 8-oxodG/A mismatch (40, 41). Mut Y, at higher than 1:1 protein-substrate molar ratio, forms a covalent intermediate with its substrate involving Lys-142 (41) but has little or no AP lyase
activity (40, 41). It has been recently shown that the single amino
acid substitution Lys-142 to Ala generates a Mut Y protein retaining
its DNA glycosylase activity but incising DNA at abasic site by a
-
elimination mechanism without the formation of a Schiff base
intermediate (42). This mutant protein has just the opposite properties
of the Fpg P2G. These two observations point out that it is possible to
dissociate the formation of the Schiff base complex from the incision
of the DNA at abasic sites.
The results point out the different role of the N-terminal proline of
the Fpg protein in the processing of the different substrates. However,
it is not excluded that the amino acid substitution could modify the
environment and/or the role of some specific amino acid(s) in the
active site of the protein. For example, we have shown that the
mutation P2G in the FpgP2G mutant did not change the overall structure
of this protein as determined by measuring the acrylamide quenching and
the lifetime of tryptophane fluorescence (43). However, subtle changes
were observed in the structure dynamics of the P2G mutant at 20 °C,
indicating that the tryptophane residues are differently surrounded as
compared with the wild-type protein. The FpgP2E protein is devoid of
any enzymatic activity but has a binding constant similar to the FpgP2G
mutant. There are neither changes in the structure dynamics of FpgP2E
at 20 °C nor at 4 °C, which means that its conformation at
20 °C is the same as at 4 °C, whereas wild-type Fpg, FpgP2G, and
FpgK57G exhibit changes under such conditions. The lack of the
structure dynamics at variant temperatures and/or the presence of the
first Met of the protein could explain the total lack of any enzymatic activity of the Fpg P2E protein.
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ACKNOWLEDGEMENTS |
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We thank Drs. J. Lhomme and J. F. Constant (UMR 5616 CNRS, Grenoble) for the gift of oligonucleotide containing the tetrahydrofuran residue and for helpful discussion and Dr. J. Derancourt (UPR 1086 CNRS, Montpellier) for protein sequencing.
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FOOTNOTES |
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* This work was supported by European Community Grant ENV4-CT97-0505 and by funds from Fondation pour la Recherche Medicale (fellowship to O. S.) and Association pour la Recherche sur le Cancer.The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
To whom correspondence should be addressed. Tel.: 33-1-42114824;
Fax: 33-1-42114454; E-mail: jlaval@igr.fr.
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ABBREVIATIONS |
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The abbreviations used are: 8-oxoG, 7,8-dihydro-8-oxoguanine; Fapy, 2,6-diamino-4-hydroxy-5-N-methylformamidopyrimidine; AP, apurinic/apyrimidinic, abasic; PAGE, polyacrylamide gel electrophoresis.
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