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J. Biol. Chem., Vol. 275, Issue 47, 36498-36501, November 24, 2000
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,
,
**
From the
Laboratory of Molecular Genetics
and
Laboratory of Structural Biology, National Institute of
Environmental Health Sciences, Research Triangle Park,
North Carolina 27709 and § Department of Chemistry and
¶ UNLV Cancer Institute, University of Nevada, Las Vegas,
Nevada 89154-4003
Received for publication, August 1, 2000, and in revised form, September 15, 2000
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ABSTRACT |
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Eukaryotic DNA mismatch repair requires the
concerted action of several proteins, including proliferating cell
nuclear antigen (PCNA) and heterodimers of MSH2 complexed with either
MSH3 or MSH6. Here we report that MSH3 and MSH6, but not MSH2, contain N-terminal sequence motifs characteristic of proteins that bind to
PCNA. MSH3 and MSH6 peptides containing these motifs bound PCNA, as did
the intact Msh2-Msh6 complex. This binding was strongly reduced when
alanine was substituted for conserved residues in the motif. Yeast
strains containing alanine substitutions in the PCNA binding motif of
Msh6 or Msh3 had elevated mutation rates, indicating that these
interactions are important for genome stability. When human MSH3 or
MSH6 peptides containing the PCNA binding motif were added to a human
cell extract, mismatch repair activity was inhibited at a step
preceding DNA resynthesis. Thus, MSH3 and MSH6 interactions with PCNA
may facilitate early steps in DNA mismatch repair and may also be
important for other roles of these eukaryotic MutS homologs.
The mutation rate of an organism is reduced by the ability
of the general DNA mismatch repair
(MMR)1 system to correct DNA
replication errors. In eukaryotes, MMR is initiated when one of two
protein complexes binds to mismatches (reviewed in Refs. 1-3). The
MutS Although the signal that directs mismatch repair to the newly
replicated strand in eukaryotic cells is unknown, repair of mismatched
duplexes in extracts of eukaryotic cells can be directed to one strand
by a discontinuity in the DNA backbone. We previously suggested that
one-strand discontinuity that might serve as a strand
discrimination signal is the primer terminus at the replication fork
and that PCNA may link DNA replication and mismatch repair to
facilitate recognition and repair of errors in the nascent strand (4).
PCNA is the essential sliding clamp that topologically encircles DNA
and physically associates with DNA polymerase Because these data reveal important roles for PCNA in MMR, we are
attempting to identify interactions of PCNA with mismatch repair
proteins and investigate their functional importance. Here we take
advantage of previous studies (reviewed in Refs. 5 and 11) showing that
PCNA interacts with several other proteins involved in DNA replication
and repair (12-17). These proteins share a common amino acid motif
with the consensus sequence Qxxhxxaa (see Fig.
1). A p21 peptide containing this motif binds to the interdomain
connector loop of PCNA (18), which is present three times in the
trimeric PCNA sliding clamp. The present study was motivated by the
observation that the consensus PCNA binding motif is present at the N
termini of MSH3 and MSH6. We provide evidence that these motifs mediate
physical interactions with PCNA and that these interactions are
important for the function of MSH3 and MSH6.
Materials--
N-terminal peptides of hMSH6 and hMSH3 containing
wild type or mutant PCNA binding motifs (see Fig. 1B) were
synthesized by Research Genetics (Huntsville, AL). Materials for the
MMR assays have been described (19).
Construction of Plasmids--
Bacterial expression plasmids were
constructed to produce glutathione S-transferase (GST)
fusion proteins containing amino acids 28-47 of yeast
Saccharomyces cerevisiae Msh3 (GST-yMsh3), 22-41 of S. cerevisiae Msh6 (GST-yMsh6), 18-37 of human
MSH3 (GST-hMSH3), 18-37 of human MSH3 with an F27A/F28A substitution
(GST-hMSH3, F27A/F28A), 1-20 of human MSH6 (GST-hMSH6), or 1-20 of
human MSH6 with an F10A/F11A substitution (GST-hMSH6, F10A/F11A). These
plasmids were made by ligating annealed pairs of
oligonucleotides2 into an
EcoRI/XhoI-digested pGEX-4T-1 vector (Amersham
Pharmacia Biotech). They each have a stop codon after the last MSH3 or
MSH6 codon and a unique HindIII restriction site to
facilitate screening during subcloning. The correct sequence was
confirmed by DNA sequencing. Plasmids for yeast and human PCNA and GST
fusion proteins for human FEN1 and DNA ligase I were as described (13,
16, 20). pGEX-4T-3 without insert was used to produce GSTp.
Assays for PCNA Binding--
Proteins were expressed in
Escherichia coli strain BL21(DE3) by induction with 0.8 mM isopropyl-
To test interactions with Msh2-Msh6, yeast PCNA was overexpressed in
E. coli, purified as described (21), and coupled to Affi-gel
15 beads (Bio-Rad Laboratories) according to the manufacturer's instructions. Wild type and mutant yMsh2-yMsh6 heterodimer was purified
as described.3 20 µg of
either Msh2-Msh6 complex was incubated with 20 µl of PCNA beads, or
BSA beads as a negative control, for 1 h at 4 °C in 20 mM Tris-HCl (pH 7.4), 200 mM NaCl, 1 mM DTT, 0.1 mM EDTA, 0.01% Nonidet P-40, and
10% glycerol. Beads were washed 6 times with 20 mM
Tris-HCl (pH7.4), 1 M NaCl, 1 mM DTT, 0.1 mM EDTA, 0.01% Nonidet P-40, and 10% glycerol. Beads were
resuspended in an equal volume of 2× Laemmli loading buffer and
subjected to SDS-PAGE. Proteins were transferred to a polyvinylidene
difluoride membrane and probed with an antibody to a peptide of amino
acids 280-301 of yMSH6. This antibody reacts with both yMsh6 and yMsh2.
Construction of Yeast Strains and Measurements of Mutation
Rates--
A yMSH6 integration vector was constructed by
subcloning a 5.3-kb EcoRI/BamHI fragment from the
centromeric plasmid pMMR83 (from L. Prakash, University of Texas
Medical Branch, Galveston, TX) into the integration vector
YIplac211. A yMSH3 integration vector was constructed by
subcloning a 4-kb KpnI/PstI fragment from the
centromeric plasmid pPM611 (from L. Prakash) into YIplac211. The PCNA
binding motifs were altered by site-directed mutagenesis using
Pfu turbo polymerase (Stratagene) and mutant
oligonucleotides (Genosys). Integration vectors were linearized with
AflII and placed into E203 (msh3 and
msh6) (22) or SJR938 (23). Integrants were selected as
described (24), mutations were verified by DNA sequencing and mutation
rates were determined as described (25).
DNA Mismatch Repair--
Procedures for measuring MMR
activity have been described (19). Repair reactions (25 µl) contained
0-400 µM hMSH3 peptide (amino acids 18-37) or hMSH6
peptide (amino acids 1-20).
MSH3 and MSH6 Contain Consensus PCNA Binding Motifs Not Found in
MSH2--
Taq MutS protein contains five domains (26), and
sequence alignments suggest that human and yeast MSH2, MSH3, and MSH6
proteins share these five domains (Fig.
1A). However, MSH3 and MSH6
contain distinct N-terminal amino acid sequences not found in
Taq MutS or in MSH2 (Fig. 1A). These regions of
MSH3 and MSH6 encode the sequence Qxxhxxaa (Fig.
1B), where h and a are hydrophobic and aromatic amino acids,
respectively. Flanking this consensus motif are several charged amino
acids that may contribute to binding (reviewed in Ref. 11).
PCNA Interacts with MSH3 and MSH6 Peptides Containing the
Binding Motifs--
Using glutathione-agarose affinity beads in a
pull-down assay previously used to demonstrate PCNA interaction with
FEN1, we first examined the ability of human PCNA to interact with
human and yeast MSH3 and MSH6 peptides. Human PCNA bound to GST fusion proteins containing short peptide sequences with the putative PCNA
binding motifs of hMSH3 (Fig. 2,
panel A, lane 5), hMSH6 (lane 7),
yMsh3 (lane 9), and yMsh6 (lane 10). These
results are similar to PCNA binding to GST fusion proteins containing
the PCNA binding motifs of hFEN1 and hDNA ligase I (Fig. 2, panel A, lanes 2 and 3). Substituting
alanines for the conserved phenylalanines, which abolishes PCNA binding
to the DNA ligase I peptide (lane 4) (16), eliminated PCNA
binding by hMSH3 (lane 6) and hMSH6 (lane 8).
Next, we examined the ability of yeast PCNA to bind to yeast Msh3 and
Msh6 fusion proteins. Because yeast PCNA is 29 kDa and nearly
comigrates with the fusion proteins in SDS-PAGE gels, complexes
isolated using the pull-down assay were treated with thrombin to
release the Msh peptides and any associated PCNA into the supernatant.
Analysis of the supernatants (Fig. 2, panel B,
left) showed that yeast PCNA bound to fusion proteins of
yMsh3 (lane 2), yMsh6 (lane 3) and hFEN1
(lane 4), but not to GST alone (lane 1). Parallel
experiments with human PCNA (Fig. 2, panel B,
right) confirmed its ability to bind to fusion proteins of yMsh3 (lane 6), yMSH6 (lane 7), and hFen1
(lane 8) but not to GST alone (lane 5). These
experiments also demonstrated that the GST moiety generated by thrombin
cleavage did not contribute to the band intensity at 29 kDa in the
experiments with yeast PCNA (lanes 1-4). When the
bead-associated material after cleavage was analyzed (not shown), the
GST moiety was found in approximately equal amounts and no intact
fusion proteins were seen, indicating that the cleavage reaction was
complete.
PCNA Interacts with the Msh2-Msh6 Heterodimer--
We next
examined binding of the intact Msh2-Msh6 heterodimer to yPCNA attached
to Affi-gel beads. Wild type Msh2-Msh6 bound to these beads (Fig.
2C) but not to beads to which BSA had been attached (not
shown). This result is similar to a previous demonstration that yPCNA
binds to Msh2-Msh3 but not to Msh2 alone (7). PCNA binding was strongly
reduced when the heterodimer contained wild type Msh2 and mutant Msh6
with alanine substituted for conserved amino acids in the PCNA binding
motif (Fig. 2C).
Alteration of PCNA Binding Motifs Yield Mutators--
To examine
the functional importance of the yeast Msh3 and Msh6 PCNA binding
motifs, we constructed haploid yeast strains with alanine substituted
for conserved residues in the motifs and measured mutation rates
in vivo. We used a highly sensitive reporter gene that
monitors the rate of Lys+ reversion via single-base
deletions in a run of 14 A·T base pairs in the Lys2 gene
(25). An msh3/msh6 double mutant strain had an 11,000-fold
higher mutation rate than a wild type strain (Table I), reflecting inactivation of Msh2-Msh6-
and Msh2-Msh3-dependent mismatch repair. However,
msh3 and msh6 single mutant strains had reversion
rates that were 16- and 200-fold higher, respectively, than the wild
type yeast strain (Table I). These smaller increases are expected based
on the redundancy of these pathways (27) and reflect the contribution
of wild type Msh6 and Msh3 to repair. However, substituting alanine for
conserved residues in the PCNA binding motif of either MSH3
or MSH6 increased reversion rates about 20-fold relative to
the respective wild type genes (Table I). The strain with alanine
substitutions in the PCNA binding motif of MSH3 also had a
10-fold higher rate of reversion at a run of 10 G·C base pairs (23)
compared with wild type (Table I), and the strain with alanine
substitutions in the PCNA binding motif of MSH6 had a
mutation rate at the CAN1 locus that was 2-fold higher than
the msh3/MSH6 yeast strain (Table I).
Inhibition of MMR Activity by MSH Peptides Containing the PCNA
Binding Motif--
Next, we measured MMR activity in extracts of human
TK6 cells in the absence or presence of N-terminal hMSH3 and hMSH6
peptides that contain this motif. We reasoned that addition of hMSH3 or hMSH6 PCNA binding peptides to the mismatch repair reaction might compete with native MSH3 or MSH6 for binding to PCNA, thus preventing repair. With the MMR assay used (19), any effect results from inhibition of MMR at a step prior to resynthesis of DNA (4). As shown
in Fig. 3, the extract alone efficiently
repaired a G·G mismatch and a 2-base insertion mismatch. Addition of
hMSH3 or hMSH6 peptides inhibited repair of both mismatches in a
concentration-dependent manner. Addition of peptides with
alanines replacing the conserved phenylalanines did not inhibit
repair.
We have identified consensus PCNA binding motifs in MSH3 and
MSH6 and have clearly shown that these N-terminal residues interact with PCNA. Given the presence of this motif, interaction with PCNA was
anticipated based on previous demonstrations that several other
proteins interact with PCNA via this conserved motif (12-17). Our
results with the yeast Msh3 peptide are consistent with a previous
study (7) showing an interaction between yeast PCNA and the yeast
MSH2-MSH3 heterodimer but not with MSH2 alone. The data with the human
MSH6 peptide and intact Msh2-Msh6 are also consistent with hMSH6
binding to a hPCNA affinity column (8). The elevated mutation rates of
yeast strains with mutations in these PCNA binding motifs suggest that
interactions between PCNA and both MSH3 and MSH6 are important for
genome stability. The observed mutator phenotypes may reflect reduced
repair of mismatches recognized by MSH2-MSH3 and MSH2-MSH6. This
possibility is consistent with the inhibition of strand-specific MMR at
a step preceding DNA resynthesis observed when MSH3 or MSH6 PCNA
binding peptides are added to MMR reactions catalyzed by an extract of
human cells (Fig. 3).
Substitutions in the MSH3 and MSH6 PCNA binding motif that strongly
reduced binding to PCNA (Fig. 2) yielded mutation rates that were not
as high as in strains completely devoid of Msh3 or Msh6 (Table I),
indicating retention of some MMR function. Precedent for partial repair
activity comes from previous studies showing that Fen1 and DNA ligase I
participate with reduced efficacy in long-patch base excision repair
when similar substitutions are present in their PCNA binding motifs
(20, 28, 29). Partial retention of MMR function might reflect residual
PCNA interactions with Msh2-Msh3 and Msh2-Msh6 at other sites or with
other MMR proteins in a multiprotein complex. For example, yeast
two-hybrid analysis indicates that PCNA interacts with Mlh1 (4), and
human PCNA co-immunoprecipitates in a complex containing MLH1 and PMS2 (6). Any direct interactions of PCNA with MutL homologues may be at
sites other than the interdomain connector loop of PCNA, because we did
not find consensus PCNA binding motifs in either Mlh1 or Pms1.
It is also possible that the intermediate mutator phenotypes of
strains with substitutions in the Msh3 and Msh6 PCNA binding motifs
reflect the importance of PCNA interactions for one form of MMR but not
another. Just as replication enzymology differs on the leading and
lagging strands, so too might MMR enzymology differ, e.g. at
the origin, during chain elongation, or during Okazaki fragment
processing. The role of PCNA may also depend on the relative locations
of the mismatch and the strand discrimination signal. For example, the
nick that can serve as a strand discrimination signal in
vitro can be either 5' or 3' to the mismatch. The PCNA binding
motif of MSH3 and MSH6 interacts with one of three potential binding
sites in trimeric PCNA, potentially leaving two other binding sites on
PCNA available for binding by other proteins. This may include a
subunit of DNA polymerase
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INTRODUCTION
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
heterodimer consists of the MutS
homologs MSH2 and MSH6 and is involved in the recognition and repair of base-base and small insertion/deletion mismatches. MutS
is comprised of MSH2 and MSH3 and is primarily responsible for
binding to and correcting insertion/deletion mutations. Other proteins
participate in MMR, including heterodimers of MutL homologs, PCNA,
exonuclease I, replication protein A, replication factor C, and
DNA polymerase
. Working in concert, these proteins complete a DNA
excision/resynthesis reaction that specifically corrects errors in the
nascent strand (1-3).
to enhance its
processivity (reviewed in Ref. 5). PCNA is required at an early step in
DNA mismatch repair that precedes excision of the mismatch (4), as well
as for the DNA resynthesis that follows mismatch excision (6). Yeast
PCNA has been suggested to interact with Mlh1 in vivo (4),
and it interacts with the Msh2-Msh3 heterodimer in vitro
(7). Human PCNA can be co-immunoprecipitated with MSH2, MLH1, and PMS2
(6), and a PCNA affinity column binds MSH2 and MSH6 (8). Yeast strains
with certain mutant PCNA alleles exhibit a mutator phenotype that is
epistatic with mutations in mismatch repair genes (4, 7, 9, 10). One of
these alleles, pol30-104, is lethal in combination with a
null mutation in RAD52, and this synthetic lethality is
suppressed by a mutation in MSH2 (9). This suggests that
this mutant PCNA may reduce strand discrimination such that nicking of
both strands yields lethal double strand breaks.
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EXPERIMENTAL PROCEDURES
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
-D-thiogalactopyranoside. Cells
were lysed in ice-cold 50 mM Tris-HCl, 150 mM
NaCl, 0.2 mg/ml lysozyme, 2 mM EDTA, 1 mM
benzamidine, 0.5 mM phenylmethylsulfonyl fluoride (pH 7.4).
Binding assay mixtures contained 80 µl of 40% glutathione-agarose
beads (Sigma), 300 µl of lysate from cells expressing GST or GST
fusion protein, and 400 µl of lysate from cells expressing human or
yeast PCNA. Mixtures were incubated for 2 h at 4 °C and then
washed five times with 0.8 ml of 50 mM Tris-HCl, 150 mM NaCl (pH 7.4). For binding assays with human PCNA,
protein complexes were eluted by heating to 100 °C with 80 µl of
2× Laemmli SDS sample buffer, separated on a 12% SDS polyacrylamide
gel, and stained with Coomassie Blue. For binding assays with yeast
PCNA, the washed bead mixtures were resuspended in 100 µl of
phosphate-buffered saline containing 5 units thrombin (Amersham
Pharmacia Biotech) and incubated for 3 h at room temperature. Beads were pelleted by centrifugation, and 6 µl of supernatant was
analyzed as above. To characterize proteins associated with the beads
after cleavage, the supernatant was removed, beads were washed, and
proteins were eluted with 80 µl of 2× SDS sample buffer.
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RESULTS
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES

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Fig. 1.
Alignment of yeast and human MutS homologs.
Panel A, putative domain organization of MSH2, MSH3, and
MSH6 proteins in comparison to Taq MutS. Taq MutS
domains (26) are indicated in Roman numerals, and the PCNA
binding motifs of MSH3 and MSH6 are designated as PBM.
Panel B, alignment of the PCNA binding motifs of human and
yeast MSH3 and MSH6 with those of other proteins that interact with
PCNA. Amino acids residue numbers for each protein flank the
peptides.

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Fig. 2.
Interaction of MSH3 and MSH6 peptides with
PCNA. The analysis was performed as described under
"Experimental Procedures." Migration of human (34 kDa) and yeast
(apparent molecular mass, 29 kDa) PCNA and GST fusion peptides
are indicated. Lanes M show molecular mass standards of 200, 116, 97, 66, 55, 36, 31, 21, and 14 kDa. Panel A, human PCNA
binding to human and yeast MSH3 and MSH6 peptides. Despite the use of a
lon ompT protease-deficient bacterial strain for protein
expression and inclusion of protease inhibitors, partial degradation
was observed for some of the GST fusion proteins. As seen previously
(16), the GST-hLigase I fusion protein was more susceptible to
degradation than its F8A/F9A derivative, and a similar trend is evident
for the hMSH3 and MSH6 fusion proteins. Panel B, yeast and
human PCNA binding to yeast Msh3 and Msh6 peptides. Panel C,
immunoblot of intact wild type yeast Msh2-Msh6 complex or
Msh2-Msh6-KQFF mutant complex to detect binding to yPCNA attached to
Affi-gel 15 beads (lanes 1 and 2). Lane
3 illustrates that the Msh2-Msh6-KQFF mutant complex does not bind
to BSA attached to Affi-gel 15 beads. Similarly, the intact wild type
yeast Msh2-Msh6 complex does not bind to BSA attached to Affi-gel 15 beads (not shown).
Mutator effect of mutations in PCNA binding motifs of MSH6 and MSH3

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Fig. 3.
Inhibition of MMR activity by MSH3 and MSH6
PCNA binding peptides. Reactions were performed as described under
"Experimental Procedures," using M13mp2 DNA substrates containing a
G·G mismatch at nucleotide 88 or a 2-base insertion mismatch at
nucleotide 90 of the LacZ gene. The (+) strand is
covalently closed and encodes colorless plaques, whereas the (-)
strand codes for blue plaques and contains a nick at nucleotide
264.
Unrepaired heteroduplexes yield mixed plaques in an MMR-deficient
E. coli strain, whereas repair in the extract decreases the
percentage of mixed plaques and increases the colorless to blue plaque
ratio, because the nick directs repair to the (-) strand. The
change in the ratio of colorless to blue plaques indicated that repair
was indeed strand-specific. All repair values reflect scoring of at
least 500 plaques. Closed boxes, wild type peptides;
open boxes, peptides with alanines substituted for the
conserved phenylalanines.
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DISCUSSION
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEDURES
RESULTS
DISCUSSION
REFERENCES
, the replicative polymerase suggested to
participate in DNA resynthesis during MMR (6, 30). Through this
physical linkage, mismatches that escape proofreading at the primer
terminus may be efficiently recognized just after emerging from the
polymerase. The mismatch may then be removed by a 3'-exonuclease
(identity unknown) via excision of a small number of nucleotides in
what may be an extended form of proofreading. Alternative and not
mutually exclusive models (reviewed in Refs. 1 and 2) are suggested by
the fact that the eukaryotic MMR system can correct a mismatch that is
hundreds of base pairs from a nick. Thus, PCNA might enhance processive movement of the MMR complex as it searches for a distant signal. In any
MMR model, the asymmetry of both the MSH2-MSH6 heterodimer and PCNA may
be important for orienting the MMR machinery to allow discrimination
between the template and nascent strand. MSH3 and MSH6 also participate
in other processes in cells, including cell cycle checkpoint control,
apoptosis, repair of DNA strand breaks, transcription-coupled excision
repair of DNA lesions, and recombination. To the extent that PCNA
participates in these transactions, the ability of MSH3 and MSH6 to
bind to PCNA may be important to their recruitment and functions in
modulating cell survival and spontaneous and induced mutagenesis.
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ACKNOWLEDGEMENTS |
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We thank Wei Yang for information on the structure of Taq MutS and Youri Pavlov, Polina Shcherbakova, and Leroy Worth for critical comments on the manuscript.
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FOOTNOTES |
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* 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.: 919-541-2644; Fax: 919-541-7613; E-mail: kunkel@niehs.nih.gov.
Published, JBC Papers in Press, September 25, 2000, DOI 10.1074/jbc.C000513200
2 The sequences of the oligonucleotides used in this study are available upon request.
3 The wild type and mutant Msh2-Msh6 complexes were each highly purified in 1:1 stoichiometry. K. Drotschmann and T. A. Kunkel, manuscript in preparation.
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ABBREVIATIONS |
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The abbreviations used are: MMR, DNA mismatch repair; PCNA, proliferating cell nuclear antigen; FEN1, flap endonuclease 1; GST, glutathione S-transferase; y, yeast; h, human; BSA, bovine serum albumin; DTT, dithiothreitol; PAGE, polyacrylamide gel electrophoresis.
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