The Phe-X-Glu DNA binding motif of MutS. The role of hydrogen bonding in mismatch recognition

8-oxoguanine incorporation into DNA repeats in vitro and mismatch recognition by MutSalpha

DNA 8-oxoguanine (8-oxoG) causes transversions and is also implicated in frameshifts. We previously identified the dNTP pool as a likely source of mutagenic DNA 8-oxoG and demonstrated that DNA mismatch repair prevented oxidation-related frameshifts in mononucleotide repeats. Here, we show that both Klenow fragment and DNA polymerase α can utilize 8-oxodGTP and incorporate the oxidized purine into model frameshift targets. Both polymerases incorporated 8-oxodGMP opposite C and A in repetitive DNA sequences and efficiently extended a terminal 8-oxoG. The human MutSα mismatch repair factor recognized DNA 8-oxoG efficiently in some contexts that resembled frameshift intermediates in the same C or A repeats. DNA 8-oxoG in other slipped/mispaired structures in the same repeats adopted configurations that prevented recognition by MutSα and by the OGG1 DNA glycosylase thereby rendering it invisible to DNA repair. These findings are consistent with a contribution of oxidative DNA damage to frameshifts. They also suggest how mismatch repair might reduce the burden of DNA 8-oxoG and prevent frameshift formation.

A set of nonpolar thymidine nucleoside analogues with gradually increasing size

[structure: see text] We describe a series of nonpolar nucleoside analogues having similar shapes and gradually increasing size. The structure of the nucleobase thymine was mimicked with toluene derivatives, replacing O2/O4 with hydrogen, fluorine, chlorine, bromine, and iodine. Glycosidic bonds were formed by reactions of lithiated 2,4-dihalotoluenes with a deoxyribonolactone derivative. Structural analysis by NMR showed similar conformations across the series. The compounds are useful for study of the biological recognition of nucleotides and nucleic acids.

Determination of protein-DNA binding constants and specificities from statistical analyses of single molecules: MutS-DNA interactions

Atomic force microscopy (AFM) is a powerful technique for examining the conformations of protein–DNA complexes and determining the stoichiometries and affinities of protein–protein complexes. We extend the capabilities of AFM to the determination of protein–DNA binding constants and specificities. The distribution of positions of the protein on the DNA fragments provides a direct measure of specificity and requires no knowledge of the absolute binding constants. The fractional occupancies of the protein at a given position in conjunction with the protein and DNA concentrations permit the determination of the absolute binding constants. We present the theoretical basis for this analysis and demonstrate its utility by characterizing the interaction of MutS with DNA fragments containing either no mismatch or a single mismatch. We show that MutS has significantly higher specificities for mismatches than was previously suggested from bulk studies and that the apparent low specificities are the result of high affinity binding to DNA ends. These results resolve the puzzle of the apparent low binding specificity of MutS with the expected high repair specificities. In conclusion, from a single set of AFM experiments, it is possible to determine the binding affinity, specificity and stoichiometry, as well as the conformational properties of the protein–DNA complexes.

A series of nonpolar thymidine analogues of increasing size: DNA base pairing and stacking properties

[reaction: see text] We describe the properties in DNA of a set of five nonpolar nucleoside mimics in which shape is similar but size is increased gradually. The compounds vary in the size of their exocyclic substituents, which range from hydrogen to iodine, and are designed to test the steric effects of nucleosides, nucleotides, and DNA in biological systems in a systematic way. We describe the conversion of toluene, 2,4-difluorotoluene, 2,4-dichlorotoluene, 2,4-dibromotoluene, and 2,4-diiodotoluene deoxyribosides into suitably protected phosphoramidite derivatives and their incorporation into synthetic DNAs. Studies of their behavior in the context of hexamer and dodecamer duplexes were carried out, with comparison to natural thymine. Thermal melting data with compounds in 5' dangling positions showed that all five compounds stack more strongly than thymine, and all the dihalo-substituted cases stack more strongly than the unsubstituted toluene case. Stacking correlated with surface area and hydrophobicity, both of which increase across the series. In base-pairing studies, all five compounds showed destabilized pairing opposite natural bases (relative to thymine-adenine pairing), as expected. Notably, pairing among the nonpolar base analogues was considerably more stable, and some of the pairs involving the largest analogues showed stability equal to that of a natural thymine-adenine pair. The results establish the base pairing properties of a potentially useful new series of biochemical probes for DNA-protein interactions and also identify a set of new, stable hydrophobic base pairs for designed genetic pairing systems.

Developing the use of mismatch binding proteins for discovering rare somatic mutations

A method for detecting rare, unknown, somatic mutations could allow presymptomatic cancer screening from human fluids. Immobilized mismatch binding protein can bind DNA heteroduplexes while allowing homoduplexes to be washed away, thus enriching for rare mutations. We examined the potential use, for mutation enrichment, of a fusion protein of maltose binding protein and the mismatch binding protein TaqMutS (MBP-MutS). Unlabeled and fluorescent-labeled oligonucleotides, either perfectly complementary or with single nucleotide mismatches or deletions, were combined to form homo- or heteroduplexes that were then mixed at low ratios of hetero- to homoduplexes and enriched for heteroduplexes. Enrichment was observed using a capillary DNA sequencer. A single base deletion oligonucleotide was enriched by a factor of 29, and a mismatch oligonucleotide was enriched by a factor of 2. N-1 oligonucleotide synthesis fragments were enriched more than were mismatches, suggesting that these deletion fragments may compete for MutS and impede enrichment of mismatches. Purification of oligonucleotides by high pressure liquid chromatography or polyacrylamide gel electrophoresis failed to remove n-1 fragments, thus overcoming this obstacle to enrichment of mismatch mutations may require alternative strategies, such as developing new purification methods or avoiding the use of synthetic oligonucleotides before enrichment.

DNA mismatch binding activities in Chlorella pyrenoidosa extracts and affinity isolation of G-T mismatch binding proteins

DNA mismatch recognition proteins contained in the extracts of unicellular alga Chlorella pyrenoidosa were isolated by affinity adsorption and 2-D gel electrophoresis. Incubation of the algal extracts with a 38-mer duplex oligonucleotide carrying a single DNA simple mispair generated a few gel retardation complexes. G-T mispair was recognized significantly better than C-T, G-G, G-A, and C-C mispairs by the algal extracts and these extracts bound very weakly to G-A and C-C mispairs, displaying a universal trend of mismatch binding efficiency. The levels of mismatch recognition complexes were slightly increased in the presence of 1 mM ATP. Two 13-kDa G-T binding polypeptides possessing pIs of 5.3 and 5.5 were isolated after resolving affinity-captured proteins by 2-D gel electrophoresis and the two factors were found to bind 5.5- and 2.8-fold stronger to heteroduplex than to homoduplex DNA, respectively. No proteins significantly homologous to the two algal G-T binding proteins were found by peptide mass fingerprinting (PMF). The sequence of a peptide generated from trypsin-cleavage of one G-T binding factor (pI 5.5) could be aligned with the amino acid sequences that form the C-terminal active sites of human and mouse mismatch-specific uracil/thymine-DNA glycosylases, suggesting the possibility of this factor as an algae- or a Chlorella-specific DNA mismatch glycosylase.

Correcting errors in synthetic DNA through consensus shuffling

Although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1-3 random errors/kb of DNA. Here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic DNA. In this method, errors are revealed as mismatches by re-hybridization of the population. The DNA is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding protein (MutS). PCR assembly of the remaining fragments yields a new population of full-length sequences enriched for the consensus sequence of the input population. We show that two iterations of consensus shuffling improved a population of synthetic green fluorescent protein (GFPuv) clones from approximately 60 to >90% fluorescent, and decreased errors 3.5- to 4.3-fold to final values of approximately 1 error per 3500 bp. In addition, two iterations of consensus shuffling corrected a population of GFPuv clones where all members were non-functional, to a population where 82% of clones were fluorescent. Consensus shuffling should facilitate the rapid and accurate synthesis of long DNA sequences.

Impact of mutS inactivation on foreign DNA acquisition by natural transformation in Pseudomonas stutzeri

In prokaryotic mismatch repair the MutS protein and its homologs recognize the mismatches. The mutS gene of naturally transformable Pseudomonas stutzeri ATCC 17587 (genomovar 2) was identified and characterized. The deduced amino acid sequence (859 amino acids; 95.6 kDa) displayed protein domains I to IV and a mismatch-binding motif similar to those in MutS of Escherichia coli. A mutS::aac mutant showed 20- to 163-fold-greater spontaneous mutability. Transformation experiments with DNA fragments of rpoB containing single nucleotide changes (providing rifampin resistance) indicated that mismatches resulting from both transitions and transversions were eliminated with about 90% efficiency in mutS+. The mutS+ gene of strain ATCC 17587 did not complement an E. coli mutant but partially complemented a P. stutzeri JM300 mutant (genomovar 4). The declining heterogamic transformation by DNA with 0.1 to 14.6% sequence divergence was partially alleviated by mutS::aac, indicating that there was a 14 to 16% contribution of mismatch repair to sexual isolation. Expression of mutS+ from a multicopy plasmid eliminated autogamic transformation and greatly decreased heterogamic transformation, suggesting that there is strong limitation of MutS in the wild type for marker rejection. Remarkably, mutS::aac altered foreign DNA acquisition by homology-facilitated illegitimate recombination (HFIR) during transformation, as follows: (i) the mean length of acquired DNA was increased in transformants having a net gain of DNA, (ii) the HFIR events became clustered (hot spots) and less dependent on microhomologies, which may have been due to topoisomerase action, and (iii) a novel type of transformants (14%) had integrated foreign DNA with no loss of resident DNA. We concluded that in P. stutzeri upregulation of MutS could enforce sexual isolation and downregulation could increase foreign DNA acquisition and that MutS affects mechanisms of HFIR.

Analysis of the functional domains of the mismatch repair homologue Msh1p and its role in mitochondrial genome maintenance

Mitochondrial DNA (mtDNA) repair occurs in all eukaryotic organisms and is essential for the maintenance of mitochondrial function. Evidence from both humans and yeast suggests that mismatch repair is one of the pathways that functions in overall mtDNA stability. In the mitochondria of the yeast Saccharomyces cerevisiae, the presence of a homologue to the bacterial MutS mismatch repair protein, MSH1, has long been known to be essential for mitochondrial function. The mechanisms for which it is essential are unclear, however. Here, we analyze the effects of two point mutations, msh1-F105A and msh1-G776D, both predicted to be defective in mismatch repair; and we show that they are both able to maintain partial mitochondrial function. Moreover, there are significant differences in the severity of mitochondrial disruption between the two mutants that suggest multiple roles for Msh1p in addition to mismatch repair. Our overall findings suggest that these additional predicted functions of Msh1p, including recombination surveillance and heteroduplex rejection, may be primarily responsible for its essential role in mtDNA stability.

Cloning of the mismatch recognition protein MSH2 from zebrafish (Danio rerio) and its developmental stage-dependent mRNA expression

Eukaryotic mismatch repair of simple base mispairs and small insertion-deletion loops is activated by the binding of a heterodimeric complex composed of MutS homolog 2(MSH2) and MSH6. Here we report the cloning of zebrafish (Danio rerio) MSH2 (zMSH2) cDNA that has an open reading frame of 2811 nucleotides encoding a polypeptide of 936 amino acids. The deduced amino acid sequence of zMSH2 shares a 69% identity to both human and mouse MSH2. The zMSH2 protein contains a putative tyrosine-42 mismatch-contacting residue located at the N-terminal mismatch recognition region and four C-terminal ATP-binding consensus sequences conserved among MutS homologs. The 105-kDa recombinant zMSH2 bound apparently stronger to a G-T heteroduplex than to a homoduplex probe as shown by a gel shift assay. A preferential expression of both zMSH2 and zMSH6 mRNA in early embryos was found by Northern blot analysis. Whole mount in situ hybridization revealed a major expression of zMSH2 in different regions of the brain, including eyes, telencephalon, and the fourth ventricle in 12- to 48-h-old embryos. The production of zMSH2 mRNA gradually decreased in more mature 60- to 120-h-old zebrafish, reflecting a positive correlation between the amount of proliferating cells and MSH gene expression.

DNA mismatch repair: molecular mechanisms and biological function

DNA mismatch repair (MMR) guards the integrity of the genome in virtually all cells. It contributes about 1000-fold to the overall fidelity of replication and targets mispaired bases that arise through replication errors, during homologous recombination, and as a result of DNA damage. Cells deficient in MMR have a mutator phenotype in which the rate of spontaneous mutation is greatly elevated, and they frequently exhibit microsatellite instability at mono- and dinucleotide repeats. The importance of MMR in mutation avoidance is highlighted by the finding that defects in MMR predispose individuals to hereditary nonpolyposis colorectal cancer. In addition to its role in postreplication repair, the MMR machinery serves to police homologous recombination events and acts as a barrier to genetic exchange between species.

Direct IBD mapping: identical-by-descent mapping without genotyping

Direct identical-by-descent (IBD) mapping is a technique, that combines genomic mismatch scanning (GMS) and DNA microarray technology, for mapping regions shared IBD between two individuals without locus-by-locus genotyping or sequencing. The lack of reagents has limited its widespread application. In particular, two key reagents have been limiting, 1). mismatch repair proteins MutS, L and H, and 2). genomic microarrays for identifying the genomic locations of the GMS-selected IBD fragments. Here, we describe steps that optimized the procedure and resources that will facilitate the development of direct IBD mapping.

Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates

We have refined a series of isomorphous crystal structures of the Escherichia coli DNA mismatch repair enzyme MutS in complex with G:T, A:A, C:A and G:G mismatches and also with a single unpaired thymidine. In all these structures, the DNA is kinked by approximately 60 degrees upon protein binding. Two residues widely conserved in the MutS family are involved in mismatch recognition. The phenylalanine, Phe 36, is seen stacking on one of the mismatched bases. The same base is also seen forming a hydrogen bond to the glutamate Glu 38. This hydrogen bond involves the N7 if the base stacking on Phe 36 is a purine and the N3 if it is a pyrimidine (thymine). Thus, MutS uses a common binding mode to recognize a wide range of mismatches.

Msh2 separation of function mutations confer defects in the initiation steps of mismatch repair

In eukaryotes the MSH2-MSH3 and MSH2-MSH6 heterodimers initiate mismatch repair (MMR) by recognizing and binding to DNA mismatches. The MLH1-PMS1 heterodimer then interacts with the MSH proteins at or near the mismatch site and is thought to act as a mediator to recruit downstream repair proteins. Here we analyzed five msh2 mutants that are functional in removing 3' non-homologous tails during double-strand break repair but are completely defective in MMR. Because non-homologous tail removal does not require MSH6, MLH1, or PMS1 functions, a characterization of the msh2 separation of function alleles should provide insights into early steps in MMR. Using the Taq MutS crystal structure as a model, three of the msh2 mutations, msh2-S561P, msh2-K564E, msh2-G566D, were found to map to a domain in MutS involved in stabilizing mismatch binding. Gel mobility shift and DNase I footprinting assays showed that two of these mutations conferred strong defects on MSH2-MSH6 mismatch binding. The other two mutations, msh2-S656P and msh2-R730W, mapped to the ATPase domain. DNase I footprinting, ATP hydrolysis, ATP binding, and MLH1-PMS1 interaction assays indicated that the msh2-S656P mutation caused defects in ATP-dependent dissociation of MSH2-MSH6 from mismatch DNA and in interactions between MSH2-MSH6 and MLH1-PMS1. In contrast, the msh2-R730W mutation disrupted MSH2-MSH6 ATPase activity but did not strongly affect ATP binding or interactions with MLH1-PMS1. These results support a model in which MMR can be dissected into discrete steps: stable mismatch binding and sensing, MLH1-PMS1 recruitment, and recycling of MMR components.

High-fidelity in vivo replication of DNA base shape mimics without Watson-Crick hydrogen bonds

We report studies testing the importance of Watson-Crick hydrogen bonding, base-pair geometry, and steric effects during DNA replication in living bacterial cells. Nonpolar DNA base shape mimics of thymine and adenine (abbreviated F and Q, respectively) were introduced into Escherichia coli by insertion into a phage genome followed by transfection of the vector into bacteria. Genetic assays showed that these two base mimics were bypassed with moderate to high efficiency in the cells and with very high efficiency under damage-response (SOS induction) conditions. Under both sets of conditions, the T-shape mimic (F) encoded genetic information in the bacteria as if it were thymine, directing incorporation of adenine opposite it with high fidelity. Similarly, the A mimic (Q) directed incorporation of thymine opposite itself with high fidelity. The data establish that Watson-Crick hydrogen bonding is not necessary for high-fidelity replication of a base pair in vivo. The results suggest that recognition of DNA base shape alone serves as the most powerful determinant of fidelity during transfer of genetic information in a living organism.

A porphyrin C-nucleoside incorporated into DNA

[reaction: see text] A free porphyrin coupled on 2-deoxy-D-ribose was synthesized and incorporated into DNA via phosphoramidite chemistry. Substitution at the ends of a 5'-modified self-complementary duplex was found to be thermally and thermodynamically stabilizing. The porphyrin moiety strongly intercalates in the duplex when located near the center, and retains its fluorescence properties in DNA.

A highly effective nonpolar isostere of deoxyguanosine: synthesis, structure, stacking, and base pairing

We describe the preparation and structure of the deoxyribonucleoside of 4-fluoro-6-methylbenzimidazole, abbreviated dH (8), which acts as a close shape mimic of the nucleoside deoxyguanosine. The nucleoside is prepared from 2-fluoro-4-methylaniline in seven steps. The X-ray crystal structure reveals a (-sc) glycosidic orientation, an S conformation for the deoxyribose moiety, and quite close shape mimicry of guanine by the substituted benzimidazole. Conformational studies by (1)H NMR and (1)H-(1)H ROESY experiments reveal an S-type conformation and an anti glycosidic orientation in solution (D(2)O), essentially the same as that of deoxyguanosine. Base-stacking studies in a "dangling end" context reveal that the benzimidazole base mimic stacks more strongly than all four natural bases, and more strongly than its counterpart guanine by 1.1 kcal/mol. Base-pairing studies in a 12mer DNA duplex show that, like other nonpolar nucleoside isosteres, H is destabilizing and nonselective when paired opposite natural bases. However, when paired opposite another nonpolar isostere, difluorotoluene (F), a mimic of thymine, the pair exhibits stability approaching that of its natural analogue, a G-T (wobble) base pair. The nucleoside analogue dH will be useful in studies of protein-DNA interactions, and the H-F base pair will serve as a structurally and thermodynamically close mimic of G-T in studies of DNA mismatch repair enzymes.

Dominant Saccharomyces cerevisiae msh6 mutations cause increased mispair binding and decreased dissociation from mispairs by Msh2-Msh6 in the presence of ATP

A previous study described four dominant msh6 mutations that interfere with both the Msh2-Msh6 and Msh2-Msh3 mismatch recognition complexes (Das Gupta, R., and Kolodner, R. D. (2000) Nat. Genet. 24, 53-56). Modeling predicted that two of the amino acid substitutions (G1067D and G1142D) interfere with protein-protein interactions at the ATP-binding site-associated dimer interface, one (S1036P) similarly interferes with protein-protein interactions and affects the Msh2 ATP-binding site, and one (H1096A) affects the Msh6 ATP-binding site. The ATPase activity of the Msh2-Msh6-G1067D and Msh2-Msh6-G1142D complexes was inhibited by GT, +A, and +AT mispairs, and these complexes showed increased binding to GT and +A mispairs in the presence of ATP. The ATPase activity of the Msh2-Msh6-S1036P complex was inhibited by a GT mispair, and it bound the GT mispair in the presence of ATP, whereas its interaction with insertion mispairs was unchanged compared with the wild-type complex. The ATPase activity of the Msh2-Msh6-H1096A complex was generally attenuated, and its mispair-binding behavior was unaffected. These results are in contrast to those obtained with the wild-type Msh2-Msh6 complex, which showed mispair-stimulated ATPase activity and ATP inhibition of mispair binding. These results indicate that the dominant msh6 mutations cause more stable binding to mispairs and suggest that there may be differences in how base base and insertion mispairs are recognized.

DNA binding properties of the yeast Msh2-Msh6 and Mlh1-Pms1 heterodimers

We describe here our recent studies of the DNA binding properties of Msh2-Msh6 and Mlh1-Pms1, two protein complexes required to repair mismatches generated during DNA replication. Mismatched DNA binding by Msh2-Msh6 was probed by mutagenesis based on the crystal structure of the homologous bacterial MutS homodimer bound to DNA. The results suggest that several amino acid side chains inferred to interact with the DNA backbone near the mismatch are critical for repair activity. These contacts, which are different in Msh2 and Msh6, likely facilitate stacking and hydrogen bonding interactions between side chains in Msh6 and the mismatched base, thus stabilizing a kinked DNA conformation that permits subsequent repair steps coordinated by the Mlh1-Pms1 heterodimer. Mlh1-Pms1 also binds to DNA, but independently of a mismatch. Mlh1-Pms1 binds short DNA substrates with low affinity and with a slight preference for single-stranded DNA. It also binds longer duplex DNA molecules, but with a higher affinity indicative of cooperative binding. Indeed, imaging by atomic force microscopy reveals cooperative DNA binding and simultaneous interaction with two DNA duplexes. The novel DNA binding properties of Mlh1-Pms1 may be relevant to signal transduction during DNA mismatch repair and to recombination, meiosis and cellular responses to DNA damage.

Asymmetric recognition of DNA local distortion. Structure-based functional studies of eukaryotic Msh2-Msh6

Crystal structures of bacterial MutS homodimers bound to mismatched DNA reveal asymmetric interactions of the two subunits with DNA. A phenylalanine and glutamate of one subunit make mismatched base-specific interactions, and residues of both subunits contact the DNA backbone surrounding the mismatched base, but asymmetrically. A number of amino acids in MutS that contact the DNA are conserved in the eukaryotic Msh2-Msh6 heterodimer. We report here that yeast strains with amino acids substituted for residues inferred to interact with the DNA backbone or mismatched base have elevated spontaneous mutation rates consistent with defective mismatch repair. Purified Msh2-Msh6 with substitutions in the conserved Phe(337) and Glu(339) in Msh6 thought to stack or hydrogen bond, respectively, with the mismatched base do have reduced DNA binding affinity but normal ATPase activity. Moreover, wild-type Msh2-Msh6 binds with lower affinity to mismatches with thymine replaced by difluorotoluene, which lacks the ability to hydrogen bond. The results suggest that yeast Msh2-Msh6 interacts asymmetrically with the DNA through base-specific stacking and hydrogen bonding interactions and backbone contacts. The importance of these contacts decreases with increasing distance from the mismatch, implying that interactions at and near the mismatch are important for binding in a kinked DNA conformation.