Influence of pH on the conformation and stability of mismatch base-pairs in DNA

Brown, Tom; Leonard, Gordon A.; Booth, Ewan D.; Kneale, Geoff

doi:10.1016/0022-2836(90)90320-l

Cited by 108 publications

(89 citation statements)

References 12 publications

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“…Moreover, the C6-keto group of mismatched G, presented in the major groove as in G(syn)-A(anti), is less critical for SpMYH reactivity than MutY by comparing the activities of both enzymes with A/G and A/2AP mismatches. The N-1 of adenine (located in the minor groove) is protonated in the A/C mispair (52). The difference of cleavage on A/C mismatch by SpMYH and MutY may be related to the A/C structure.…”

Section: Discussionmentioning

confidence: 99%

Characterization of the Recombinant MutY Homolog, an Adenine DNA Glycosylase, from Yeast Schizosaccharomyces pombe

Fawcett

1998

Journal of Biological Chemistry

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The mutY homolog (SpMYH) gene from a cDNA library of Schizosaccharomyces pombe encodes a protein of 461 amino acids that displays 28 and 31% identity to Escherichia coli MutY and human MutY homolog (MYH), respectively. Expressed SpMYH is able to complement an E. coli mutY mutant to reduce the mutation rate. Similar to E. coli MutY protein, purified recombinant SpMYH expressed in E. coli has adenine DNA glycosylase and apurinic/apyrimidinic lyase activities on A/G-and A/7,8-dihydro-8-oxoguanine (8-oxoG)-containing DNA. However, both enzymes have different salt requirements and slightly different substrate specificities. SpMYH has greater glycosylase activity on 2-aminopurine/G and A/2-aminopurine but weaker activity on A/C than E. coli MutY. Both enzymes also have different substrate binding affinity and catalytic parameters. Although SpMYH has great affinity to A/8-oxoG-containing DNA as MutY, the binding affinity to A/G-containing DNA is substantially lower for SpMYH than MutY. SpMYH has similar reactivity to both A/G-and A/8-oxoG-containing DNA; however, MutY cleaves A/G-containing DNA about 3-fold more efficiently than it does A/8-oxoG-containing DNA. Thus, SpMYH is the functional eukaryotic MutY homolog responsible for reduction of 8-oxoG mutational effect.Cellular and organism aging have been correlated with accumulated DNA damage (1, 2). Oxygen is metabolized inside the cell by a series of one-electron reductions with the generation of reactive and potentially damaging intermediates called reactive oxygen species (3). The frequency of oxidative damage to DNA has been estimated at 10 4 lesions/cell/day in humans (4). 8- ) is one of the most stable products of oxidative DNA damage. The formation of GO in DNA, if not repaired, can lead to misincorporation of A opposite to the GO lesion and result in G:C to T:A transversions (5-8). In Escherichia coli, a family of enzymes, MutY, MutM, and MutT, is involved in defending against the mutagenic effects of GO lesions (9 -11). The MutT protein has nucleotide triphosphatase activity, which eliminates 8-oxo-dGTP from the nucleotide pool (12). The MutM protein (Fpg protein) provides a second level of defense by removing both mutagenic GO adducts and ring-opened purine lesions (13)(14)(15)(16). The E. coli MutY is an adenine glycosylase that is responsible for the correction of A/GO as well as A/G and A/C mismatches (9,(17)(18)(19)(20)(21)(22). MutY removes misincorporated adenines paired with GO lesions and reduces the GO mutational effects. Recent results show that MutY and the N-terminal catalytic domain can be trapped in a stable covalent enzyme-DNA intermediate in the presence of sodium borohydride (23)(24)(25) and support the hypothesis that MutY contains both DNA glycosylase and AP lyase activities.MutY homologous (MYH) activities have been identified in human HeLa (26) and calf thymus (27) extracts. Both human and calf MYH systems share similar features with the E. coli mutY-dependent pathway: mismatch specificities to A/G, A/C, and A/GO, and cleavage of the A ...

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Section: Discussionmentioning

confidence: 99%

Characterization of the Recombinant MutY Homolog, an Adenine DNA Glycosylase, from Yeast Schizosaccharomyces pombe

Fawcett

1998

Journal of Biological Chemistry

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“…The structures of oligonucleotides with AoC or AoG within different flanking sequences have been studied by x-ray crystallography and NMR (1-4, 34-38). The AoC mispair has been shown to be stabilized by protonation of adenine (34). In contrast, an AoG mismatch can adopt different conformations: A(anti)/G(anti), A(syn)/G(anti), or A(anti)/G(syn) (1)(2)(3)(4)(35)(36)(37).…”

Section: Discussionmentioning

confidence: 99%

Escherichia coli MutY protein has both N-glycosylase and apurinic/apyrimidinic endonuclease activities on A.C and A.G mispairs.

Tsai-Wu

Liu

1992

Proc. Natl. Acad. Sci. U.S.A.

141

143

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In Escherichia coli the mutY (or micA)-dependent DNA mismatch repair pathway can convert AoG and AoC mismatches to C-G and G-C base pairs, respectively, through a short repair-tract mechanism. The MutY protein has been purified to near homogeneity from an E. coli overproducer strain. Purified MutY has been shown to contain both N-glycosylase and 3' apurinic/apyrimidinic (AP) endonuclease activities. The N-glycosylase removes the mispaired adenines of AoG and AoC mismatches, and the AP endonuclease acts on the first phosphodiester bond 3' to the AP sites. The N-glycosylase and the nicking (combined N-glycosylase and AP endonuclease) activities copurifiled through multiple chromatographic steps without a change in relative specific activities. (5) and also can arise from genetic recombination between two closely related sequences. There are two pathways capable of repairing AoG mismatches in Escherichia coli. One is dependent on ATP, dam methylation, and mutHLSU gene functions (6-13). The other is dependent on mutY(or micA) and polA functions but not the above three factors (14-17). The dam-dependent pathway can repair some AoG mismatches to either C0G or A-T base pairs depending on the state of methylation. The mutY (or micA)-dependent pathway acts on AoG mismatches to restore C-G base pairs exclusively (15,17).In the absence of ATP, extracts from mutY (or micA) mutants cannot bind, nick, or repair heteroduplex DNA containing AoG mismatches (14, 18). The defect in AoG mismatch repair of mutY, a mutator, suggests that this repair process is responsible for the reduction of C-G-to-A-T transversions. The mutY (or micA) mutants are also defective in repairing AoC mismatches in transfected A heteroduplex DNAs (16). Recent cloning and sequence analyses showed mutY and micA are different alleles of one gene (18,19). The mutY gene encodes a 39.1-kDa protein with homology to E. coli endonuclease III, which has both glycosylase and 3' apurinic/apyrimidinic (AP) endonuclease activities (20-22).The AP endonuclease activity of endonuclease III is the result of the enzyme catalyzing a 3-elimination reaction (23).

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“…Of our 78 selected mutants, 50 have the potential to form either AÁC or GÁU mismatches at positions 787, 795 (Table 1). Since protonated AÁC (A ÁC) and GÁU are known to be isomorphous (Brown et al, 1990;Hunter et al, 1986), we measured the melting pro®le of the wild-type 790 sequence at pH 7 and at pH 5.3 (Figure 3). Both curves are biphasic with transitions at 20 to 30 C and 60 to 70 C. The higher melting transition is oligonucleotide concentration independent, indicating unimolecular unfolding of the hairpin.…”

Section: Thermodynamic Analysismentioning

confidence: 99%

In vivo determination of RNA Structure-Function relationships: analysis of the 790 loop in ribosomal RNA 1 1Edited by D. E. Draper

Lee

Varma

SantaLucia

et al. 1997

Journal of Molecular Biology

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Influence of pH on the conformation and stability of mismatch base-pairs in DNA

Cited by 108 publications

References 12 publications

Characterization of the Recombinant MutY Homolog, an Adenine DNA Glycosylase, from Yeast Schizosaccharomyces pombe

Characterization of the Recombinant MutY Homolog, an Adenine DNA Glycosylase, from Yeast Schizosaccharomyces pombe

Escherichia coli MutY protein has both N-glycosylase and apurinic/apyrimidinic endonuclease activities on A.C and A.G mispairs.

In vivo determination of RNA Structure-Function relationships: analysis of the 790 loop in ribosomal RNA 1 1Edited by D. E. Draper

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