X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine.

Lipscomb, Leigh Ann; Peek, Mary Elizabeth; Morningstar, Marshall L.; Verghis, Susan M.; Miller, Elizabeth M.; Rich, Alexander; Essigmann, John M.; Williams, Loren Dean

doi:10.1073/pnas.92.3.719

Cited by 213 publications

(188 citation statements)

References 38 publications

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“…Yeast Pol also replicates through an 8-oxoG lesion as efficiently and accurately as through an undamaged G (11). An 8-oxoG in the anti conformation pairs with C involving the same three hydrogen bonds as in the G ⅐ C base pair; however, the template strand is significantly distorted in the vicinity of the lesion in the 8-oxoG ⅐ C pair (23,26,29,34). Because of the considerable template distortion in this base pair, replicative polymerases prefer to insert an A opposite 8-oxoG (11,39).…”

Section: Discussionmentioning

confidence: 99%

Requirement of Watson-Crick Hydrogen Bonding for DNA Synthesis by Yeast DNA Polymerase η

Washington

Helquist

Kool

et al. 2003

Molecular and Cellular Biology

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Classical high-fidelity DNA polymerases discriminate between the correct and incorrect nucleotides by using geometric constraints imposed by the tight fit of the active site with the incipient base pair. Consequently, Watson-Crick (W-C) hydrogen bonding between the bases is not required for the efficiency and accuracy of DNA synthesis by these polymerases. DNA polymerase (Pol) is a low-fidelity enzyme able to replicate through DNA lesions. Using difluorotoluene, a nonpolar isosteric analog of thymine unable to form W-C hydrogen bonds with adenine, we found that the efficiency and accuracy of nucleotide incorporation by Pol are severely impaired. From these observations, we suggest that W-C hydrogen bonding is required for DNA synthesis by Pol; in this regard, Pol differs strikingly from classical high-fidelity DNA polymerases.Classical DNA polymerases, such as T7 and Escherichia coli Klenow, synthesize DNA with high fidelity, and they are unable to replicate through DNA lesions (7). By contrast, the eukaryotic polymerase (Pol) is a low-fidelity enzyme (16,28,45) with the ability to replicate through DNA lesions. Pol is unique among eukaryotic DNA polymerases in its proficient ability to replicate through UV-induced cyclobutane pyrimidine dimers (CPDs) (15). Remarkably, both yeast and human Pol insert A's opposite the two T's of a cis-syn thyminethymine (TT) dimer with the same efficiency and accuracy as they insert A's opposite undamaged template bases (16,44). In addition to TT dimers, UV light also induces the formation of CPDs at 5Ј-TC-3Ј and 5Ј-CC-3Ј sites, and genetic studies with Saccharomyces cerevisiae have indicated a role of Pol in the accurate bypass of these lesions as well (48). Because of its role in promoting the error-free bypass of CPDs, inactivation of Pol in humans causes UV hypermutability (43) and results in the cancer-prone syndrome, the variant form of xeroderma pigmentosum (14,27). Yeast Pol also replicates through an 8-oxoguanine (8-oxoG) lesion efficiently and accurately, and genetic studies with S. cerevisiae have corroborated the requirement of Pol in the error-free bypass of this DNA lesion (11).From studies done with nonpolar isosteric analogs of natural DNA bases which lack the ability to form Watson-Crick (W-C) hydrogen (H) bonds, it has been concluded that W-C H bonding is not needed for DNA synthesis by classical high-fidelity DNA polymerases (30,32,33); rather, the geometric fit of the incoming nucleotide with the templating base within the polymerase active site is the principal determinant of the efficiency and fidelity of DNA synthesis in these polymerases (7,9,22). Here we examine the effects of difluorotoluene (F), which is virtually identical in shape, size, and conformation to thymine (T) but lacks the ability to form W-C H bonds with adenine (A) (Fig. 1A), on DNA synthesis by yeast Pol. Because of the inability of F to form W-C H bonds in water (37, 38), this compound is ideal for examining the relative importance of hydrogen bonds and steric effects on DNA synthesis. P...

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Section: Discussionmentioning

confidence: 99%

Requirement of Watson-Crick Hydrogen Bonding for DNA Synthesis by Yeast DNA Polymerase η

Washington

Helquist

Kool

et al. 2003

Molecular and Cellular Biology

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“…1). In the 8-oxoG ⅐ C base pair, the glycosidic bonds of both residues are in the anti configuration, and these bases form normal WatsonCrick hydrogen bonds (25,34). In the 8-oxoG ⅐ A base pair, the glycosidic bond of the 8-oxoG residue is in the syn configuration and it base pairs along its Hoogsteen edge with A (22,29).…”

mentioning

confidence: 99%

“…In the 8-oxoG ⅐ A base pair, the glycosidic bond of the 8-oxoG residue is in the syn configuration and it base pairs along its Hoogsteen edge with A (22,29). With both 8-oxoG ⅐ C and 8-oxoG ⅐ A base pairs, the DNA adopts the normal B form (22,25,29,34); however, when 8-oxoG is in the anti configuration in the 8-oxoG ⅐ C base pair, there are significant structural perturbations of the DNA backbone at the site of the lesion (25).…”

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confidence: 99%

Mechanism of Efficient and Accurate Nucleotide Incorporation Opposite 7,8-Dihydro-8-Oxoguanine by Saccharomyces cerevisiae DNA Polymerase η

Carlson

Washington

2005

Molecular and Cellular Biology

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Most DNA polymerases incorporate nucleotides opposite template 7,8-dihydro-8-oxoguanine (8-oxoG) lesions with reduced efficiency and accuracy. DNA polymerase (Pol) , which catalyzes the error-free replication of template thymine-thymine (TT) dimers, has the unique ability to accurately and efficiently incorporate nucleotides opposite 8-oxoG templates. Here we have used pre-steady-state kinetics to examine the mechanisms of correct and incorrect nucleotide incorporation opposite G and 8-oxoG by Saccharomyces cerevisiae Pol . We found that Pol binds the incoming correct dCTP opposite both G and 8-oxoG with similar affinities, and it incorporates the correct nucleotide bound opposite both G and 8-oxoG with similar rates. While Pol incorporates an incorrect A opposite 8-oxoG with lower efficiency than it incorporates a correct C, it does incorporate A more efficiently opposite 8-oxoG than opposite G. This is mainly due to greater binding affinity for the incorrect incoming dATP opposite 8-oxoG. Overall, these results show that Pol replicates through 8-oxoG without any barriers introduced by the presence of the lesion.

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“…3,4 These lesions distort normal DNA architecture, [5][6][7][8] interfere with gene expression, 9,10 and are associated with the development of breast cancer through template-directed DNA synthesis. 11 Stromal cells reportedly play a key role in the evolution 12,13 and progression [14][15][16] of breast cancer.…”

Section: Introductionmentioning

confidence: 99%

Oxidative Changes in the DNA of Stroma and Epithelium from the Female Breast: Potential Implications for Breast Cancer

Malins

Anderson²,

Ramsey³

et al. 2006

Cell Cycle

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Reciprocal interactions between the stroma and epithelium are considered to be intimately associated with the development of breast cancer. In studies of whole breast tissues, a keen interest exists in the occurrence of the mutagenic DNA lesions 8-hydroxy-2'-deoxyguanosine and 8-hydroxy-2'-deoxyadenosine. However, there is an apparent lack of information on the presence of these lesions in the DNA of the stroma, epithelium, and myoepithelium, despite the fact that these oxidation products may significantly influence reciprocal interactions between these cell types implicated in carcinogenesis. We report age-related increases in concentrations of both lesions in the stromal DNA, which occur roughly commensurate with the known rise in breast cancer incidence between 30 and 40 years of age. However, no further increases in these concentrations occurred in the older women. Plots of lesion concentrations revealed an uneven distribution, with some younger women having relatively high concentrations and some older women having relatively low concentrations. This finding implies that while increased age is a probable factor in lesion accumulations, other factors may also be influential [e.g., cellular concentrations of reactive oxygen species (ROS)]. Distinct differences were found between the base and backbone structures of the stromal DNA from younger women (ages 17 -30), compared to older women (ages 50 -62). In addition, comparisons of matched stromal, epithelial, and myoepithelial DNA (from the same individual) showed no differences in DNA damage, suggesting a random attack by the hydroxyl radical on all three groups. Collectively, the findings imply that the structural changes in DNA described may potentially disrupt normal reciprocal interactions between the cell types, thus increasing breast cancer risk.

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X-ray structure of a DNA decamer containing 7,8-dihydro-8-oxoguanine.

Abstract: We have determined the x-ray structure of a DNA fragment containing 7,8-dihydro-8-oxoguanine (Go).

Cited by 213 publications

References 38 publications

Requirement of Watson-Crick Hydrogen Bonding for DNA Synthesis by Yeast DNA Polymerase η

Requirement of Watson-Crick Hydrogen Bonding for DNA Synthesis by Yeast DNA Polymerase η

Mechanism of Efficient and Accurate Nucleotide Incorporation Opposite 7,8-Dihydro-8-Oxoguanine by Saccharomyces cerevisiae DNA Polymerase η

Oxidative Changes in the DNA of Stroma and Epithelium from the Female Breast: Potential Implications for Breast Cancer

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