To counteract the deleterious effects of DNA damage, cells are equipped with specialized polymerases to bypass DNA lesions. Previous biochemical studies revealed that DinB family DNA polymerases, including Escherichia coli DNA polymerase IV and human DNA polymerase , efficiently incorporate the correct nucleotide opposite some N DNA is susceptible to damage by endogenous and exogenous agents (1). To minimize cell death arising from replication blockage and mutations emanating from nucleotide misincorporation opposite the damage site, cells are equipped with several pathways to repair DNA lesions (2). Additionally, cells have evolved two major mechanisms to tolerate unrepaired DNA lesions (3), including homologous recombination and translesion synthesis (TLS) 2 (3). In this regard, synthesis past many DNA lesions requires the replacement of replicative DNA polymerases with one or a few specialized polymerases, most of which belong to the Y-family (4). Along this line, phylogenetic analysis revealed five branches of Y-family polymerases, which include UmuC, DinB, polymerase , polymerase , and REV1 (4, 5). All of these, except for UmuC, are found in eukaryotic cells (4,5). Apart from the Y-family DNA polymerases, some B-family DNA polymerases also participate in TLS. These include DNA polymerase II in Escherichia coli and polymerase , which is composed of the catalytic subunit REV3 and the regulatory subunit REV7, in eukaryotic cells (4, 5). These specialized DNA polymerases are characterized by their relatively low fidelity in replicating undamaged DNA but have the capability to bypass those DNA lesions that normally block DNA synthesis by replicative DNA polymerases (4). It was advocated that specialized DNA polymerases are evolved by nature to copy DNA base damage accurately, but they no longer bear the ability to replicate unmodified DNA with high fidelity (6). The best known example of this is the efficient and accurate bypass of cis,syn-cyclobutane pyrimidine dimers by polymerase (7,8), which is encoded by the xeroderma pigmentosum-variant gene (i.e. POLH) in humans (9). Xeroderma pigmentosum-variant patients exhibit elevated susceptibility to developing skin cancer (10). Several recent studies also demonstrated that DinB DNA polymerase, a Y-family polymerase conserved in all three kingdoms of life (11), can insert the correct dCMP opposite several N 2 -substituted guanine lesions at an efficiency that is similar to or better than opposite an unmodified guanine (12)(13)(14). The x-ray crystal structure of the catalytic core of human DNA polymerase , along with primer/template DNA and an incoming nucleotide, reveals the lack of steric hindrance in the minor groove at the primer-template junction (15), which may account for the tolerance of polymerase toward the minor groove N 2 -dG lesions. By using shuttle vector technology, we also showed that DinB (i.e. polymerase IV) is the major polymerase involved in the accurate bypass of the two diastereomers of N 2 -(1-carboxyethyl)-2Ј-deoxyguanosine (N 2 -CEdG) in ...

A new type of interstrand cross-link resulting from the reaction of a DNA abasic site with a guanine residue on the opposing strand of the double helix was recently identified, but the chemical connectivity of the cross-link was not rigorously established. The work described here was designed to characterize the chemical structure and properties of dG–AP cross-links generated in duplex DNA. The approach involved characterization of the nucleoside cross-link “remnant” released by enzymatic digestion of DNA duplexes containing the dG–AP cross-link. We first carried out a chemical synthesis and complete spectroscopic structure determination of the putative cross-link remnant 9b composed of a 2-deoxyribose adduct attached to the exocyclic N2-amino group of dG. A reduced analogue of the cross-link remnant was also prepared (11b). Liquid chromatography–tandem mass spectrometric (LC-MS/MS) analysis revealed that the retention times and mass spectral properties of synthetic standards 9b and 11b matched those of the authentic cross-link remnants released by enzymatic digestion of duplexes containing the native and reduced dG–AP cross-link, respectively. These results establish the chemical connectivity of the dG–AP cross-link released from duplex DNA and provide a foundation for detection of this lesion in biological samples. The dG–AP cross-link in duplex DNA was remarkably stable, decomposing with a half-life of 22 days at pH 7 and 23 °C. The intrinsic chemical stability of the dG–AP cross-link suggests that this lesion in duplex DNA may have the power to block DNA-processing enzymes involved in transcription and replication.

Causal links exist between smoking cigarettes and cancer development. Some genotoxic agents in cigarette smoke are capable of alkylating nucleobases in DNA and higher levels of ethylated DNA lesions were observed in smokers than non-smokers. In this study, we examined comprehensively how the regioisomeric O2-, N3- and O4-ethylthymidine (O2-, N3- and O4-EtdT) perturb DNA replication mediated by purified human DNA polymerases (hPol) η, κ, and ι, yeast DNA polymerase ζ (yPol ζ), and the exonuclease-free Klenow fragment (Kf−) of Escherichia coli DNA polymerase I. Our results showed that hPol η and Kf− could bypass all three lesions and generate full-length replication products, whereas hPol ι stalled after inserting a single nucleotide opposite the lesions. Bypass carried out by hPol κ and yPol ζ differed markedly amongst the three lesions: Consistent with its known capability in bypassing efficiently the minor-groove N2-substituted 2′-deoxyguanosine lesions, hPol κ was able to bypass O2-EtdT, though it experienced great difficulty in bypassing N3-EtdT and O4-EtdT; yPol ζ was only modestly blocked by O4-EtdT, but the polymerase was highly hindered by O2-EtdT and N3-EtdT. LC-MS/MS analysis of the replication products revealed that DNA synthesis opposite O4-EtdT was highly error-prone, with dGMP being preferentially inserted, while the presence of O2-EtdT and N3-EtdT in template DNA directed substantial frequencies of misincorporation of dGMP and, for hPol ι and Kf−, dTMP. Thus, our results suggested that O2-EtdT and N3-EtdT may also contribute to the AT→TA and AT→GC mutations observed in cells and tissues of animals exposed to ethylating agents.

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O2- and O4-methylthymidine (O2-MdT and O4-MdT) can be induced in tissues of laboratory animals exposed with N-methyl-N-nitrosourea, a known carcinogen. These two O-methylated DNA adducts have been shown to be poorly repaired and may contribute to the mutations arising from exposure to DNA methylating agents. Here, in vitro replication studies with duplex DNA substrates containing site-specifically incorporated O2-MdT and O4-MdT showed that both lesions blocked DNA synthesis mediated by three different DNA polymerases, including the exonuclease-free Klenow fragment of Escherichia coli DNA polymerase I (Kf−), human DNA polymerase κ (pol κ) and Saccharomyces cerevisiae DNA polymerase η (pol η). Results from steady-state kinetic measurements and LC-MS/MS analysis of primer extension products revealed that Kf− and pol η preferentially incorporated the correct nucleotide (dAMP) opposite O2-MdT, while O4-MdT primarily directed dGMP misincorporation. While steady-state kinetic experiments showed that pol κ-mediated nucleotide insertion opposite O2-MdT and O4-MdT is highly promiscuous, LC-MS/MS analysis of primer extension products demonstrated that pol κ incorporated favorably the incorrect dGMP opposite both lesions. Our results underscored the limitation of the steady-state kinetic assay in determining how DNA lesions compromise DNA replication in vitro. In addition, the results from our study revealed that, if left unrepaired, O-methylated thymidine lesions may constitute important sources of nucleobase substitutions emanating from exposure to alkylating agents.