Tandem Base Lesions Are Generated by Hydroxyl Radical within Isolated DNA in Aerated Aqueous Solution

Bourdat, Anne-Gaëlle; Douki, Thierry; Frelon, Sandrine; Gasparutto, Didier; Cadet, Jean

doi:10.1021/ja994282i

Cited by 111 publications

(76 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…In addition, clustered lesions consisting of L and Tg on opposite strands were studied in order to compare to the tandem lesions. The same local sequences were incorporated into 16-nucleotide long duplexes (12)(13)(14)(15)(16)(17)(18)(19) in order to probe the effects of the lesions on thermal stability.…”

Section: Oligonucleotide Substrate Design and Synthesismentioning

confidence: 99%

DNA Tandem Lesion Repair by Strand Displacement Synthesis and Nucleotide Excision Repair

et al. 2008

View full text Add to dashboard Cite

DNA tandem lesions are comprised of two contiguously damaged nucleotides. This subset of clustered lesions is produced by a variety of oxidizing agents, including ionizing radiation. Clustered lesions can inhibit base excision repair (BER). We report the effects of tandem lesions composed of a thymine glycol and a 5′-adjacent 2-deoxyribonolactone (LTg) or tetrahydrofuran abasic site (FTg). Some BER enzymes that act on the respective isolated lesions do not accept the tandem lesion as a substrate. For instance, endonuclease III (Nth) does not excise thymine glycol (Tg) when it is part of either tandem lesion. Similarly, endonuclease IV (Nfo) does not incise L or F when they are in tandem with Tg. Long-patch BER overcomes inhibition by the tandem lesion. DNA polymerase β (Pol β) carries out strand displacement synthesis, following APE1 incision of the abasic site. Pol β activity is enhanced by flap endonuclease (FEN1), which cleaves the resulting flap. The tandem lesion is also incised by the bacterial nucleotide excision repair system UvrABC with almost the same efficiency as an isolated Tg. These data reveal two solutions that DNA repair systems can use to counteract the formation of tandem lesions.Isolated damaged nucleotides are believed to be the most common lesions resulting from DNA oxidation. As a result of efforts by many researchers, a great deal has been learned about how DNA lesions are repaired by base excision repair (BER) 1 and nucleotide excision repair (NER) (1-3). Recently, clusters of DNA lesions have been identified as significant components of radiation-induced damage. Clustered lesions consist of two or more damaged nucleotides within ~1.5 turns of duplex DNA and are attributed to multiple ionization events by a single radiation track. In principle, clustered lesions can contain modified nucleotides on a single strand, but biochemical studies have focused on bistranded lesions, which are possible progenitors to double strand breaks (1-11). Numerous studies have revealed the effects of clustered lesions on BER. The effects are dependent upon the nature of the lesions, as well as their proximity to one another in duplex DNA. Clustered lesions consisting of two contiguously damaged nucleotides are referred to as tandem lesions (12,13). Unlike other examples of clustered damage, tandem lesions can result from a single DNA damaging event, in which a † We are grateful for support of this research by the National Institute of General Medical Science (Grant GM-063028). This research was supported in part by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences.* To whom correspondence should be addressed. . E-mail: mgreenberg@jhu.edu. ‡ These researchers contributed equally to the research described in this paper. § Johns Hopkins University. || Laboratory of Molecular Genetics, NIEHS, NIH.1 Abbreviations: AP, abasic site; L, 2-deoxyribonolactone; F, tetrahydrofuran abasic site; Tg, thymine glycol; BER, base excision repair; LP-BER, long-patch base exc...

show abstract

Section: Oligonucleotide Substrate Design and Synthesismentioning

confidence: 99%

DNA Tandem Lesion Repair by Strand Displacement Synthesis and Nucleotide Excision Repair

et al. 2008

View full text Add to dashboard Cite

show abstract

“…Recent works have demonstrated that in dinucleoside monophosphates (11,12) and in oligonucleotides (11,13) peroxyl radicals of pyrimidine bases could efficiently react with a vicinal DNA base. Indeed, it has been recently reported that in DNA addition of pyrimidine peroxyl radicals onto the C8 of a purine base is capable of producing 8-oxodGuo involved in tandem lesions neighboring a formylamine (dF) residue (14,15). Quantitatively, formation of 8-oxodGuo/dF tandem lesions accounts for ∼10% of the generated 8-oxodGuo.…”

mentioning

confidence: 99%

HO ^• radicals induce an unexpected high proportion of tandem base lesions refractory to repair by DNA glycosylases

Bergeron

Auvré

Radicella

et al. 2010

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

123

113

View full text Add to dashboard Cite

Reaction of HO• radicals with double-stranded calf thymus DNA produces high levels of and, to a minor extent, . Formation of the hydroxylated purine lesions is explained by addition of HO • to the C8 position of the purine moiety. It has been reported that tandem lesions containing a formylamine residue neighboring 8-oxodGuo could be produced through addition of a transiently generated pyrimidine peroxyl radical onto the C8 of an adjacent purine base. Formation of such tandem lesions accounted for ≈10% of the total 8-oxodGuo. In the present work we show that addition of HO • onto the C8 of purine accounts for only ∼5% of the generated 8-oxodGuo. About 50% of the 8-hydroxylated purine lesions, including 8-oxodGuo and 8-oxodAdo, are involved in tandem damage and are produced by peroxyl addition onto the C8 of a vicinal purine base. In addition, the remaining 45% of the 8-oxodGuo are produced by an electron transfer reaction, providing an explanation for the higher yield of formation of 8-oxodGuo compared to 8-oxodAdo. Interestingly, we show that >40% of the 8-oxodGuo involved in tandem lesions is refractory to excision by DNA glycosylases. Altogether our results demonstrate that, subsequently to a single oxidation event, peroxidation reactions significantly increase the yield of formation of hydroxylated purine modifications, generating a high proportion of tandem lesions partly refractory to base excision repair.DNA damage | DNA repair | peroxidation reaction | tandem lesions F ormation of oxidatively generated DNA lesions is associated with the occurrence of degenerative diseases, cancer, and aging (1). Therefore, reactions of reactive oxygen species, and among them the highly genotoxic hydroxyl radical (HO • ), with DNA constituents have been extensively studied during the last three decades (2). 8-Oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodGuo) and, to a minor extent the corresponding adenine derivative 8-oxo-7,8-dihydro-2′-deoxyadenosine (8-oxodAdo), have been shown to be significantly generated in cellular DNA under various conditions of oxidative stress. More than 20 years ago (3) it was established that in the presence of HO• (produced either by the indirect effect of ionizing radiation or by Fenton-type reactions) the mechanism of formation of 8-hydroxylated purine lesions (8-oxoPur), including both 8-oxodGuo and 8-oxodAdo, involves addition of HO• to the C8 position of the purine bases, followed by an oxidation reaction (for a review see refs. 2 and 4). In addition, 8-oxoPur could be also produced by a one-electron oxidation process followed by hydration of the purine radical cation thus generated, producing following oxidation mainly 8-oxodGuo due to efficient charge transfer processes (5, 6) combined with the relatively low ionization potential of guanine compared to other DNA constituents.In addition, the pioneering work of Box and coworkers (7-10) suggested the possible formation of tandem lesions, constituted of two adjacent modifications. Recent works have demonstrated that in dinucleoside monophosp...

show abstract

“…The ligation mechanism involves three steps: (a) activation of the enzyme by adenylation (30), (b) formation of the intermediate by transfer of the AMP residue from the enzyme to the 5′-phosphate of the nicked DNA (30), and (c) sealing of the DNA by a transesterification reaction (28,31). The existence of clustered DNA damage (32)(33)(34)(35) and the insertion of dOGMP during replication suggests the possibility that an oxidized lesion could appear near a nick site. Furthermore, the DNA repair enzyme MutY excises adenine opposite guanine or 8-oxoG during BER (11,36,37), and complete repair requires the further action of a polymerase for insertion of dCTP opposite OG, followed by ligation (38).…”

mentioning

confidence: 99%

In Vitro Ligation of Oligodeoxynucleotides Containing C8-Oxidized Purine Lesions Using Bacteriophage T4 DNA Ligase

et al. 2007

View full text Add to dashboard Cite

Ligases conduct the final stage of repair of DNA damage by sealing a single-stranded nick after excision of damaged nucleotides and reinsertion of correct nucleotides. Depending upon the circumstances and the success of the repair process, lesions may remain at the ligation site, either in the template or at the oligomer termini to be joined. Ligation experiments using bacteriophage T4 DNA ligase were carried out with purine lesions in four positions surrounding the nick site in a total of 96 different duplexes. The oxidized lesion 8-oxo-7,8-dihydroguanosine (OG) showed, as expected, that the enzyme is most sensitive to lesions on the 3′ end of the nick compared to the 5′ end and to lesions located in the intact template strand. In general, substrates containing the OG·A mismatch were more readily ligated than OG·C. Ligations of duplexes containing the OA·T base pair (OA=8-oxo-7,8-dihydroadenosine) that could adopt an anti-anti conformation proceeded in high efficiencies. An OI·Acontaining duplex (OI = 8-oxo-7,8-dihydroinosine) behaved similarly to OG·A. Due to its low reduction potential, OG is readily oxidized to secondary oxidation products, such as the guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp) nucleosides; these lesions also contain an oxo group at the original C8 position of the purine. Ligation of oligomers containing Gh and Sp occurred when opposite A and G although the overall ligation efficiencies were much lower than most OG base pairs. Steady-state kinetic studies were carried out for representative examples of lesions in the template. K m increased by 90-100-fold for OG·C, OI·C, OI·A and OA·T containing duplexes compared to G·C. Substrates containing Gh·A, Gh·G, Sp·A and Sp·G base pairs showed K m values 20-70-fold higher than G·C while the K m value for OG·A was 5 times lower than G·C.Reactive oxygen species (ROS) 1 such as O 2 −•, HO• and H 2 O 2 are continuously produced during normal metabolic processes, and their production is augmented by inflammation and exposure to certain agents (1,2). DNA is sensitive to ROS, and in vivo oxidative damage results in DNA strand breaks, base modifications and DNA-protein cross-links (1). Unrepaired oxidative DNA damage can be mutagenic and is implicated in carcinogenesis, neurological disorders and aging (2-4). Oxidation of guanine, the most easily oxidized nucleobase (5), can lead to the commonly observed lesion 8-oxo-7,8-dihydro-2′-deoxyguanosine (OG) which is regarded as a biomarker of oxidative DNA damage in the cell (6). OG is mutagenic in the absence of repair leading to G→T transversions (7-10).OG can be removed by the base excision repair pathway (BER) (11-14) involving glycosidic bond cleavage of the damaged base followed by excision of the remaining abasic (AP) site (15). A nucleotide is inserted by a DNA polymerase, and in a final stage, the nick is sealed by a DNA ligase (16)(17)(18)(19)(20). Although DNA repair of oxidized base lesions has been extensively

show abstract

Tandem Base Lesions Are Generated by Hydroxyl Radical within Isolated DNA in Aerated Aqueous Solution

Cited by 111 publications

References 31 publications

DNA Tandem Lesion Repair by Strand Displacement Synthesis and Nucleotide Excision Repair

DNA Tandem Lesion Repair by Strand Displacement Synthesis and Nucleotide Excision Repair

HO ^• radicals induce an unexpected high proportion of tandem base lesions refractory to repair by DNA glycosylases

In Vitro Ligation of Oligodeoxynucleotides Containing C8-Oxidized Purine Lesions Using Bacteriophage T4 DNA Ligase

Contact Info

Product

Resources

About

Tandem Base Lesions Are Generated by Hydroxyl Radical within Isolated DNA in Aerated Aqueous Solution

Cited by 111 publications

References 31 publications

DNA Tandem Lesion Repair by Strand Displacement Synthesis and Nucleotide Excision Repair

DNA Tandem Lesion Repair by Strand Displacement Synthesis and Nucleotide Excision Repair

HO • radicals induce an unexpected high proportion of tandem base lesions refractory to repair by DNA glycosylases

In Vitro Ligation of Oligodeoxynucleotides Containing C8-Oxidized Purine Lesions Using Bacteriophage T4 DNA Ligase

Contact Info

Product

Resources

About

HO ^• radicals induce an unexpected high proportion of tandem base lesions refractory to repair by DNA glycosylases