Synthesis of Oligonucleotides Containing Fapy·dG (<i>N</i><sup>6</sup>-(2-Deoxy-α,β-<scp>d</scp>-erythropentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine) Using a 5‘-Dimethoxytrityl Dinucleotide Phosphoramidite

Jiang, Yu; Wiederholt, Carissa J.; Patro, Jennifer N.; Haraguchi, Kazuhiro; Greenberg, Marc M.

doi:10.1021/jo048253o

Cited by 30 publications

(33 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…FapyGua-containing oligodeoxynucleotides were a kind gift from Dr. Marc Greenberg (38). The oligodeoxynucleotides containing 5-OHUra or 8-OH-Gua were obtained from Midland Certified Reagent Co. (Midland, TX).…”

Section: Methodsmentioning

confidence: 99%

Cockayne Syndrome Group B Protein Stimulates Repair of Formamidopyrimidines by NEIL1 DNA Glycosylase

Müftüoğlu

Souza-Pinto

Doğan

et al. 2009

Journal of Biological Chemistry

View full text Add to dashboard Cite

Cockayne syndrome (CS) 6 is a segmental premature aging syndrome with progressive neurological degeneration (1). CS is caused by mutations in CS complementation groups A (CSA) or B (CSB) genes (2, 3). Approximately 80% of CS patients have mutations in the CSB gene, which encodes a 168-kDa protein belonging to the SWI/SNF2 family of chromatin remodeling proteins (4). Cells from CS patients are hypersensitive to UV radiation-induced DNA damage, and the CSB protein is required for the transcription-coupled nucleotide excision repair of UV radiation-induced DNA lesions (cyclobutane pyrimidine dimers and 6-pyrimidine-4-pyrimidone products) (5). CSB is also believed to play a role in transcription elongation and interacts with the RNA polymerase II elongation complex (6). The molecular basis of the progressive neurological defects in CS patients, however, remains unknown; it has been proposed that neurological symptoms in CS may be due to defective repair and/or processing of oxidative DNA damage in CSB-deficient cells (7).Oxidative DNA damage can be caused by endogenous and exogenous agents. Reactive oxygen species, including highly reactive hydroxyl radicals, are formed as byproducts of normal metabolism, mostly during the process of mitochondrial respiration. It has been estimated that up to 2% of all the O 2 consumed by respiration may be released as reactive oxygen species (8, 9). The central nervous system relies exclusively on mitochondria to generate ATP through oxidative metabolism. As a result, neurons are susceptible to increased levels of oxidative stress, and elevated levels of reactive oxygen species have been implicated in the etiology of neurodegenerative diseases including Alzheimer, Parkinson, and Huntington diseases and amyotrophic lateral sclerosis (for a review, see Ref. 10).Hydroxyl radicals attack DNA bases and the sugar-phosphate DNA backbone, generating modified bases and singlestranded DNA (ssDNA) breaks, respectively (11). Many oxida-

show abstract

Section: Methodsmentioning

confidence: 99%

Cockayne Syndrome Group B Protein Stimulates Repair of Formamidopyrimidines by NEIL1 DNA Glycosylase

Müftüoğlu

Souza-Pinto

Doğan

et al. 2009

Journal of Biological Chemistry

View full text Add to dashboard Cite

show abstract

“…FapyG-or FapyA-containing oligonucleotides were synthesized as described previously (17,18). The oligonucleotides were characterized by electrospray ionization mass spectroscopy, and the spectra showing the expected fragment masses are presented in Supplemental Fig.…”

Section: Methodsmentioning

confidence: 99%

“…A method for the synthesis of oligonucleotides containing FapyG and FapyA at defined sites was recently developed (17,18). Here, we have reported the first study of the repair of FapyG and FapyA in these oligonucleotides, using nuclear and mitochondrial extracts of wild type and mice deficient in the two major glycosylases for the repair of oxidative DNA damage, OGG1 and NTH1.…”

mentioning

confidence: 99%

Repair of Formamidopyrimidines in DNA Involves Different Glycosylases

Souza-Pinto

Haraguchi

et al. 2005

Journal of Biological Chemistry

Self Cite

180

148

View full text Add to dashboard Cite

The oxidatively induced DNA lesions 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA) are formed abundantly in DNA of cultured cells or tissues exposed to ionizing radiation or to other free radical-generating systems. In vitro studies indicate that these lesions are miscoding, can block the progression of DNA polymerases, and are substrates for base excision repair. However, no study has yet addressed how these lesions are metabolized in cellular extracts. The synthesis of oligonucleotides containing FapyG and FapyA at defined positions was recently reported. These constructs allowed us to investigate the repair of Fapy lesions in nuclear and mitochondrial extracts from wild type and knock-out mice lacking the two major DNA glycosylases for repair of oxidative DNA damage, OGG1 and NTH1. The background level of FapyG/FapyA in DNA from these mice was also determined. Endogenous FapyG levels in liver DNA from wild type mice were significantly higher than 8-hydroxyguanine levels. FapyG and FapyA were efficiently repaired in nuclear and mitochondrial extracts from wild type animals but not in the glycosylasedeficient mice. Our results indicated that OGG1 and NTH1 are the major DNA glycosylases for the removal of FapyG and FapyA, respectively. Tissue-specific analysis suggested that other DNA glycosylases may contribute to FapyA repair when NTH1 is poorly expressed. We identified NEIL1 in liver mitochondria, which could account for the residual incision activity in the absence of OGG1 and NTH1. FapyG and FapyA levels were significantly elevated in DNA from the knock-out mice, underscoring the biological role of OGG1 and NTH1 in the repair of these lesions.A large number of DNA base modifications are formed by oxidative damage to DNA (for review, see Ref. 1). Some of these lesions are generated at high rates, even in the absence of exogenous DNA-damaging agents. For instance, it was estimated that 100 -500 8-hydroxyguanines 3 are formed per day in a human cell (2). 8-oxoG is one of the most studied DNA lesions, and it is often used as a biomarker of oxidative DNA damage. However, ring-opened formamidopyrimidine lesions, 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA), are formed at equal or higher levels than 8-oxoG after oxidative stress (3-5). These lesions result from hydroxyl radical attack on guanine and adenine, respectively, followed by one-electron reduction of the hydroxyl adduct radicals (1), which are also intermediates in the formation of 8-oxoG and 8-oxoA (6). Formation of Fapy lesions in DNA upon UV radiation has also been reported (7). FapyA (8) and FapyG (9) are miscoding in vitro, both directing the preferential misincorporation of adenine opposite the lesions by a bacterial DNA polymerase (Klenow exo Ϫ ). Experiments using the methylated analogue of FapyG, i.e. 2,6-diamino-4-hydroxy-5-Nmethylformamidopyrimidine (Me-FapyG), have suggested that formamidopyrimidines might also constitute blocks to DNA poly...

show abstract

“…Commercially available DNA synthesis reagents were obtained from Glen Research Inc (Sterling, VA). Oligodeoxyribonucleotides containing Fapy•dG or Fapy•dA were prepared as described previously (22,23,32). Oligodeoxyribonucleotides containing Tg or 5,6-dihydro-2′-deoxyuridine (dHU) were prepared using commercially available reagents and protocols provided by the manufacturer (Glen Research).…”

Section: Methodsmentioning

confidence: 99%

“…An important consequence of this is that such experiments do not provide insight into the enzyme's ability to prevent mutations. Recently, chemical syntheses of oligonucleotides containing Fapy•dA or Fapy•dG were reported (22,23,32). We have taken advantage of these substrates to examine formamidopyrimidine excision by Endo III and Endo VIII when the lesions are opposite each of the four native nucleotides.…”

Section: Introductionmentioning

confidence: 99%

Excision of formamidopyrimidine lesions by endonucleases III and VIII is not a major DNA repair pathway in Escherichia coli

Wiederholt¹

2005

Nucleic Acids Research

View full text Add to dashboard Cite

Proper maintenance of the genome is of great importance. Consequently, damaged nucleotides are repaired through redundant pathways. We considered whether the genome is protected from formamidopyrimidine nucleosides (Fapy•dA, Fapy•dG) via a pathway distinct from the Escherichia coli guanine oxidation system. The formamidopyrimidines are produced in significant quantities in DNA as a result of oxidative stress and are efficiently excised by formamidopyrimidine DNA glycosylase. Previous reports suggest that the formamidopyrimidine nucleosides are substrates for endonucleases III and VIII, enzymes that are typically associated with pyrimidine lesion repair in E.coli. We investigated the possibility that Endo III and/or Endo VIII play a role in formamidopyrimidine nucleoside repair by examining Fapy•dA and Fapy•dG excision opposite all four native 2′-deoxyribonucleotides. Endo VIII excises both lesions more efficiently than does Endo III, but the enzymes exhibit similar selectivity with respect to their action on duplexes containing the formamidopyrimidines opposite native deoxyribonucleotides. Fapy•dA is removed more rapidly than Fapy•dG, and duplexes containing purine nucleotides opposite the lesions are superior substrates compared with those containing formamidopyrimidine–pyrimidine base pairs. This dependence upon opposing nucleotide indicates that Endo III and Endo VIII do not serve as back up enzymes to formamidopyrimidine DNA glycosylase in the repair of formamidopyrimidines. When considered in conjunction with cellular studies [J. O. Blaisdell, Z. Hatahet and S. S. Wallace (1999) J. Bacteriol., 181, 6396–6402], these results also suggest that Endo III and Endo VIII do not protect E.coli against possible mutations attributable to formamidopyrimidine lesions.

show abstract

Synthesis of Oligonucleotides Containing Fapy·dG (N⁶-(2-Deoxy-α,β-d-erythropentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine) Using a 5‘-Dimethoxytrityl Dinucleotide Phosphoramidite

Cited by 30 publications

References 34 publications

Cockayne Syndrome Group B Protein Stimulates Repair of Formamidopyrimidines by NEIL1 DNA Glycosylase

Cockayne Syndrome Group B Protein Stimulates Repair of Formamidopyrimidines by NEIL1 DNA Glycosylase

Repair of Formamidopyrimidines in DNA Involves Different Glycosylases

Excision of formamidopyrimidine lesions by endonucleases III and VIII is not a major DNA repair pathway in Escherichia coli

Contact Info

Product

Resources

About

Synthesis of Oligonucleotides Containing Fapy·dG (N6-(2-Deoxy-α,β-d-erythropentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine) Using a 5‘-Dimethoxytrityl Dinucleotide Phosphoramidite

Cited by 30 publications

References 34 publications

Cockayne Syndrome Group B Protein Stimulates Repair of Formamidopyrimidines by NEIL1 DNA Glycosylase

Cockayne Syndrome Group B Protein Stimulates Repair of Formamidopyrimidines by NEIL1 DNA Glycosylase

Repair of Formamidopyrimidines in DNA Involves Different Glycosylases

Excision of formamidopyrimidine lesions by endonucleases III and VIII is not a major DNA repair pathway in Escherichia coli

Contact Info

Product

Resources

About

Synthesis of Oligonucleotides Containing Fapy·dG (N⁶-(2-Deoxy-α,β-d-erythropentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine) Using a 5‘-Dimethoxytrityl Dinucleotide Phosphoramidite