Structures of base pairs with 5-(hydroxymethyl)-2'-deoxyuridine in DNA determined by NMR spectroscopy

Mellac, Sophie; Fazakerley, G. Victor; Sowers, Lawrence C.

doi:10.1021/bi00081a025

Cited by 42 publications

(46 citation statements)

References 41 publications

(33 reference statements)

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“…The structures of duplexes containing both HmU:A and HmU:G base pairs have been studied by NMR spectroscopy (9). The replacement of a thymine residue by HmU in a T:A base pair does not alter overall DNA conformation or Watson-Crick base pairing, consistent with the replacement of T by HmU in some bacteriophage.…”

Section: Discussionmentioning

confidence: 77%

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An unexpectedly high excision capacity for mispaired 5-hydroxymethyluracil in human cell extracts

Rusmintratip

Sowers

2000

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

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The oxidation of thymine in DNA can generate a base pair between 5-hydroxymethyluracil (HmU) and adenine, whereas the oxidation and deamination of 5-methylcytosine (5mC) in DNA can generate a base pair between HmU and guanine. Using synthetic oligonucleotides containing HmU at a defined site, HmU-DNA glycosylase activities in HeLa cell and human fibroblast cell extracts have been observed. An HmU-DNA glycosylase activity that removes HmU mispaired with guanine has been measured. Surprisingly, the HmU:G excision activity is 60 times greater than the corresponding HmU:A activity, even though the expected rate of formation of the HmU:A base pair exceeds that of the HmU:G base pair by a factor of 10 7 . The HmU:G mispair would arise from the 5mC:G base pair, and, if unrepaired, would give rise to a transition mutation. The observation of an unexpectedly high HmU:G glycosylase activity suggests that human cells may encounter the HmU:G mispair much more frequently than expected. The conversion of 5mC to HmU must be considered as a potential pathway for the generation of 5mC to T transition mutations, which are often found in human tumors. Oxidative DNA damage has been implicated in cancer and aging (1-3). The oxidation of the thymine methyl group of a T:A base pair can generate 5-hydroxymethyluracil (HmU; refs. 4 and 5). The biological implications of this DNA damage are currently unclear; however, the laboratories of Ames (6) and Teebor (7) have identified a specific glycosylase in higher eukaryotes that removes HmU from an HmU:A base pair in DNA. The need for DNA repair activities is generally discussed within the context of removing lesions that miscode or block the progression of a DNA or RNA polymerase. However, HmU is not miscoding (8), it does not perturb DNA structure (9, 10), and it does not impede polymerases (11,12). Indeed, in some bacteriophage, HmU completely replaces T (13).In the absence of an obvious need for the removal of HmU, the existence of the HmU-DNA glycosylase activity led to the proposal that the role of this activity was to remove HmU that could arise in DNA by a second pathway-the oxidation and deamination of 5-methylcytosine (5mC; refs. 7, 14, and 15). In support of this hypothesis, it was demonstrated that the HmU-DNA glycosylase is found only in higher eukaryotes that have 5mC in the genome (16). The methylated CpG dinucleotide is a reactive center for several carcinogens (17-19), and transition mutations at this site are frequently observed in human tumors (20 -22). Recently, the apparent involvement of altered cytosine methylation patterns in the development of human cancer has renewed interest in understanding chemical mechanisms that perturb cytosine methylation patterns (23)(24)(25)(26)(27).In the studies that initially identified HmU-DNA glycosylase activity, the substrate was the DNA of HmU-containing bacteriophage (6, 7). In these bacteriophage, the HmU replaces T and therefore pairs with A. Because HmU pairs with only A during polymerase-directed DNA synthesis, the preparation ...

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Section: Discussionmentioning

confidence: 77%

“…The need for DNA repair activities is generally discussed within the context of removing lesions that miscode or block the progression of a DNA or RNA polymerase. However, HmU is not miscoding (8), it does not perturb DNA structure (9,10), and it does not impede polymerases (11,12). Indeed, in some bacteriophage, HmU completely replaces T (13).…”

mentioning

confidence: 99%

An unexpectedly high excision capacity for mispaired 5-hydroxymethyluracil in human cell extracts

Rusmintratip

Sowers

2000

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

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“…The 60-fold increased activity towards 5-hmeU : G over 5-hmeU : A may seem surprising, since by far the major route of formation of 5-hmeU is thought to be by oxidation of the methyl-group in thymine (Rusmintratip and Sowers, 2000). However, 5-hmeU : G mispairs may cause G : C to A : T transition mutations, while 5-hmeU : G may not, since 5-hmeU is not miscoding (Levy and Teebor, 1991), does not block polymerases (Vilpo and Vilpo, 1995), and does not perturb DNA structure (Mellac et al, 1993;Pasternack et al, 1996). These results may indicate that 5-hmeU : G mispairs may be generated more frequently than assumed, although decisive experimental evidence supporting this view is still missing.…”

Section: Other Activities For Removal Of 5-hmu From Dnamentioning

confidence: 98%

Uracil in DNA – occurrence, consequences and repair

2002

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“…However, there is some experimental evidence suggesting that DNA oxidation may not be the main source of 5-hmUra in cellular DNA. The 5-hmUra:Ade base pair generated during the oxidation reaction is not miscoding and does not perturb the DNA structure [24,25]. Indeed, in some bacteriophage 5-hmUra completely replaces thymine [26].…”

Section: Epigenetic Marks In Human Leukocytes and Spermmentioning

confidence: 99%

Comparison of the Absolute Level of Epigenetic Marks 5-Methylcytosine, 5-Hydroxymethylcytosine, and 5-Hydroxymethyluracil Between Human Leukocytes and Sperm1

Guz

Gackowski

Foksiński

et al. 2014

Biology of Reproduction

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5-Methylcytosine is one of the most important epigenetic modifications and has a profound impact on embryonic development. After gamete fusion, there is a widespread and rapid active demethylation process of sperm DNA, which suggests that the paternal epigenome has an important role during embryonic development. To better understand the epigenome of sperm DNA and its possible involvement in a developing embryo, we determined epigenetic marks in human sperm DNA and in surrogate somatic tissue leukocytes; the analyzed epigenetic modifications included 5-methyl-2 0 -deoxycytidine, 5-hydroxymethyl-2 0 -deoxycytidine, and 5-hydroxymethyl-2 0 -deoxyuridine. For absolute determination of the modification, we used liquid chromatography with UV detection and tandem mass spectrometry techniques with isotopically labeled internal standards. Our analyses demonstrated, for the first time to date, that absolute global values of 5-methyl-2 0 -deoxycytidine, 5-hydroxymethyl-2 0 -deoxycytidine, and 5-hydroxymethyl-2 0 -deoxyuridine in sperm are highly statistically different from those observed for leukocyte DNA, with respective mean values of 3.815% versus 4.307%, 0.797 versus 2.945 per 10 4 deoxynucleosides, and 5.209 versus 0.492 per 10 6

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Structures of base pairs with 5-(hydroxymethyl)-2'-deoxyuridine in DNA determined by NMR spectroscopy

Cited by 42 publications

References 41 publications

An unexpectedly high excision capacity for mispaired 5-hydroxymethyluracil in human cell extracts

An unexpectedly high excision capacity for mispaired 5-hydroxymethyluracil in human cell extracts

Uracil in DNA – occurrence, consequences and repair

Comparison of the Absolute Level of Epigenetic Marks 5-Methylcytosine, 5-Hydroxymethylcytosine, and 5-Hydroxymethyluracil Between Human Leukocytes and Sperm1

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