Mapping Structurally Defined Guanine Oxidation Products along DNA Duplexes: Influence of Local Sequence Context and Endogenous Cytosine Methylation

Ming, Xun; Matter, Brock; Song, Matthew; Veliath, Elizabeth; Shanley, Ryan; Jones, R. A. C.; Tretyakova, Natalia

doi:10.1021/ja411636j

Cited by 38 publications

(56 citation statements)

References 92 publications

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“…DNA sequences containing runs of guanine are hot spots for oxidative damage (45)(46)(47), which could serve as an endogenous source of G4DNA after partial degradation or excision repair. We used H 2 O 2 because it is known to cause oxidative damage to FIGURE 2.…”

Section: Resultsmentioning

confidence: 99%

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Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress

Byrd¹,

Zybailov

Maddukuri³

et al. 2016

Journal of Biological Chemistry

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Cells engage numerous signaling pathways in response to oxidative stress that together repair macromolecular damage or direct the cell toward apoptosis. As a result of DNA damage, mitochondrial DNA or nuclear DNA has been shown to enter the cytoplasm where it binds to "DNA sensors," which in turn initiate signaling cascades. Here we report data that support a novel signaling pathway in response to oxidative stress mediated by specific guanine-rich sequences that can fold into G-quadruplex DNA (G4DNA). In response to oxidative stress, we demonstrate that sequences capable of forming G4DNA appear at increasing levels in the cytoplasm and participate in assembly of stress granules. Identified proteins that bind to endogenous G4DNA in the cytoplasm are known to modulate mRNA translation and participate in stress granule formation. Consistent with these findings, stress granule formation is known to regulate mRNA translation during oxidative stress. We propose a signaling pathway whereby cells can rapidly respond to DNA damage caused by oxidative stress. Guanine-rich sequences that are excised from damaged genomic DNA are proposed to enter the cytoplasm where they can regulate translation through stress granule formation. This newly proposed role for G4DNA provides an additional molecular explanation for why such sequences are prevalent in the human genome.

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Section: Resultsmentioning

confidence: 99%

“…It is known that DNA sequences containing runs of guanine residues are more reactive with hydroxyl radicals than guanine residues scattered throughout the genome (45,46,58). Guanine oxidation does reduce the thermal stability of G-quadruplexes; however, G4DNA structures can still form in the presence of 8-oxo-dG (59,60).…”

Section: Discussionmentioning

confidence: 99%

Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress

Byrd¹,

Zybailov

Maddukuri³

et al. 2016

Journal of Biological Chemistry

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“…In vivo, all cytosines in CpG sites are methylated, which may increase the reactivity and mutation frequency of the neighbor guanine in tumors. 39,46,65 For 248/245, the oxidation reactivity ratio was 4.1, which is larger than that for mutations. This could be related to the first guanine in codon 245 (GGC) being a CpG site, making the guanine more reactive in vivo, resulting in a smaller mutation ratio.…”

Section: Discussionmentioning

confidence: 76%

“…Stable isotope labeling of DNA has been widely used with mass spectrometry to examine the reactive sites and cytosine methylation on the formation of 8-oxodG and downstream oxidation products of reactions with nitrosoperoxycarbonate and riboflavin-mediated photolysis. 39 This approach detects the amount of 8-oxodG and other products formed, but isotopic labeling syntheses and enzymatic oligonucleotide digestion are required.…”

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confidence: 99%

Direct LC-MS/MS Detection of Guanine Oxidations in Exon 7 of the p53 Tumor Suppressor Gene

Jiang

Malla

et al. 2017

Anal. Chem.

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Oxidation of DNA by reactive oxygen species (ROS) yields 8-oxo-7,8-dihydroguanosine (8-oxodG) as primary oxidation product, which can lead to downstream G to T transversion mutations. DNA mutations are nonrandom, and mutations at specific codons are associated with specific cancers, as widely documented for the p53 tumor suppressor gene. Here, we present the first direct LC-MS/MS study (without isotopic labeling or hydrolysis) of primary oxidation sites of p53 exon 7. We oxidized a 32 base pair (bp) double-stranded (ds) oligonucleotide representing exon 7 of the p53 gene. Oxidized oligonucleotides were cut by a restriction endonuclease to provide small strands and enable positions and amounts of 8-oxodG to be determined directly by LC-MS/MS. Oxidation sites on the oligonucleotide generated by two oxidants, catechol/Cu2+/NADPH and Fenton’s reagent, were located and compared. Guanines in codons 243, 244, 245, and 248 were most frequently oxidized by catechol/Cu2+/NADPH with relative oxidation of 5.6, 7.2, 2.6, and 10.7%, respectively. Fenton’s reagent oxidations were more specific for guanines in codons 243 (20.3%) and 248 (10.4%). Modeling of docking of oxidizing species on the ds-oligonucleotide were consistent with the experimental codon oxidation sites. Significantly, codons 244 and 248 are mutational “hotspots” in nonsmall cell and small cell lung cancers, supporting a possible role of oxidation in p53 mutations leading to lung cancer.

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“…12 DNA II was designed to examine the effects of inserted mismatch base pair A/A between Py U and continuous G site. Aliquots of double-stranded (ds) DNA I and II samples were prepared by annealing equimolar amounts of desired DNA complements, and then molecular crowders were added.…”

Section: •+mentioning

confidence: 99%

Effects of Molecular-crowding on Electron Transfer and Oxidative Damage in Pyrene-modified Oligonucleotides

2018

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We examined guanine damages caused by photoinduced electron transfer (ET) in biomimetic environments using pyrenemodified oligonucleotides and molecular crowders. As a result, guanine damage induced by ET in full-matched DNA was decreased under viscous crowding conditions. On the other hand, behaviors of mismatched DNA revealed that throughspace ET between pyrene moiety and the consecutive guanine site was promoted under molecular-crowding conditions.Keywords: Guanine damage | DNA-mediated electron transfer | Molecular crowdingMechanisms of electron transfer (ET) through double helical DNA have been elucidated by extensive studies using electron donors and acceptors bound to DNA.1 It is well known that a hole injected by a photooxidant moves through base stacking and oxidizes DNA at a guanine (G) site, which is the most easily oxidized base. Oxidative damage within the genome is one of the important themes involving DNA-mediated ET.2 DNAmediated ET within the nucleosome structure has been examined by a rhodium intercalator 3 and an anthraquinone 4 as photooxidants. Moreover, a recent study revealed that DNA-mediated ET played an important role in primase functions.5 To clarify chemical roles of ET in vivo, we need to study DNA-mediated ET under crowded conditions, because the intracellular environment is highly crowded with 2040 wt % various biomolecules. Crowding by biomolecules causes changes in structures and stabilities of DNA as well as enzymatic reactivities to DNA. 6 Thus, DNA-mediated ET and DNA oxidative damages will also be affected by large amounts of coexisting molecules that change molecular diffusion rates, associations of molecules, solvent polarity, and water activity. Herein we investigated the effect of the surrounding medium on DNA damage via photoinduced ET using pyrene-modified oligonucleotides and found that molecular crowding mediums affected the efficiency of oxidative damage and the path of photoinduced ET in DNA.In this study, 5-(pyrenylethynyl)-2¤-deoxyuridine ( Py U) was used as a hole injector in DNA. The photoexcited Py U works as both hole and electron injectors for DNA-mediated ET.79 ET initiated by hole injection from the excited Py U can be evaluated by decomposition of guanines under air. It is advantageous for the study that the alkynylpyrene moiety of Py U is hardly quenched by oxygen and has long absorption wavelength. 10DNA sequences used in this investigation are shown in Figure 1. A pyrene molecule incorporated onto the 5-position of uracil via ethynyl linkage is located in DNA major groove, thus maintaining the the hydrogen bonding with adenine. 7 The DNA strands were designed to examine molecular-crowding effects on intrastrand ET in DNA. As DNA I, three adenines are embedded between Py U and GG. Continuous guanine (G) site 11 with the lowest oxidation potential is considered to trap a hole injected from the excited Py U via DNA-mediated ET and to generate guanine radical cation (G •+ ) at the GG site. Other guanines paired with C were replaced by inosines (inosine, I),...

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Mapping Structurally Defined Guanine Oxidation Products along DNA Duplexes: Influence of Local Sequence Context and Endogenous Cytosine Methylation

Cited by 38 publications

References 92 publications

Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress

Evidence That G-quadruplex DNA Accumulates in the Cytoplasm and Participates in Stress Granule Assembly in Response to Oxidative Stress

Direct LC-MS/MS Detection of Guanine Oxidations in Exon 7 of the p53 Tumor Suppressor Gene

Effects of Molecular-crowding on Electron Transfer and Oxidative Damage in Pyrene-modified Oligonucleotides

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