Measurement of Postreplicative DNA Metabolism and Damage in the Rodent Brain

Determination and Quantification of Acetaldehyde, Acetone, and Methanol in Hand Sanitizers Using Headspace GC/MS: Effect of Storage Time and Temperature

Accurate determination of the concentration of alcohols and their metabolites is important in forensics and in several life science areas. A new headspace gas chromatography-mass spectrometry method has been developed to quantify alcohols and their oxidative products using isotope-labeled internal standards. The limit of detection (LOD) of the analytes in the developed method was 0.211 µg/mL for methanol, 0.158 µg/mL for ethanol, 0.157 µg/mL for isopropanol, 0.010 µg/mL for n-propanol, 0.157 µg/mL for acetone, and 0.209 µg/mL for acetaldehyde. The precision and accuracy of the method were evaluated, and the relative standard deviation percentages were found to be less than 3%. This work demonstrates the application of this method, specifically in quantifying the concentration of oxidative products of alcohol and other minor alcohols found in hand sanitizers, which have become an essential household item since the COVID-19 pandemic. Apart from the major components, the minor alcohols found in hand sanitizers include methanol, isopropanol, and n-propanol. The concentration range of these minor alcohols found in ethanol-based hand sanitizer samples was as follows: methanol, 0.000921-0.0151 mg/mL; isopropanol, 0.454-13.8 mg/mL; and n-propanol, 0.00474-0.152 mg/mL. In ethanol-based hand sanitizers, a significant amount of acetaldehyde (0.00623-0.231 mg/mL) was observed as an oxidation product, while in the isopropanol-based hand sanitizer, acetone (0.697 mg/mL) was observed as an oxidation product. The concentration of acetaldehyde in ethanol-based hand sanitizers significantly increased with storage time and temperature, whereas no such increase in acetone concentration was observed in isopropanol-based hand sanitizers with storage time and temperature. In two of the selected hand sanitizers, the acetaldehyde levels increased by almost 200% within a week when stored at room temperature. Additionally, exposing the hand sanitizers to a temperature of 45 °C for 24 h resulted in a 100% increase in acetaldehyde concentration. On the contrary, the acetone level remained constant upon the change in storage time and temperature.

Chemical and enzymatic modifications of 5-methylcytosine at the intersection of DNA damage, repair, and epigenetic reprogramming

The DNA of all living organisms is persistently damaged by endogenous reactions including deamination and oxidation. Such damage, if not repaired correctly, can result in mutations that drive tumor development. In addition to chemical damage, recent studies have established that DNA bases can be enzymatically modified, generating many of the same modified bases. Irrespective of the mechanism of formation, modified bases can alter DNA-protein interactions and therefore modulate epigenetic control of gene transcription. The simultaneous presence of both chemically and enzymatically modified bases in DNA suggests a potential intersection, or collision, between DNA repair and epigenetic reprogramming. In this paper, we have prepared defined sequence oligonucleotides containing the complete set of oxidized and deaminated bases that could arise from 5-methylcytosine. We have probed these substrates with human glycosylases implicated in DNA repair and epigenetic reprogramming. New observations reported here include: SMUG1 excises 5-carboxyuracil (5caU) when paired with A or G. Both TDG and MBD4 cleave 5-formyluracil and 5caU when mispaired with G. Further, TDG not only removes 5-formylcytosine and 5-carboxycytosine when paired with G, but also when mispaired with A. Surprisingly, 5caU is one of the best substrates for human TDG, SMUG1 and MBD4, and a much better substrate than T. The data presented here introduces some unexpected findings that pose new questions on the interactions between endogenous DNA damage, repair, and epigenetic reprogramming pathways.

Spectroscopic and in vitro investigations of Fe2+/α-Ketoglutarate-dependent enzymes involved in nucleic acid repair and modification

The activation of molecular oxygen for the highly selective functionalization and repair of DNA and RNA nucleobases is achieved by α-ketoglutarate (α-KG)/iron-dependent dioxygenases. Enzymes of special interest are the human homologs AlkBH of Escherichia coli EcAlkB and ten-eleven translocation (TET) enzymes. These enzymes are involved in demethylation or dealkylation of DNA and RNA, although additional physiological functions are continuously being revealed. Given their importance, studying enzyme-substrate interactions, turnover and kinetic parameters is pivotal for the understanding of the mode of action of these enzymes. Diverse analytical methods, including X-ray crystallography, UV/Vis absorption, electron paramagnetic resonance (EPR), circular dichroism (CD) and NMR spectroscopy have been employed to study the changes in the active site and the overall enzyme structure upon substrate, cofactor and inhibitor addition. Several methods are now available to assess activity of these enzymes. By discussing limitations and possibilities of these techniques for EcAlkB, AlkBH and TET we aim to give a comprehensive synopsis from a bioinorganic point of view, addressing researchers from different disciplines working in the highly interdisciplinary and rapidly evolving field of epigenetic processes and DNA/RNA repair and modification.

Preparation of Internal Standards for 2D-UPLC-MS/MS Quantification of Noncanonical DNA Bases

Reliable quantitative analysis of DNA modification using liquid chromatography coupled with tandem mass spectrometry requires stable isotope-labeled internal standards. Only some of them are commercially available. Here we present a method allowing for the synthesis of [¹³C₁₀,¹⁵N₂]-5-methyl-2'-deoxycytidine from [¹³C₁₀,¹⁵N₂]-2'-deoxythymidine. We also describe an approach for the oxidation of [¹³C₁₀,¹⁵N₂]-5-methyl-2'-deoxycytidine and [¹³C₁₀,¹⁵N₂]-2'-deoxythymidine with Na₂S₂O₈, leading to the generation of [¹³C₁₀,¹⁵N₂]-5-formyl-2'-deoxycytidine, [¹³C₁₀,¹⁵N₂]-5-carboxy-2'-deoxycytidine or [¹³C₁₀,¹⁵N₂]-5-(hydroxymethyl)-2'-deoxyuridine, correspondingly. Moreover, we provide optimized protocols for the oxidation of [¹³C₅,¹⁵N₂]-thymine to [¹³C₁₀,¹⁵N₂]-5-hydroxymethyluracil, [¹³C₁₀,¹⁵N₂]-5-formyluracil, and [¹³C₁₀,¹⁵N₂]-5-carboxyuracil using Na₂S₂O₈.

New perspectives on the roles of pyrimidines in the central nervous system

Since 1956, when exogenous uridine and cytidine were found to be necessary for the maintenance of perfused rat brain function, the co-existence of de novo synthesis, salvage pathways and removal of pyrimidine bases in the CNS has been a controversial subject. Here, we review studies on metabolites and enzymes of pyrimidine metabolism through more than 60 years. In view of known and newly-described inherited pyrimidine and purine disorders - some with complex clinical profiles of neurological impairments - we underline the necessity to investigate how the different pathways work together in the developing brain and then sustain plasticity, regeneration and neuro-transmission in the adult CNS. Experimentally, early incorporation studies in animal brain slices and homogenates with radio-labelled nucleosides or precursors demonstrated salvage activity or de novo synthesis. Later, the nucleoside transporters and organic anionic transporters underlying uptake of metabolites and anti-pyrimidine drugs in the CNS were identified. Recently, the expression of de novo enzymes in glial cells and neurons was verified using (immuno) histochemical and in-situ-hybridization techniques. Adult brain was shown to take up or produce all pyrimidine (deoxy) ribonucleosides or, after uptake and phosphorolysis of nucleosides, to make use of ribose for different purposes, including energy. More recently, non-canonical pyrimidine bases (5mC, 5hmC) have been found most notably in brain, pointing to considerable postreplicative DNA metabolism, with the need for pyrimidine-specific enzymes. Even more perspectives are emerging, with advances in genome analysis and in the manipulation of expression from the gene.

Formation and repair of oxidatively generated damage in cellular DNA

In this review article, emphasis is placed on the critical survey of available data concerning modified nucleobase and 2-deoxyribose products that have been identified in cellular DNA following exposure to a wide variety of oxidizing species and agents including, hydroxyl radical, one-electron oxidants, singlet oxygen, hypochlorous acid and ten-eleven translocation enzymes. In addition, information is provided about the generation of secondary oxidation products of 8-oxo-7,8-dihydroguanine and nucleobase addition products with reactive aldehydes arising from the decomposition of lipid peroxides. It is worth noting that the different classes of oxidatively generated DNA damage that consist of single lesions, intra- and interstrand cross-links were unambiguously assigned and quantitatively detected on the basis of accurate measurements involving in most cases high performance liquid chromatography coupled to electrospray ionization tandem mass spectrometry. The reported data clearly show that the frequency of DNA lesions generated upon severe oxidizing conditions, including exposure to ionizing radiation is low, at best a few modifications per 106 normal bases. Application of accurate analytical measurement methods has also allowed the determination of repair kinetics of several well-defined lesions in cellular DNA that however concerns so far only a restricted number of cases.