Controlled potential electro-oxidation of genomic DNA

Spatially Selective Electrochemical Cleavage of a Polymerase-Nucleotide Conjugate

Novel enzymatic methods are poised to become the dominant processes for de novo synthesis of DNA, promising functional, economic, and environmental advantages over the longstanding approach of phosphoramidite synthesis. Before this can occur, however, enzymatic synthesis methods must be parallelized to enable production of multiple DNA sequences simultaneously. As a means to this parallelization, we report a polymerase-nucleotide conjugate that is cleaved using electrochemical oxidation on a microelectrode array. The developed conjugate maintains polymerase activity toward surface-bound substrates with single-base control and detaches from the surface at mild oxidative voltages, leaving an extendable oligonucleotide behind. Our approach readies the way for enzymatic DNA synthesis on the scale necessary for DNA-intensive applications such as DNA data storage or gene synthesis.

Standards for Quantitative Measurement of DNA Damage in Mammalian Cells

As the potential applications of DNA diagnostics continue to expand, there is a need for improved methods and standards for DNA analysis. This report describes several methods that could be considered for the production of reference materials for the quantitative measurement of DNA damage in mammalian cells. With the focus on DNA strand breaks, potentially useful methods for assessing DNA damage in mammalian cells are reviewed. The advantages and limitations of each method, as well as additional concerns with respect to reference material development, are also discussed. In conclusion, we outline strategies for developing candidate DNA damage reference materials that could be adopted by research laboratories in a wide variety of applications.

Development of a Reference Method and Materials for Quantitative Measurement of UV-Induced DNA Damage in Mammalian Cells: Comparison of Comet Assay and Cell Viability

Application of DNA damage diagnostic tests is rapidly growing, in particular for ovarian, prostate, and skin cancers; environmental monitoring; chronic and degenerative diseases; and male infertility. Such tests suffer from significant variability among different laboratories due the lack of standardization, experimental validation, and differences in data interpretation. Reference methods and materials for quantitative measurement of UVA-induced DNA damage in mammalian cells are frequently needed. In this study, we examined the use of the single-cell gel electrophoresis (comet) assay to assess the UVA-induced DNA damage in surface-attached Chinese hamster ovary (CHO) cells treated with a photosensitizer as a candidate cellular oxidative damage reference material. We found that the comet images became diffused and the viability of the cells decreased substantially (>20%) as the UVA dose and benzo [a] pyrene (BaP) concentration exceeded 6.3 J/cm² and 10⁻⁶ mol/L BaP. Maintaining the conditions of exposure within this range can improve DNA damage measurement fidelity, particularly if used as a quantitative reference method and to produce materials considered as an in vitro standard for the comet assay.

Inactivation behavior and intracellular changes in Escherichia coli during electro-oxidation process using Ti/Sb-SnO2/PbO2 anode: Elucidation of the disinfection mechanism

This study investigates the behavior and intracellular changes in Escherichia coli (model organism) during electro-oxidation with Ti/Sb-SnO₂/PbO₂ anode in a chlorine free electrochemical system. Preliminary studies were conducted to understand the effect of initial E. coli concentration and applied current density on disinfection. At an applied current density 30 mA cm^-2, 7 log reduction of E. coli was achieved in 75 min. The role of reactive oxygen species' (ROS) in E.coli disinfection was evaluated, which confirmed hydroxyl (•OH) radical as the predominant ROS in electro-oxidation. Observations were carried out at cell and molecular level to understand E.coli inactivation mechanism. Scanning electron microscopy images confirmed oxidative damage of the cell wall and irreversible cell death. Intracellular and extracellular protein quantification and genetic material release further confirmed cell component leakage due to cell wall rupture and degradation due to •OH radical interaction. Change in cell membrane potential suggests the colloidal nature of E. coli cells under applied current density. Plasmid deoxyribonucleic acid degradation study confirmed fragmentation and degradation of released genetic material. Overall, effective disinfection could be achieved by electro-oxidation, which ensures effective inactivation and prevents regrowth of E. coli. Disinfection of real wastewater was achieved in 12 min at an applied current density 30 mA cm^-2. Real wastewater study further confirmed that effective disinfection is possible with a low cost electrode material such as Ti/Sb-SnO₂/PbO₂. Energy consumed during disinfection was determined to be 4.978 kWh m^-3 for real wastewater disinfection at applied current density 30 mA cm^-2. Cost of operation was estimated and stability of the electrode was studied to evaluate the feasibility of large scale operation. Relatively low energy and less disinfection time makes this technology suitable for field scale applications.

Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches

The determination of the redox properties of nucleobases is of paramount importance to get insight into the charge-transfer processes in which they are involved, such as those occurring in DNA-inspired biosensors. Although many theoretical and experimental studies have been conducted, the value of the one-electron oxidation potentials of nucleobases is not well-defined. Moreover, the most appropriate theoretical protocol to model the redox properties has not been established yet. In this work, we have implemented and evaluated different static and dynamic approaches to compute the one-electron oxidation potentials of solvated nucleobases. In the static framework, two thermodynamic cycles have been tested to assess their accuracy against the direct determination of oxidation potentials from the adiabatic ionization energies. Then, the introduction of vibrational sampling, the effect of implicit and explicit solvation models, and the application of the Marcus theory have been analyzed through dynamic methods. The results revealed that the static direct determination provides more accurate results than thermodynamic cycles. Moreover, the effect of sampling has not shown to be relevant, and the results are improved within the dynamic framework when the Marcus theory is applied, especially in explicit solvent, with respect to the direct approach. Finally, the presence of different tautomers in water does not affect significantly the one-electron oxidation potentials.

Electroanalysis of Biomolecules: Rational Selection of Sensor Construction

Methods of electrochemical analysis of biological objects based on the reaction of electro-oxidation/electro-reduction of molecules are presented. Polymer nanocomposite materials that modify electrodes to increase sensitivity of electrochemical events on the surface of electrodes are described. Examples of applications electrochemical biosensors constructed with nanocomposite material for detection of biological molecules are presented, advantages and drawbacks of different applications are discussed.

On the relevance of hydroxyl radical to purine DNA damage

Hydroxyl radical (HO^•) is the most reactive toward DNA among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms. HO^• is generated also by exogenous sources such as ionizing radiations. In this review we focus on the purine DNA damage by HO^• radicals. In particular, emphasis is given on mechanistic aspects for the various lesion formation and their interconnections. Although the majority of the purine DNA lesions like 8-oxo-purine (8-oxo-Pu) are generated by various ROS (including HO^•), the formation of 5',8-cyclopurine (cPu) lesions in vitro and in vivo relies exclusively on the HO^• attack. Methodologies generally utilized for the purine lesions quantification in biological samples are reported and critically discussed. Recent results on cPu and 8-oxo-Pu lesions quantification in various types of biological specimens associated with the cellular repair efficiency as well as with distinct pathologies are presented, providing some insights on their biological significance.

Genotoxic Effects of Etoposide, Bleomycin, and Ethyl Methanesulfonate on Cultured CHO Cells: Analysis by GC-MS/MS and Comet Assay

To evaluate methods for analysis of genotoxic effects on mammalian cell lines, we tested the effect of three common genotoxic agents on Chinese hamster ovary (CHO) cells by single-cell gel electrophoresis (comet assay) and gas chromatography-tandem mass spectrometry (GC-MS/MS). Suspension-grown CHO cells were separately incubated with etoposide, bleomycin, and ethyl methanesulfonate and analyzed by an alkaline comet assay and GC-MS/MS. Although DNA strand breaks were detected by the comet assay after treatment with all three agents, GC-MS/MS could only detect DNA nucleobase lesions oxidatively induced by bleomycin. This demonstrates that although GC-MS/MS has limitations in detection of genotoxic effects, it can be used for selected chemical genotoxins that contribute to oxidizing processes. The comet assay, used in combination with GC-MS/MS, can be a more useful approach to screen a wide range of chemical genotoxins as well as to monitor other DNA-damaging factors.

Cellular Reference Materials for DNA Damage Using Electrochemical Oxidation

Reference materials are needed to quantify the level of DNA damage in cells, to assess sources of measurement variability and to compare results from different laboratories. The comet assay (single cell gel electrophoresis) is a widely used method to determine DNA damage in the form of strand breaks. Here we examine the use of electrochemical oxidation to produce DNA damage in cultured mammalian cells and quantify its percentage using the comet assay. Chinese hamster ovary (CHO) cells were grown on an indium tin oxide electrode surface and exposed 12 h to electrochemical potentials ranging from 0.5 V to 1.5 V (vs Ag/AgCl). The resulting cells were harvested and analyzed by comet and a cell viability assay. We observed a linear increase in the percentage (DNA in tail) of strand breaks along with a loss of cell viability with increasing oxidation potential value. The results indicate that electrochemically induced DNA damage can be produced in mammalian cells under well-controlled conditions and could be considered in making a cellular reference material for the comet assay.

Correlation of polyphenol content and antioxidant capacity of selected teas and tisanes from Brazilian market

Abstract In this work, it was evaluated the phenolic content, redox behavior and antioxidant capacity of several selected teas and tisanes from Brazilian market. The samples were classified as simple (single herb) or composed (blend of two or more herbs). In addition, complementary multivariate statistical approaches were used to identify the correlation and interdependence between the amount of major phytocomponents, such as phenols and flavonoids, as well as the antioxidant activity of the products. Results showed that the total polyphenol and total flavonoid concentrations are correlated to thermodynamic feasibility of reactive oxygen species reduction. The statistical modeling differentiated the results datasets in principal components, whose flavonoid content presented itself as the main parameter to segregate data between simple and composed products. On the other hand, the whole polyphenol content, in both teas and tisanes, was more relevant regarding their antioxidant capacity than the flavonoids content. Considering that the manufactures do not display the real amount of each herb in the labels of the composed products, it was not possible to confirm whether the blends of several species lead to a substantial enhancement on their antioxidant capacity. Furthermore, the redox profile and overall polyphenol content suggest that the consumption of green and black teas as well as traditional yerba mate may be worthwhile in preventing ailments associated with oxidative stress in Brazilian population. Notwithstanding, further clinical studies are required to validate this hypothesis.