Electrochemical simulation of oxidation processes involving nucleic acids monitored with electrospray ionization-mass spectrometry

Electrochemical Simulation of the Oxidative Capsaicin Metabolism

Capsaicin, primarily known as the pungent ingredient in hot peppers, is rapidly metabolized in the human body by enzymatic processes altering the pharmacological as well as toxicological properties. Herein, the oxidative transformation of capsaicin was investigated in vitro with electrochemistry as well as human liver microsomal incubations. The reaction mixtures were analyzed with liquid chromatography-mass spectrometry. Structure elucidation involved accurate mass measurements and multistage tandem mass spectrometry experiments. In total, 126 transformation products were detected. Electrochemistry provided evidence for 101 transformation products and the microsomal incubations for 46 species. 21 compounds were observed with both approaches. Identified oxidative pathways likely occurring during the phase I metabolism included dehydrogenation, O-demethylation, and hydroxylation reactions as well as combinations thereof. Furthermore, trapping of reactive intermediates either with glutathione or with electrochemically activated ribonucleosides provided evidence for the possible production of phase II metabolites and covalent adducts with a genetic material. Evidence for the occurrence of some capsaicin metabolites in humans was obtained by urine screening.

The Dynamics of Hole Transfer in DNA

High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.

On-line electrochemistry/electrospray ionization mass spectrometry (EC-ESI-MS) system for the study of nucleosides and nucleotides oxidation products

The main aim of present investigation was to study the oxidation products of nucleosides and nucleotides with the use of on-line electrochemistry/electrospray ionization mass spectrometry (EC-ESI-MS) system. The conditions applied in the system were optimized in complex manner, involving study of the impact of working electrodes or sample solvent on the oxidation of tested compounds and their ionization in mass spectrometry. Finally 5 mM of ammonium acetate was used selected and pH 3 was used for positive ionization mode, while pH 7 was applied for negative ionization in mass spectrometry. It was shown that utilization of both ionization modes is indispensable in order to detect and identify all of oxidation products. Furthermore the identification of compounds obtained using the EC-ESI-MS system was done and results were compared with known metabolites of studied compounds. These products are associated with specific disease states, or may be a potential metabolites. Moreover the analysis of urine samples by liquid chromatography coupled with mass spectrometry confirmed the possibility of using EC-ESI-MS technique to simulate the metabolism of nucleosides and nucleotides, since the oxidation products have also been identified in urine samples.

Characterization of background noise in capture-based targeted sequencing data

Background

Targeted deep sequencing is increasingly used to detect low-allelic fraction variants; it is therefore essential that errors that constitute baseline noise and impose a practical limit on detection are characterized. In the present study, we systematically evaluate the extent to which errors are incurred during specific steps of the capture-based targeted sequencing process.

Results

We removed most sequencing artifacts by filtering out low-quality bases and then analyze the remaining background noise. By recognizing that plasma DNA is naturally fragmented to be of a size comparable to that of mono-nucleosomal DNA, we were able to identify and characterize errors that are specifically associated with acoustic shearing. Two-thirds of C:G > A:T errors and one quarter of C:G > G:C errors were attributed to the oxidation of guanine during acoustic shearing, and this was further validated by comparative experiments conducted under different shearing conditions. The acoustic shearing step also causes A > G and A > T substitutions localized to the end bases of sheared DNA fragments, indicating a probable association of these errors with DNA breakage. Finally, the hybrid selection step contributes to one-third of the remaining C:G > A:T and one-fifth of the C > T errors.

Conclusions

The results of this study provide a comprehensive summary of various errors incurred during targeted deep sequencing, and their underlying causes. This information will be invaluable to drive technical improvements in this sequencing method, and may increase the future usage of targeted deep sequencing methods for low-allelic fraction variant detection.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-017-1275-2) contains supplementary material, which is available to authorized users.

Perspective on electrospray ionization and its relation to electrochemistry

The phenomenon of electrospraying of liquids is presented from the perspective of the electrochemistry involved. Basics of current and liquid flow in the capillary and spray tip are discussed, followed by specifics of charging and discharging of the sprayed liquid surface. Fundamental theories and numerical modeling relating electrospray current to solution and spray parameters are described and then compared with our own experimentally obtained data. The method of mapping potentials and currents inside the electrospray capillary by using an inserted electrically-isolated small wire probe electrode is discussed in detail with illustrations from new and published data. Based on these experimentally obtained results, a new mathematical model is derived. The introduced "nonlinear resistor electrospray capillary model" divides the electrospray capillary into small sections, adds their contributions, and then, by transition to infinitely small section thickness, produces analytical formulas that relate current and potential maps to other properties of the electrospraying liquid: primarily conductivity and current density. The presentation of the model is undertaken from an elementary standpoint, and it offers the possibility to obtain quantitative information regarding operating parameters from typical analytical systems subjected to electrospray. The model stresses simplicity and ease of use; examples applying experimental data are shown and some predictions of the model are also presented. The developed nonlinear resistor electrospray capillary model is intended to provide a new quantitative basis for improving the understanding of electrochemical transformations occurring in the electrospray emitter. A supplemental material section gives full derivation of the model and discusses other consequences.

Mass spectrometric methods for monitoring redox processes in electrochemical cells

Electrochemistry (EC) is a mature scientific discipline aimed to study the movement of electrons in an oxidation-reduction reaction. EC covers techniques that use a measurement of potential, charge, or current to determine the concentration or the chemical reactivity of analytes. The electrical signal is directly converted into chemical information. For in-depth characterization of complex electrochemical reactions involving the formation of diverse intermediates, products and byproducts, EC is usually combined with other analytical techniques, and particularly the hyphenation of EC with mass spectrometry (MS) has found broad applicability. The analysis of gases and volatile intermediates and products formed at electrode surfaces is enabled by differential electrochemical mass spectrometry (DEMS). In DEMS an electrochemical cell is sampled with a membrane interface for electron ionization (EI)-MS. The chemical space amenable to EC/MS (i.e., bioorganic molecules including proteins, peptides, nucleic acids, and drugs) was significantly increased by employing electrospray ionization (ESI)-MS. In the simplest setup, the EC of the ESI process is used to analytical advantage. A limitation of this approach is, however, its inability to precisely control the electrochemical potential at the emitter electrode. Thus, particularly for studying mechanistic aspects of electrochemical processes, the hyphenation of discrete electrochemical cells with ESI-MS was found to be more appropriate. The analytical power of EC/ESI-MS can further be increased by integrating liquid chromatography (LC) as an additional dimension of separation. Chromatographic separation was found to be particularly useful to reduce the complexity of the sample submitted either to the EC cell or to ESI-MS. Thus, both EC/LC/ESI-MS and LC/EC/ESI-MS are common.

Synthesis of 2'-deoxy-1'-homo-N-nucleosides with anti-influenza activity by catalytic methyltrioxorhenium (MTO)/H2O2 oxyfunctionalization

This paper describes a new route for the synthesis of 1'-homo-N-nucleoside derivatives by means of either methyltrioxorhenium (MTO) or supported MTO catalysts, with H(2)O(2) as the primary oxidant. Under these selective conditions, the oxyfunctionalization of the heterocyclic ring and the N heteroatom oxidation were operative processes, regardless of the type of substrate used, that is, purine or pyrimidine derivatives. In addition, the oxidation of 1'-homo-N-thionucleosides, showed the occurrence of site-specific oxidative nucleophilic substitutions of the heterocyclic ring. The MTO/H(2)O(2) system showed, in general, high reactivity under both homogeneous and heterogeneous conditions, affording the final products with high conversion values of substrates and from medium to high yields. Many of the novel 1'-homo-N-nucleoside analogues were active against the influenza A virus, without any cytotoxic effects, retaining their activity in both protected and unprotected forms.

Ascorbic acid for homogenous redox buffering in electrospray ionization-mass spectrometry

Electrospray ionization (ESI) involves the dispersion of a liquid containing analytes of interest into a fine aerosol by applying a high potential difference to the sample solution with respect to a counter electrode. Thus, from the electrochemical point of view, the ESI source represents a two-electrode controlled-current electrochemical flow cell. The electroactive compounds part of the solvent sprayed may be altered by occurring electrolysis (oxidation in positive ion mode and reduction in negative ion mode). These reactions can be troublesome in the context of unknown identification and quantification. In the search for a simple, inexpensive, and efficient way to suppress electrochemical oxidation in positive ESI, the usability of ascorbic acid, hydroquinone, and glutathione for homogenous redox buffering was tested. Performance of the antioxidants was assessed by analyzing pharmaceutical compounds covering a broad range of functional groups prone to oxidation. Different emitter setups were applied for continuous infusion, flow injection, and liquid chromatography/mass spectrometry experiments. Best performance was obtained with ascorbic acid. In comparison to hydroquinone and glutathione, ascorbic acid offered superior antioxidant activity, a relatively inert oxidation product, and hardly any negative effect on the ionization efficiency of analytes. Furthermore, ascorbic acid suppressed the formation of sodiated forms and was able to induce charge state reduction. Only in the very special case of analyzing a compound isobaric to ascorbic acid, interference with the low-abundant [ascorbic acid+H](+) signal may become a point of attention.

An optimized electrochemistry-liquid chromatography-mass spectrometry method for studying guanosine oxidation

Oxidative stress can disrupt the integrity of genetic material. Due to its importance in the pathogenesis of different kinds of disease, including neurodegenerative disease, cardiovascular disease and cancer, major efforts are put into the elucidation of mechanisms involved. Herein, the combination of electrochemistry/liquid chromatography/mass spectrometry (EC/LC/MS) is presented as convenient, fast and simple method to study nucleic acids oxidation. Guanosine was selected as test compound. 8-Hydroxyguanosine and (guanosine-H)₂ were identified as primary oxidation products. Oxidation was accomplished in an electrochemical thin-layer cell integrated in the flow path of the autosampler of the chromatographic system. The reaction mixture was separated and mass analyzed by LC/MS. The use of LC was found to be particularly beneficial to resolve isobaric oxidation products. Another advantage of the setup used was the ability to decouple the electrochemical cell and the electrospray ionization source from each other eliminating any kind of cell potential interaction. Separation of EC from LC/MS, furthermore, facilitates method optimization. Experimental parameters were optimized for both techniques independently. Highest yields and best detectability of oxidation products were obtained with 10 mM ammonium formate at physiological pH delivered at a flow rate of 2.5-5 μL/min through the electrochemical cell.

Formation and characterization of covalent guanosine adducts with electrochemistry-liquid chromatography-mass spectrometry

Chemicals can interact with the genetic material giving rise to the formation of covalent adducts. These alterations can lead to adverse consequences, including cancer, reproductive impairment, development anomalies, or genetic diseases. In search for an assay allowing identification of hazardous compounds that might form covalent adducts with nucleic acids, electrochemistry (EC)/liquid chromatography (LC)/mass spectrometry (MS) is presented. EC/LC/MS is a purely instrumental approach. EC is used for oxidative activation, LC for the fractionation of the reaction mixture, and MS for the detection and characterization of the reaction products. To test the system capabilities, we investigated the formation of covalent adducts produced by guanosine and acetaminophen (APAP). Electrochemical activation of mixtures of guanosine and APAP gave rise to the formation of four isomers of (guanosine + APAP-2H). Mass voltammograms as well as dose–response-curves were used to obtain insights in the mechanism of adduct formation. These experiments revealed that a mechanism involving radical intermediates is favored. The initial step of adduct formation is the conversion of both APAP and guanosine into radicals via one-electron–one-proton reactions. Among different competing reaction pathways, the generated radical intermediates undergo intermolecular reactions to form covalent adducts between guanosine and APAP.