Separation procedures capable of revealing DNA adducts

Smart sensor for assessment of oxidative/nitrative stress biomarkers using a dual-imprinted electrochemical paper-based analytical device

We present a novel dual-imprinted electrochemical paper-based analytical device (Di-ePAD) to simultaneously determine 8-hydroxy-2'-deoxyguanosine (8-OHdG) and 3-nitrotyrosine (3-NT) and assess oxidative and nitrative biomarkers in urine and plasma samples. The Di-ePAD was designed with hydrophobic barrier layers formed on filter paper to provide three-dimensional circular reservoirs and assembled electrodes. The molecularly imprinted polymer (MIP) was synthesized using a silica nanosphere decorated with silver nanoparticles (SiO₂@AgNPs) as a core covered with dual-analyte imprinted sites on the polymer to recognize selectively and bind the target biomarkers. This strategy drives monodispersity and enhances the conductivity of the resulting MIP core-shell products. 3-NT-MIP and 8-OHdG-MIP were synthesized by successively coating the surface of SiO₂@AgNPs with l-Cysteine via the thiol group, then terminating with MIP shells. The dual imprinted core-shell composites possess attractive properties for the target biomarkers' sensing, including catalytic activity, selectivity, and good conductivity. The Di-ePAD revealed excellent linear dynamic ranges of 0.01-500 μM for 3-NT and 0.05-500 μM for 8-OHdG, with detection limits of 0.0027 μM for 3-NT and 0.0138 μM for 8-OHdG. This newly developed method based on the synergistic effects of SiO₂@AgNPs combined with promising properties of MIP offers outstanding selectivity, sensitivity, reproducibility, simplicity, and low cost for quantitative analysis of 3-NT and 8-OHdG. The proposed Di-ePAD showed good accuracy and precision when applied to actual samples, including urine and serum samples validated by a conventional HPLC method.

OUP accepted manuscript

HPLC-PDA, LC-MS/MS methods were developed for simultaneous determination of a group of oxidative stress biomarkers (OSBs); 2dA, 2dC, 2dU, 3NLT, 5HMU and 8OHdG in 10 simulated artificial body fluids. O-phosphoric acid and methanol composed mobile phases A and B for gradient elution in HPLC-PDA using ODS-2 column. Linearity obtained for 1.0×10-6-1.0×10-4M range. LODs were 1.73×10-6, 1.19×10-6, 2.59×10-6, 1.40×10-6, 2.21×10-6 and 4.07×10-6M for 2dU, 8OHdG, 2dA, 2dC, 5HMU and 3NLT, respectively. LOQs were 5.29×10-6, 4.02×10-6, 6.82×10-6, 4.02×10-6, 6.82×10-6 and 9.92×10-6M. About 10 mM aqueous ammonium acetate solution and methanol containing 0.1% (v/v) formic acid composed mobile phases A and B for gradient elution in LC-MS/MS. Linearity obtained for 1.0×10-8-1.0×10-6M range. LODs were 2.88×10-10, 1.01×10-8, 3.38×10-9, 1.36×10-7, 1.81×10-7 and 1.40×10-8M for 2dU, 8OHdG, 2dA, 2dC, 5HMU and 3NLT, respectively. LOQs were 9.37×10-10, 3.22×10-8, 1.91×10-8, 4.53×10-7, 5.90×10-7 and 2.18×10-8M. Both methods were validated using ICH Q2(R1) guideline. Specificity, linearity, range, accuracy, precision, reproducibility, LOD, LOQ and recovery were achieved. Chemometric analysis was performed on raw PDA and MS data to check their significance for discrimination of OSBs. Sets of single and triple quadrupole fragmentations were evaluated for principle component analysis. Chosen number of PCs successfully distinguished OSBs of interest.

Evaluation of Type-A Endonucleases for the Quantitative Analysis of DNA Damage due to Exposure to Acetaldehyde Using Capillary Electrophoresis

The substrate selectivities of three endonucleases were studied quantitatively using capillary zone electrophoresis to find one giving N²-ethyl(Et)-2'-deoxyguanosine-5'-monophosphate (5'-dGMP) and cyclic 1,N²-propano(CPr)-5'-dGMP from DNAs damaged by acetaldehyde (AA). Six 2'-deoxyribonucleoside-5'-monophosphates to be quantified in the hydrolysis solutions of DNAs, namely, Et-5'-dGMP, CPr-5'-dGMP, and four authentic ones, were completely separated using a 100 mM borate running buffer solution having an optimized pH of 9.67. Using the present method, nuclease reactions of nuclease S1 (NS1), nuclease P1 (NP1), and nuclease Bal 31 to 2'-deoxyribonucleoside-5'-monophosphates from damaged Calf thymus (CT-) DNAs were monitored. The CT-DNAs were prepared by treatment with AA to generate Et-guanine or CPr-guanine internally. Bal 31 hydrolyzed the damaged CT-DNAs to yield Et-5'-dGMP and CPr-5'-dGMP quantitatively. The two 5'-dGMP adducts were not detected in the hydrolysis solutions using NS1 or NP1. Bal 31 can be a suitable nuclease for analyzing DNA damages caused by AA.

Constructing a novel 8-hydroxy-2'-deoxyguanosine electrochemical sensor and application in evaluating the oxidative damages of DNA and guanine

8-Hydroxy-2'-deoxyguanosine (8-OHdG) is commonly identified as a biomarker of oxidative DNA damage. In this work, a novel and facile 8-OHdG sensor was developed based on the multi-walled carbon nanotubes (MWCNTs) modified glassy carbon electrode (GCE). It exhibited good electrochemical responses toward the oxidation of 8-OHdG, and the linear ranges were 5.63×10(-8)-6.08×10(-6)M and 6.08×10(-6)-1.64×10(-5)M, with the detection limit of 1.88×10(-8)M (S/N=3). Moreover, the fabricated sensor was applied for the determination of 8-OHdG generated from damaged DNA and guanine, respectively, and the oxidation currents of 8-OHdG increased along with the damaged DNA and guanine within certain concentrations. These results could be used to evaluate the DNA damage, and provide useful information on diagnosing diseases caused by mutation and deficiency of the immunity system.

Assessment of DNA damage by micellar electrokinetic chromatography

A simple and inexpensive MEKC method, which is able to assess base damage within DNA samples, is illustrated. After heat-acid hydrolysis of the DNA samples, both the percentage of each canonical DNA base and the relative amount of uncanonical DNA bases can be measured. This method is useful for an evaluation of the integrity of PCR templates used in several fields of investigation.

Voltammetric behaviour of free DNA bases, methylcytosine and oligonucleotides at disposable screen printed graphite electrode platforms

Improvements in analytical methods for the determination and quantification of methylcytosine in DNA are vital since it has the potential to be used as a biomarker to detect different diseases in the first stage such as in the case of carcinomas and sterility. In this work we utilized screen printed graphite electrodes (SPGE) for studying the electrochemical response of all free DNA bases, methylcytosine and short oligonucleotides by cyclic voltammetry (CV) and square wave voltammetry (SWV). CV and SWV responses of free DNA bases and methylcytosine have been investigated by using SPGE platforms and the feasibility of detecting and quantifying cytosine and methylcytosine as free DNA moieties has been evaluated as a function of pH, concentration and the presence of the other free DNA bases in solution simultaneously. Repeatability of using SWV has been performed for the electrochemical behavior of both 250 μM cytosine and 250 μM methylcytosine in the presence of 25 μM guanine, with coefficient of variations of 6.9% and 2.6% respectively based upon peak current (N = 5). Six-mer oligonucleotides with a sequence 5'-XXXCGC-3', where the XXX motif corresponds to TTT, TTA, TAA and AAA have been performed using SWV in 0.1 M acetate buffer pH 5.0 to explore how the DNA base position effects the electrooxidation of guanine and cytosine into the oligonucleotide. Furthermore SWV comparisons of the electrooxidation of the oligonucleotides 5'-CGCGCG-3' and its methylated 5'-mCGmCGmCG-3' have been performed with concentrations in acetate buffer solutions, and the interaction of both oligonucleotides with the graphitic surface of the SPGE has been demonstrated by fitting well-known adsorption models such as Freundlich and Langmuir kinetics according to the SWV current response of guanine, cytosine and methylcytosine into the oligonucleotide.

Separation of purine and pyrimidine bases and nucleosides by hydrophilic interaction chromatography

The separation of 12 model compounds chosen among purine and pyrimidine bases and nucleosides was studied by using hydrophilic interaction chromatography (HILIC). The compounds investigated were small molecules with relevant properties for biomedical and pharmaceutical studies. The mixture of pyrimidines and purines was applied on a ZIC-HILIC 150 x 2.1 mm, 5 microm, and two TSKgel Amide-80 150 x 2.0 mm, 5 microm and 3 microm particle size columns. The retention of the analytes was studied by varying ACN%, ammonium formate concentration, pH, and column temperature. The results obtained confirmed the elution order of nucleobases, nucleosides, and nucleotides based on their hydrophobicity. The retention mechanism of the columns was studied considering the models used for describing partitioning and surface adsorption. The influence on retention of chromatographic conditions (ACN%, salt concentration, pH, and temperature) was described and discussed for both columns. The optimization of the conditions studied allowed to assess a gradient method for the separation of the 12 analytes. The developed method is a valuable alternative to existing methods for the separation of the compounds concerned.

Determination of 8-hydroxy-2'deoxyguanosine in Urine Using HPLC With Electrochemical Detection

Endogenous cell metabolism and different chemicals, drugs, ionising radiation, solar light, cigarette smoking, and air pollution can induce oxidative damage to DNA. Oxidative DNA damage is involved in the development of different diseases, aging, and cancer. Urine 8-hydroxy-2'deoxyguanosine (8-oxodG) is widely accepted as a biomarker of the "whole body" oxidative DNA damage. The aim of this study was to introduce a method for determination 8-oxodG in spot urine samples using high-performance liquid chromatography with electrochemical detection. In the tested range of 50 nmol L-1to 400 nmol L-1, the calibration curve was linear (r2=0.9995) and the limit of detection was 3 nmol L-1. Concentrations of 8-oxodG ranged between 3.0 nmol L-1and 48.0 nmol L-1, which is in accordance with values reported for healthy individuals in other studies.

Ochratoxin A: An overview on toxicity and carcinogenicity in animals and humans

Ochratoxin A (OTA) is a ubiquitous mycotoxin produced by fungi of improperly stored food products. OTA is nephrotoxic and is suspected of being the main etiological agent responsible for human Balkan endemic nephropathy (BEN) and associated urinary tract tumours. Striking similarities between OTA-induced porcine nephropathy in pigs and BEN in humans are observed. International Agency for Research on Cancer (IARC) has classified OTA as a possible human carcinogen (group 2B). Currently, the mode of carcinogenic action by OTA is unknown. OTA is genotoxic following oxidative metabolism. This activity is thought to play a central role in OTA-mediated carcinogenesis and may be divided into direct (covalent DNA adduction) and indirect (oxidative DNA damage) mechanisms of action. Evidence for a direct mode of genotoxicity has been derived from the sensitive 32P-postlabelling assay. OTA facilitates guanine-specific DNA adducts in vitro and in rat and pig kidney orally dosed, one adduct comigrates with a synthetic carbon (C)-bonded C8-dG OTA adduct standard. In this paper, our current understanding of OTA toxicity and carcinogenicity are reviewed. The available evidence suggests that OTA is a genotoxic carcinogen by induction of oxidative DNA lesions coupled with direct DNA adducts via quinone formation. This mechanism of action should be used to establish acceptable intake levels of OTA from human food sources.

Voltammetric behaviour of DNA bases at a screen-printed carbon electrode and its application to a simple and rapid voltammetric method for the determination of oxidative damage in double stranded DNA

Screen-printed carbon electrodes (SPCEs) have been investigated as possible sensors to identify gamma-irradiation induced oxidative damage in double stranded (ds) DNA. Studies were undertaken to explore the possibility of using both cyclic voltammetry and differential pulse voltammetry to identify changes due to oxidative damage. Initially, guanine, adenine and 8-oxoguanosine were examined and it was found possible to differentiate them from their voltammetric responses. The voltammetric response of 8-oxoguanosine was found to be linear over the concentration range 1-400 microM, with a slope of 0.0296 microA microM(-1) (R2 value of 0.9984), in the presence of 2mM concentrations of guanine and adenine. Investigations were made into harnessing these findings to identify oxidative damage in gamma-irradiated dsDNA. The presence of oxidative damage in these samples was readily identifiable, and the magnitude of the voltammetric response was found to be dose dependant (R2=0.9919). A simple sample preparation step involving only the dissolution of double stranded DNA sample in the optimised electrolyte (0.1M acetate buffer pH 4.5) was required. This report appears to be first describing the use of a SPCE to detect DNA damage which can be related to the dose of gamma-radiation used.

Investigation of enzymatic behavior of benzonase/alkaline phosphatase in the digestion of oligonucleotides and DNA by ESI-LC/MS

We have developed an ion-pairing HPLC-MS method that has sufficient separation power, selectivity, and sensitivity to investigate the enzymatic behavior of benzonase/alkaline phosphatase upon digestion of oligonucleotides and DNA. Mass spectrometry revealed that this enzyme pair can nonspecifically digest oligonucleotides and DNA into fragments ranging from 2 to 10 nucleotides, i.e., sizes suitable for routine mass spectrometric measurements. Trimers, tetramers, and pentamers are the most prominent digested products. This makes benzonase/alkaline phosphatase a promising choice for DNA and DNA adduct related studies that require a nonspecific enzyme. A computer software program developed in-house was critical in automating the processing of mass spectral data. The methodology described here provides a systematic approach for evaluating the behavior of DNA-cleaving enzymes by mass spectrometry.

Development of the adductome approach to detect DNA damage in humans

The development of new strategies designed to detect DNA damage caused by oxidative stress and other means may advance our understanding of the roles of such types of damage in the etiology of cancers, in aging processes, and as biomarkers of exposure. A DNA adduct detection method that uses liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) to detect multiple DNA adducts in human lung tissue is reported herein. This adductome analysis strategy is designed to detect the neutral loss of 2 -deoxyribose from positively ionized 2 -deoxynucleoside adducts in multiple reaction ion monitoring mode (MRM) transmitting the [M + H](+) > [M + H - 116](+) transition over a total of 374 transitions in the mass range from m/z 228.8 to m/z 602.8. Data analysis is optimized and coupled with a comprehensive manual screening process designed to minimize the number of artifactual adducts appearing in the final analysis. In the final analysis, putative adducts were organized into an adductome map and unambiguous confirmation of selected oxidative adducts were made by stable isotope dilution and comparison to authentic standards. The future applications of this method are discussed.

Further arguments in favour of direct covalent binding of Ochratoxin A (OTA) after metabolic biotransformation

Ochratoxin A (OTA) is nephrotoxic to all animal species, carcinogenic for rats and mice and probably implicated in human Balkan endemic nephropathy and the associated urothelial tract tumour. Controversial results concerning genotoxicity and biotransformation of OTA have been generated. By (32)P post-labelling technique, a dose- and time-dependent DNA adduct formation is observed in vivo and in vitro. Use of several inducers or inhibitors of biotransforming enzymes (including cytochrome P 450, cyclooxygenase, lipoxygenase, glutathione-S-transferase), demonstrated that OTA is biotransformed into genotoxic derivatives damaging for DNA. Authentic C8dG-OTA standards have been synthesized by photo-oxidation. Both of them (C-C8 & O-C8) co-migrate on TLC with two adducts formed by in vitro incubation of OTA in the presence of kidney microsomes, and in vivo in kidney of pig or rodent fed OTA as well as in kidney and bladder tumour of humans exposed to OTA. Several OTA metabolites have been isolated from tissues or cells treated by OTA. The open ring lactone (OP-OTA) and quinone OTA (OTQ) are genotoxic.

Liquid chromatography-electrospray ionization-mass spectrometry: the future of DNA adduct detection

Over the past 40 years considerable emphasis has been placed on the development of accurate and sensitive methods for the detection and quantitation of DNA adducts. The formation of DNA adducts resulting from the covalent interaction of genotoxic carcinogens with DNA, derived from exogenous and endogenous sources, either directly or following metabolic activation, can if not repaired lead to mutations in critical genes such as those involved in the regulation of cellular growth and subsequent development of cancer. The major analytical challenge has been to detect levels of DNA adducts at the level of 0.1-1 adducts per 10(8) unmodified DNA bases using only low microgram amounts of DNA, and with high specificity and accuracy, in humans exposed to genotoxic carcinogens derived from occupational, environmental, dietary and life-style sources. In this review we will highlight the merits as well as discuss the progress made by liquid chromatography coupled to electrospray ionization mass spectrometry as a method for DNA adduct detection.

Analysis of nucleic acid constituents by on-line capillary electrophoresis-mass spectrometry

This review is focused on the capillary electrophoresis-mass spectrometric (CE-MS) analysis of nucleic acid constituents in the broadest sense, going from nucleotides and adducted nucleotides over nucleoside analogues to oligonucleotides. These nucleic acid constituents play an important role in a variety of biochemical processes. Hence, their isolation, identification, and quantification will undoubtedly help reveal the process of life and disease mechanisms, such as carcinogenesis, and can also be useful for antitumor and antiviral drug research to provide valuable information about mechanism of action, pharmacokinetics, pharmacodynamics, toxicity, therapeutic drug level monitoring, and quality control related to this substance class. Fundamental investigations into their structure, the search for modifications, the occurrence and biochemical impact of structural variation amongst others, are therefore of great value. In view of the related bioanalytical procedures, the coupling of CE to MS has emerged as a powerful tool for the analysis of the complex mixtures of nucleic acid constituents: CE confers rapid analysis and efficient resolution, while MS provides high selectivity and sensitivity with structural characterization of minute amounts of compound. After an introduction about the biochemical and analytical perspectives on the nucleic acid constituents, the different modes of CE used in this field of research as well as the relevant CE-MS interfaces and the difficulties associated with quantitative CE-MS are briefly discussed. A large section is finally devoted to field-oriented applications.

Capillary electrophoresis - mass spectrometry: survey on developments and applications 2003-2004

The major developments and applications related to CE-MS over the last two years (2003-2004) and most of the reviews and applications found in the ISI Web of Science and publisher data bases are presented in a tabulated way. This article complements our previous review "Capillary electrophoresis - mass spectrometry: 15 years of developments and applications", Electrophoresis, 2003, 24, 3837-3867 for the last two years 2003-2004. All cited articles were analyzed in a way to illustrate (i) in which journals CE-MS-related papers were mostly found over the last decades and (ii) which commercial CE-, MS-instrumentations or CE-MS combinations were mostly used in the European, Asian, and American continent. Additionally, like it was done in our last review, the reader will rapidly find applications classified as forensics, environment, bioanalytics, pharmaceutics, and metabolites.