Chemical selectivity of nucleobase adduction relative to in vivo mutation sites on exon 7 fragment of p53 tumor suppressor gene

Damage to p53 tumor suppressor gene is found in half of all human cancers. Databases integrating studies of large numbers of tumors and cancer cell cultures show that mutation sites of specific p53 codons are correlated with specific types of cancers. If the most frequently damaged p53 codons in vivo correlate with the most frequent chemical damage sites in vitro, predictions of organ-specific cancer risks might result. Herein, we describe LC-MS/MS methodology to reveal codons with metabolite-adducted nucleobases by LC-MS/MS for oligonucleotides longer than 20 base pairs. Specifically, we used a known carcinogen, benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (BPDE) to determine the most frequently adducted nucleobases within codons. We used a known sequence of 32 base pairs (bp) representing part of p53 exon 7 with 5 possible reactive hot spots. This is the first nucleobase reactivity study of a double stranded DNA p53 fragment featuring more than 20 base pairs with multiple reactive sites. We reacted the 32 bp fragment with benzo[a]pyrene metabolite BPDE that undergoes nucleophilic substitution by DNA bases. Liquid chromatography-mass spectrometry (LC-MS/MS) was used for sequencing of oligonucleotide products from the reacted 32 bp fragment after fragmentation by a restriction endonuclease. Analysis of the adducted p53 fragment compared with unreacted fragment revealed guanines of codons 248 and 244 as most frequently targeted, which are also mutated with high frequency in human tumors. Codon 248 is mutated in non-small cell and small cell lung, head and neck, colorectal and skin cancer, while codon 244 is mutated in small cell lung cancer, all of which involve possible BDPE exposure. Results suggest the utility of this approach for screening of adducted p53 gene by drugs and environmental chemicals to predict risks for organ specific cancers.     

A reagentless DNA biosensor based on cathodic electrochemiluminescence at a C/CxO1−x electrode

A reagentless signal-on electrochemiluminescence (ECL) biosensor for DNA hybridization detection was developed based on the quenching effect of ferrocene (Fc) on intrinsic cathodic ECL at thin oxide covered glassy carbon (C/C_xO_1−x) electrodes. To construct the DNA biosensor, molecular beacon (MB) modified with ferrocene (3′-Fc) was attached to a C/C_xO_1−x electrode via the covalent bound between labeled amino (5′-NH₂) and surface functional groups. It was found that the immobilization of the probe on the electrode surface mainly depended on the fraction of surface carbonyl moiety. When a complementary target DNA (cDNA) was present, the stem-loop of MB on the electrode was converted into a linear double-helix configuration due to hybridization, resulting in the moving away of Fc from the electrode surface, and the restoring of the cathodic ECL signal. The restoration of the ECL intensity was linearly changed with the logarithm of cDNA concentration in the range of 1.0 × 10⁻¹¹ to 7.0 × 10⁻⁸ M, and the detection limit was ca. 5.0 pM (S/N = 3). Additionally, single-base mismatched DNA can be effectively discriminated from the cDNA. The great advantage of the biosensor lies in its simplicity and cost-effective with ECL generated from the electrode itself, and no adscititious luminophore is required.     

High resolution mass spectrometry based profiling of diet-related deoxyribonucleic acid adducts

Exposure of DNA to endo- and exogenous DNA binding chemicals can result in the formation of DNA adducts and is believed to be the first step in chemically induced carcinogenesis. DNA adductomics is a relatively new field of research which studies the formation of known and unknown DNA adducts in DNA due to exposure to genotoxic chemicals. In this study, a new UHPLC-HRMS(/MS)-based DNA adduct detection method was developed and validated. Four targeted DNA adducts, which all have been linked to dietary genotoxicity, were included in the described method; O⁶-methylguanine (O⁶-MeG), O⁶-carboxymethylguanine (O⁶-CMG), pyrimidopurinone (M1G) and methylhydroxypropanoguanine (CroG). As a supplementary tool for DNA adductomics, a DNA adduct database, which currently contains 123 different diet-related DNA adducts, was constructed. By means of the newly developed method and database, all 4 targeted DNA adducts and 32 untargeted DNA adducts could be detected in different DNA samples. The obtained results clearly demonstrate the merit of the described method for both targeted and untargeted DNA adduct detection in vitro and in vivo, whilst the diet-related DNA adduct database can distinctly facilitate data interpretation.     

Geno-Tox: Cell Array Biochip for Genotoxicity Monitoring and Classification

In vitro genotoxicity tests detect carcinogens that are thought to act primarily via a mechanism involving direct genetic damage. In this study, we constructed a Geno-Tox cell array chip for genotoxicity testing; eight recombinant bioluminescent bacteria were used to successfully fabricate a Geno-Tox cell array chip. Four well-characterized DNA damage chemicals were selected to determine the capabilities of this Geno-Tox array chip, and each strain of the chip was distinctly responsive, according to the specific mode of genotoxic action. Therefore, this Geno-Tox cell array chip could be implemented to characterize and understand the genotoxic modes of impact; thus, it could be used to provide the genotoxic mechanism of action for new drugs or unknown or newly synthesized chemicals in food and the environment.     

A bioluminescence test for genotoxic agents

Mutagenic chemicals and agents that damage DNA are potential carcinogens. Recently, a new method has been developed to determine just how genotoxic these agents are by testing their ability to restore the luminescence of dark mutants of luminous bacteria in vivo.     

Cyclic voltammetric detection of chemical DNA damage induced by styrene oxide in natural dsDNA layer-by-layer films using methylene blue as electroactive probe

In this work, an electrochemical sensor for detecting damage of natural double-stranded DNA (dsDNA) was constructed based on PSS/{PDDA/dsDNA}₃ layer-by-layer films, where PSS was poly(styrene sulfonate) and PDDA was poly(diallyldimethyl ammonium). When the PSS/{PDDA/dsDNA}₃ films assembled on pyrolytic graphite (PG) electrodes were immersed into methylene blue (MB) solution and loaded MB into the films, the formed PSS/{PDDA/dsDNA}₃-MB films in blank buffers at pH 7.0 showed a reversible cyclic voltammetric (CV) peak pair at −0.23 V vs. SCE for MB redox couple. In blank solutions, the MB loaded into the films was released gradually from the films, but the complete reloading of MB into the films could be realized by immersing the films into MB solution again, indicating the good reversibility of MB incorporation. However, after incubation in the solution of known genotoxic agent styrene oxide (SO), the damaged PSS/{PDDA/dsDNA}₃-MB films could not return to their original and fully-loaded state with reloading of MB, and showed smaller CV peak currents than those of intact PSS/{PDDA/dsDNA}₃-MB films. The relative peak current ratio, I_p,I/I_p,III, where I_p,I was the anodic peak current of intact DNA films in blank buffers after fully loading with MB and I_p,III was that of SO-damaged DNA films after reloading with MB, increased linearly with the incubation time with SO in the range of 5–40 min with a damage rate of 0.0099 min⁻¹. While the formation of SO adducts with dsDNA had no substantial effect on the dsDNA conformation, the steric hindrance of SO adducts with guanine or adenine blocked the intercalation of MB into the base pairs of dsDNA, resulting in the decrease of CV peak currents of loaded MB. The specific intercalation of MB into dsDNA base pairs and the sensitive electrochemical response of MB, combined with the unique feature of loading reversibility of MB in the DNA layer-by-layer films, make the difference in CV response between the intact and damaged dsDNA films become pronounced in the “loading/release/reloading” procedure. This may provide a new and general approach for constructing a biosensor for screening genetoxic chemicals in vitro.     

In-situ monitoring of cell-secreted lactate by electrochemiluminescence sensing under biomimetic microfluidic confinement

Cell migration proceeds in 3D matrices in vivo, which can naturally switch to distinct phenotypes for better invasion in confined microenvironments. The studies of important metabolites under confinement are extremely meaningful for comprehensive insights into cancer metastasis. The integration of cell confinement device and analytical techniques is a key point for in-situ analysis of significant metabolites in vitro.Herein, an electrochemiluminescence(ECL) sensing platform was designed for in-s...     

Spatial regulation of a common precursor from two distinct genes generates metabolite diversity

In secondary metabolite biosynthesis, core synthetic genes such as polyketide synthase genes usually encode proteins that generate various backbone precursors. These precursors are modified by other tailoring enzymes to yield a large variety of different secondary metabolites. The number of core synthesis genes in a given species correlates, therefore, with the number of types of secondary metabolites the organism can produce. In our study, heterologous expression of all the A. terreus NRPS-like genes showed that two NRPS-like proteins, encoded by atmelA and apvA, release the same natural product, aspulvinone E. In hyphae this compound is converted to aspulvinones whereas in conidia it is converted to melanin. The genes are expressed in different tissues and this spatial control is probably regulated by their own specific promoters. Comparative genomics indicates that atmelA and apvA might share a same ancestral gene and the gene apvA is located in a highly conserved region in Aspergillus species that contains genes coding for life-essential proteins. Our data reveal the first case in secondary metabolite biosynthesis in which the tissue specific production of a single compound directs it into two separate pathways, producing distinct compounds with different functions. Our data also reveal that a single trans-prenyltransferase, AbpB, prenylates two substrates, aspulvinones and butyrolactones, revealing that genes outside of contiguous secondary metabolism gene clusters can modify more than one compound thereby expanding metabolite diversity. Our study raises the possibility of incorporation of spatial, cell-type specificity in expression of secondary metabolites of biological interest and provides new insight into designing and reconstituting their biosynthetic pathways.     

Analytical methods in DNA and protein adduct analysis

DNA or protein adducts are reaction products of endogenous or exogenous chemicals and cellular macromolecules. Adducts are useful in toxicological studies and/or human biomonitoring exercises. In particular, DNA damage provides invaluable information for risk analysis. Second, metabolites or conjugates can be regarded as markers of phase II reactions though they may not give accurate information about the levels of reactive and damage-provoking reactive compounds or intermediates. Electrophiles are often short-lived molecules and therefore difficult to monitor. In contrast, adducts are often chemically stable, though their levels in biological samples are low, which makes their detection challenging. The assay of adducts is similar to the analysis of any other trace organic molecule, i.e. problems with the matrix and small amounts of analytes in samples. The ³²P-postlabelling assay is a specific method for DNA adducts but immunochemical and fluorescence-based methods have been developed which can detect adducts linked to both DNA and protein. Tandem mass spectrometry, particularly if combined with ultrahigh-performance liquid chromatography, is currently the recommended detection technique; however investigators are striving to develop novel ways to achieve greater sensitivity. Standards are a prerequisite in adduct analysis, but unfortunately they are seldom commercially available.     

Comparison of DNA‐Reactive Metabolites from Nitrosamine and Styrene Using Voltammetric DNA/Microsomes Sensors

Voltammetric sensors made with films of polyions, double‐stranded DNA and liver microsomes adsorbed layer‐by‐layer onto pyrolytic graphite electrodes were evaluated for reactive metabolite screening. This approach features simple, inexpensive screening without enzyme purification for applications in drug or environmental chemical development. Cytochrome P450 enzymes (CYPs) in the liver microsomes were activated by an NADPH regenerating system or by electrolysis to metabolize model carcinogenic compounds nitrosamine and styrene. Reactive metabolites formed in the films were trapped as adducts with nucleobases on DNA. The DNA damage was detected by square‐wave voltammetry (SWV) using Ru(bpy) as a DNA‐oxidation catalyst. These sensors showed a larger rate of increase in signal vs. reaction time for a highly toxic nitrosamine than for the moderately toxic styrene due to more rapid reactive metabolite‐DNA adduct formation. Results were consistent with reported in vivo TD₅₀ data for the formation of liver tumors in rats. Analogous polyion/ liver microsome films prepared on 500 nm silica nanoparticles (nanoreactors) and reacted with nitrosamine or styrene, provided LC‐MS or GC analyses of metabolite formation rates that correlated well with sensor response.     

Secondary Metabolites of Purpureocillium lilacinum

Fungi can synthesize a wealth of secondary metabolites, which are widely used in the exploration of lead compounds of pharmaceutical or agricultural importance. Beauveria, Metarhizium, and Cordyceps are the most extensively studied fungi in which a large number of biologically active metabolites have been identified. However, relatively little attention has been paid to Purpureocillium lilacinum. P. lilacinum are soil-habituated fungi that are widely distributed in nature and are very important biocontrol fungi in agriculture, providing good biological control of plant parasitic nematodes and having a significant effect on Aphidoidea, Tetranychus cinnbarinus, and Aleyrodidae. At the same time, it produces secondary metabolites with various biological activities such as anticancer, antimicrobial, and insecticidal. This review attempts to provide a comprehensive overview of the secondary metabolites of P. lilacinum, with emphasis on the chemical diversity and biological activity of these secondary metabolites and the biosynthetic pathways, and gives new insight into the secondary metabolites of medical and entomogenous fungi, which is expected to provide a reference for the development of medicine and agrochemicals in the future.     

Identification of chemicals and their metabolites from PHY906, a Chinese medicine formulation,in the plasma of a patient treated with irinotecan and PHY906 using liquid chromatography/tandem mass spectrometry (LC/MS/MS)

Traditional Chinese Medicine (TCM) is increasingly being used in combination with Western medicine. In general, TCM is comprised of multiple components in sharp contrast to Western medicine, where a single active chemical is used. Presently, there are no well-established standards for most of the chemical compounds of TCM and their respective metabolites. Moreover, there are no formal analytical methods for the identification of these chemicals, especially in trace amounts. The ability to measure the pharmacokinetic behaviors of chemicals and their metabolites from these herbal formulations are critical in understanding of the action of TCM. This paper describes the use of LC/MS/MS along with enzyme treatments and n-octanol/water partition coefficient, to investigate the chemical components of PHY906 and their metabolites in the plasma of a patient with metastatic colorectal cancer (mCRC) treated with irinotecan and PHY906. The chemicals from an aqueous extract of PHY906 and the plasma from a patient was prepared and separated on an Agilent ZORBAX-SB C₁₈ column, and eluted with acetonitrile/0.05% (v/v) formic acid. From the PHY906 aqueous extract, a total of 57 compounds and 27 metabolites were identified and tentatively assigned structures based on their identified mass spectrometry, enzyme digestion and n-octanol/water partition coefficient. In contrast, analysis of patient plasma identified only 33 chemicals and new metabolites. These findings demonstrated that LC/MS/MS was and effective and reliable method for studying the parent chemicals of the Chinese herbal medicine PHY906 and their metabolites in a patient with metastatic colorectal cancer.     

Direct electrochemiluminescence detection of oxidized DNA in ultrathin films containing [Os(bpy)2(PVP)10]2+

Direct electrochemiluminescence (ECL) involving oxidized DNA was demonstrated in ultrathin films of cationic polymer [Os(bpy)2(PVP)10]2+ [PVP = poly(vinyl pyridine)] assembled layer-by-layer with DNA or oligonucleotides. Electrochemically oxidized Os(II) sites generated ECL from films containing oxo-guanines on DNA formed by chemical oxidation using Fenton reagent. Films combining DNA, [Ru(bpy)2(PVP)10]2+, and [Os(bpy)2(PVP)10]2+ had Os(II) sites that produced ECL specific for oxidized DNA, and Ru(II) sites gave ECL from reaction with oxo-adenines, chemically damaged DNA, and possibly from cleaved DNA strands.     

Generation of 1,2-azaboretidines via reduction of ADC borane adducts

Reaction of the acyclic (diamino)carbene (ADC) :C(NiPr₂)₂ (1) with different dihaloboranes of the type RBX₂ (R = Mes, Dur; X = Cl, Br) smoothly afforded a novel class of ADC-stabilized borane adducts. For MesBBr₂ however, the reaction did not stop at the adduct level, but an uncommon rearrangement process occurred, which eventually resulted in the formation of a 5-membered boracycle after elimination of mesitylene. Chemical reduction of the ADC borane adducts by KC₈ selectively yielded air stable 1,2-azaboretidines. Detailed DFT studies suggest a reduction mechanism involving a highly reactive borylene intermediate, which is converted into the boracycles via a rearrangement/C–H activation sequence.     

Electrochemiluminescence of CdTe quantum dots as labels at nanoporous gold leaf electrodes for ultrasensitive DNA analysis

A new electrochemiluminescence (ECL) DNA assay is developed using quantum dots (QDs) as DNA labels. When nanoporous gold leaf (NPGL) electrodes are used, sensitivity of the ECL assay is remarkably increased due to ultra-thin nanopores. In this assay, target DNA (t-DNA) is hybridized with capture DNA (c-DNA) bound on the NPGL electrode, which is fabricated by conjugating amino-modified c-DNA to thioglycolic acid (TGA) modified at the activated NPGL electrode. Following that, amino-modified probe DNA is hybridized with the t-DNA, yielding sandwich hybrids on the NPGL electrode. Then, mercaptopropionic acid-capped CdTe QDs are labeled to the amino group end of the sandwich hybrids. Finally, in the presence of S₂O₈²⁻ as coreactant, ECL emission of the QD-labeled DNA hybrids on the NPGL electrode is measured by scanning the potential from 0 to −2 V to record the curve of ECL intensity versus potential. The maximum ECL intensity (I_m,ECL) on the curve is proportional to t-DNA concentration with a linear range of 5 × 10⁻¹⁵ to 1 × 10⁻¹¹ mol/L. The ECL DNA assay can be used to determine DNA corresponding to mRNA in cell extracts in this study.     

New methodology for the characterization of (±)-anti-BPDE-DNA adducts and tetrol I-1 with solid-matrix phosphorescence

Novel solid-matrix phosphorescence (SMP) methods were developed for the detection and characterization of (±)-anti-benzo[a]pyrene-trans-7,8-dihydrodiol-9,10-epoxide ((±)-anti-BPDE)-DNA adducts and a hydrolysis product of the (±)-anti-BPDE-DNA adducts, tetrol I-1, by using the heavy-atom salts, thallium nitrate and sodium iodide, to enhance the solid-matrix phosphorescence. Thallium nitrate was much more effective for enhancing the SMP of the (±)-anti-BPDE-DNA adducts and tetrol I-1. Thus, the results from TlNO₃ were emphasized. The amount of TlNO₃ adsorbed on the solid matrix was varied over a wide range, and SMP intensities, lifetimes, and spectra were acquired. Fundamental equations and calculated photophysical parameters were used to interpret the data and characterize the samples. The data indicated that there were two major populations of the (±)-anti-BPDE-DNA adducts and tetrol I-1 adsorbed on the solid matrix. Because DNA was adsorbed so strongly to the solid matrix, the (±)-anti-BPDE-DNA adducts interacted in a uniform manner with increasing amounts of TlNO₃. However, tetrol I-1 responded in a more random fashion with the increase in the amount of TlNO₃. The methods developed can be used to compare the SMP of small molecular-weight metabolites and DNA samples modified at different levels of (±)-anti-BPDE. Also, the methodology can be employed for DNA samples that are adducted with any material that would give measurable SMP.     

Thermochemical properties of some vinyl chloride-induced DNA lesions: detailed view from NBO & AIM analysis

Etheno-damaged DNA adducts such as 3,N ⁴-ethenocytosine, N ²,3-ethenoguanine, and 1,N ²-ethenoguanine are associated with carcinogenesis and cell death. These inevitable damages are counteracted by glycosylase enzymes, which cleave damaged nucleobases from DNA. Escherichia coli alkyl purine DNA glycosylase is the enzyme responsible for excising damaged etheno adducts from DNA in humans. In an effort to understand the intrinsic properties of these molecules, we examined gas-phase acidity values and proton affinities (PA) of multiple sites of these molecules as well as equilibrium tautomerization and base pairing properties by quantum mechanical calculations. We also used calculations to compare the acidic and basic properties of these etheno adduct with those of the normal bases—cytosine and guanine nucleobases. We hypothesize that alkyl DNA glycosylase may cleave certain damaged nucleobases as anions and that the active site may take advantage of a nonpolar environment to favor deprotonated cytosine or guanine as a leaving group versus damaged nucleobases.     

LC-MS/MS Based Identification of Piperine Production by Endophytic Mycosphaerella sp. PF13 from Piper nigrum

Piper nigrum is very remarkable for its medicinal properties due to the presence of metabolites like piperine. Emerging understanding on the biosynthetic potential of endophytic fungi suggests the possibility to have piperine producing fungi in P. nigrum. In the current study, endophytic fungi isolated from P. nigrum were screened for the presence of piperine by liquid chromatography-tandem mass spectrometry (LC-MS/MS). This resulted in the identification of a Mycosphaerella sp. with the ability to produce piperine extracellularly. The biosynthesis of piperine (C₁₇H₁₉NO₃) by the endophytic fungal isolate was confirmed by the presence of m/z 286.1 (M + H⁺) in the LC-MS/MS analysis using positive mode ionization. This was further supported by the presence of specific fragment ions with masses 135, 143, 171 and 201 formed due to the fragmentation of piperine present in the fungal extract.     

Simultaneous determination of 8‐oxo‐2′‐deoxyguanosine and 8‐oxo‐2′‐deoxyadenosine in DNA using online column‐switching liquid chromatography/tandem mass spectrometry

Sensitive and reliable methods are required for the assessment of oxidative DNA damage, which can result from reactive oxygen species that are generated endogenously from cellular metabolism and inflammatory responses, or by exposure to exogenous agents. The development of a liquid chromatography/tandem mass spectrometry (LC/MS/MS) selected reaction monitoring (SRM) method is described, that utilises online column‐switching valve technology for the simultaneous determination of two DNA adduct biomarkers of oxidative stress, 8‐oxo‐7,8‐dihydro‐2′‐deoxyguanosine (8‐oxodG) and 8‐oxo‐7,8‐dihydro‐2′‐deoxyadenosine (8‐oxodA). To allow for the accurate quantitation of both adducts the corresponding [¹⁵N₅]‐labelled stable isotope internal standards were synthesised and added prior to enzymatic hydrolysis of the DNA samples to 2′‐deoxynucleosides. The method required between 10 and 40 µg of hydrolysed DNA on‐column for the analysis and the limit of detection for both 8‐oxodG and 8‐oxodA was 5 fmol. The analysis of calf thymus DNA treated in vitro with methylene blue (ranging from 5 to 200 µM) plus light showed a dose‐dependent increase in the levels of both 8‐oxodG and 8‐oxodA. The level of 8‐oxodG was on average 29.4‐fold higher than that of 8‐oxodA and an excellent linear correlation (r = 0.999) was observed between the two adducts. The influence of different DNA extraction procedures for 8‐oxodG and 8‐oxodA levels was assessed in DNA extracted from rat livers following dosing with carbon tetrachloride. The levels of 8‐oxodG and 8‐oxodA were on average 2.9 (p = 0.018) and 1.4 (p = 0.018) times higher, respectively, in DNA samples extracted using an anion‐exchange column procedure than in samples extracted using a chaotropic procedure, implying artefactual generation of the two adducts. In conclusion, the online column‐switching LC/MS/MS SRM method provides the advantages of increased sample throughput with reduced matrix effects and concomitant ionisation suppression, making the method ideally suited when used in conjunction with chaotropic DNA extraction for the determination of oxidative DNA damage. Copyright © 2008 John Wiley & Sons, Ltd.     

Assembly and characterization of Ag nanoparticles in PAM-g-PVA/PVP semi-interpenetrating network hydrogels

Polyacrylamide grafted poly(vinyl alcohol)/polyvinylpyrrolidone (PAM-g-PVA/PVP) semi-interpenetrating network (semi-IPN) hydrogels were designed and prepared via a simple free radical polymerization reaction process initiated by a PVA-(NH₄)₂Ce(NO₃)₆ redox system. The structure of the PAM-g-PVA/PVP semi-IPNs was characterized by a Fourier transform infrared spectroscopy. The morphologies of PAM-g-PVA/PVP hydrogels and PAM-g-PVA/PVP/Ag nanocomposite hydrogels were examined by scanning electron microscopy and transmission electron microscopy (TEM). The experimental results indicated that the PAM, PVA or PVP chains can efficiently act as stabilizing agents for Ag nanoparticles. TEM investigation of sample morphology showed the presence of nearly spherical-, square- or rectangular-shaped Ag nanoparticles with diameters ranging from 10 to 60 nm. The characteristic surface plasmon resonance band appeared at 390–400 run as a result of the immobilization of Ag nanoparticles within the hydrogel matrices. The self-assembly of Ag nanoparticles and the swelling behavior of the resulting nanocomposites can be controlled and modulated by altering the mole fraction of PVP in the PAM-g-PVA/PVP semi-IPNs.