Determination of apurinic/apyrimidinic lesions in DNA with high-performance liquid chromatography and tandem mass spectrometry

The rate of formation and stability of abasic site interstrand crosslinks in the DNA duplex

DNA interstrand crosslinks (ICLs) strands pose an impenetrable barrier for DNA replication. Different ICLs are known to recruit distinct DNA repair pathways. NEIL3 glycosylase has been known to remove an abasic (Ap) site derived DNA crosslink (Ap-ICL). An Ap-ICL forms spontaneously from the Ap site with an adjacent adenine in the opposite strand. Lack of genetic models and a poor understanding of the fate of these lesions leads to many questions about the occurrence and the toxicity of Ap-ICL in cells. Here, we investigate the circumstances of Ap-ICL formation. With an array of different oligos, we have investigated the rates of formation, the yields, and the stability of Ap-ICL. Our findings point out how different bases in the vicinity of the Ap site change crosslink formation in vitro. We reveal that AT-rich rather than GC-rich regions in the surrounding Ap site lead to higher rates of Ap-ICL formation. Overall, our data reveal that Ap-ICL can be formed in virtually any DNA sequence context surrounding a hot spot of a 5'-Ap-dT pair, albeit with significantly different rates and yields. Based on Ap-ICL formation in vitro, we attempt to predict the number of Ap-ICLs in the cell.

DNA-Protein Cross-Links Formed by Reacting Lysine with Apurinic/Apyrimidinic Sites in DNA and Human Cells: Quantitative Analysis by Liquid Chromatography-Tandem Mass Spectrometry Coupled with Stable Isotope Dilution

Accumulating evidence suggests that DNA lesion-induced DNA-protein cross-links (DPCs) interrupt normal DNA metabolic processes, such as transcription, replication, and repair, resulting in profound biological consequences, including the development of many human diseases, such as cancers. Although apurinic/apyrimidinic (AP) sites are among the most predominant DNA lesions and are in close proximity to the histone proteins that they wrap around in the nucleosome, knowledge of the chemical structure or biological consequences of their associated DPCs is limited in part due to a lack of sensitive and selective analytical methods. We developed liquid chromatography-tandem mass spectrometry coupled with a stable isotope dilution method for rigorous quantitation of DPCs formed by reacting a DNA AP site with a lysine residue. In combination with chemical derivatization with fluorenylmethoxycarbonyl chloride to form a hydrophobic conjugate, the developed LC-MS/MS method allows sensitive detection of AP site-Lys cross-links down to sub-1 adduct per 10⁶ nt. After validation using a synthetic AP site-lysine-cross-linked peptide and an oligodeoxyribonucleotide, the method was used to determine the concentration of AP site-lysine cross-links in hot acid-treated DNA and in human cells exposed to methyl methanesulfonate.

Toxicity and genotoxicity of domestic sewage sludge in the freshwater snail Biomphalaria glabrata (Say, 1818)

Waste produced in homes is one of the main sources of pollutants in freshwater ecosystems. Therefore, it is imperative to implement methodologies that aid in environmental monitoring procedures. The use of organisms as biomonitors has grown increasingly prevalent as they are models that provide data that can be adequately evaluated. In this work, we investigated the genotoxic and cytotoxic effects caused by domestic sewage sludge through an analysis of biomarkers in the mollusk Biomphalaria glabrata. For the tests, increasing concentrations of 50, 100, 150, and 500 mg L^-1 of domestic sewage sludge were standardized, in addition to control groups. Assays were performed after the mollusks were exposed to the domestic sewage sludge in acute (48 h) and chronic (15 d) manner. Toxicity tests were performed with embryonic and adult snails. The cytoplasmic and nuclear changes were analyzed in the hemocyte cells. Lastly, genotoxic damage was analyzed using the comet assay. Adult snails and embryos of B. glabrata showed no significant morphological changes. Domestic sludge caused deleterious effects on mollusks as confirmed after cell genotoxicity tests. Therefore, based on the results obtained from the analysis of B. glabrata hemocytes, we can affirm that domestic sewage sludge causes genotoxic and cytotoxic effects on mollusk cells. Therefore, it is possible to conclude that the mollusk Biomphalaria glabrata can be used as a good low-cost alternative to assist in the biomonitoring of freshwater environments. Graphical Abstract.

Thermoplastic nanofluidic devices for identifying abasic sites in single DNA molecules

DNA damage can take many forms such as double-strand breaks and/or the formation of abasic (apurinic/apyrimidinic; AP) sites. The presence of AP sites can be used to determine therapeutic efficacy of many drugs, such as doxorubicin. While there are different assays to search for DNA damage, they are fraught with limitations, such as the need for large amounts of DNA secured from millions of cells. This is challenging due to the growing importance of using liquid biopsies as a source of biomarkers for many in vitro diagnostic assays. To accommodate the mass limits imposed by the use of liquid biopsies, we report a single-molecule DNA damage assay that uses plastic nanofluidic chips to stretch DNA to near its full contour length when the channel dimensions (width and depth) are near the persistence length (∼50 nm) of double-stranded (ds) DNA. The nanofluidic chip consisted of input funnels for high loading efficiency of single DNA molecules, entropic traps to store the DNA and simultaneously load a series of nanochannels for high throughput processing, and an array of stretching nanochannels to read the AP sites. Single dsDNA molecules, which were labeled with an intercalating dye and a biotinylated aldehyde reactive probe (bARP), could be parked in the stretching nanochannels, where the AP sites were read directly using a dual-color fluorescence microscope equipped with an EMCCD camera. One color of the microscope was used to read the DNA length and the second color detected the AP sites. The nanofluidic chip was made from thermoplastics via nanoimprint lithography, which obviated the need for direct writing the devices in glass or quartz using focused ion beam milling. We show that we can read the frequency of AP sites in single dsDNA molecules with the frequency of AP sites determined by associating fluorescently-labeled streptavidin with bARP through a biotin/streptavidin complex.

Mass Spectrometric Quantitation of Apurinic/Apyrimidinic Sites in Tissue DNA of Rats Exposed to Tobacco-Specific Nitrosamines and in Lung and Leukocyte DNA of Cigarette Smokers and Nonsmokers

Metabolic activation of the carcinogenic tobacco-specific nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N'-nitrosonornicotine (NNN) results in formation of reactive electrophiles that modify DNA to produce a variety of products including methyl, 4-(3-pyridyl)-4-oxobutyl (POB)-, and 4-(3-pyridyl)-4-hydroxybutyl adducts. Among these are adducts such as 7-POB-deoxyguanosine (N7POBdG) which can lead to apurinic/apyrimidinic (AP) sites by facile hydrolysis of the base-deoxyribonucleoside bond. In this study, we used a recently developed highly sensitive mass spectrometric method to quantitate AP sites by derivatization with O-(pyridin-3-yl-methyl)hydroxylamine (PMOA) (detection limit, 2 AP sites per 108 nucleotides). AP sites were quantified in DNA isolated from tissues of rats treated with NNN and NNK and from human lung tissue and leukocytes of cigarette smokers and nonsmokers. Rats treated with 5 or 21 mg/kg bw NNK for 4 days by s.c. injection had 2-6 and 2-17 times more AP sites than controls in liver and lung DNA (p < 0.05). Increases in AP sites were also found in liver DNA of rats exposed for 10 and 30 weeks (p < 0.05) but not for 50 and 70 weeks to 5 ppm of NNK in their drinking water. Levels of N7POBG were significantly correlated with AP sites in rats treated with NNK. In rats treated with 14 ppm (S)-NNN in their drinking water for 10 weeks, increased AP site formation compared to controls was observed in oral and nasal respiratory mucosa DNA (p < 0.05). No significant increase in AP sites was found in human lung and leukocyte DNA of cigarette smokers compared to nonsmokers, although AP sites in leukocyte DNA were significantly correlated with urinary levels of the NNK metabolite 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL). This is the first study to use mass spectrometry based methods to examine AP site formation by carcinogenic tobacco-specific nitrosamines in laboratory animals and to evaluate AP sites in DNA of smokers and nonsmokers.

Complex Interactions Between Weather, and Microbial and Physicochemical Water Quality Impact the Likelihood of Detecting Foodborne Pathogens in Agricultural Water

Agricultural water is an important source of foodborne pathogens on produce farms. Managing water-associated risks does not lend itself to one-size-fits-all approaches due to the heterogeneous nature of freshwater environments. To improve our ability to develop location-specific risk management practices, a study was conducted in two produce-growing regions to (i) characterize the relationship between Escherichia coli levels and pathogen presence in agricultural water, and (ii) identify environmental factors associated with pathogen detection. Three AZ and six NY waterways were sampled longitudinally using 10-L grab samples (GS) and 24-h Moore swabs (MS). Regression showed that the likelihood of Salmonella detection (Odds Ratio [OR] = 2.18), and eaeA-stx codetection (OR = 6.49) was significantly greater for MS compared to GS, while the likelihood of detecting L. monocytogenes was not. Regression also showed that eaeA-stx codetection in AZ (OR = 50.2) and NY (OR = 18.4), and Salmonella detection in AZ (OR = 4.4) were significantly associated with E. coli levels, while Salmonella detection in NY was not. Random forest analysis indicated that interactions between environmental factors (e.g., rainfall, temperature, turbidity) (i) were associated with likelihood of pathogen detection and (ii) mediated the relationship between E. coli levels and likelihood of pathogen detection. Our findings suggest that (i) environmental heterogeneity, including interactions between factors, affects microbial water quality, and (ii) E. coli levels alone may not be a suitable indicator of food safety risks. Instead, targeted methods that utilize environmental and microbial data (e.g., models that use turbidity and E. coli levels to predict when there is a high or low risk of surface water being contaminated by pathogens) are needed to assess and mitigate the food safety risks associated with preharvest water use. By identifying environmental factors associated with an increased likelihood of detecting pathogens in agricultural water, this study provides information that (i) can be used to assess when pathogen contamination of agricultural water is likely to occur, and (ii) facilitate development of targeted interventions for individual water sources, providing an alternative to existing one-size-fits-all approaches.

The genomics of oxidative DNA damage, repair, and resulting mutagenesis

Reactive oxygen species are a constant threat to DNA as they modify bases with the risk of disrupting genome function, inducing genome instability and mutation. Such risks are due to primary oxidative DNA damage and also mediated by the repair process. This leads to a delicate decision process for the cell as to whether to repair a damaged base at a specific genomic location or better leave it unrepaired. Persistent DNA damage can disrupt genome function, but on the other hand it can also contribute to gene regulation by serving as an epigenetic mark. When such processes are out of balance, pathophysiological conditions could get accelerated, because oxidative DNA damage and resulting mutagenic processes are tightly linked to ageing, inflammation, and the development of multiple age-related diseases, such as cancer and neurodegenerative disorders. Recent technological advancements and novel data analysis strategies have revealed that oxidative DNA damage, its repair, and related mutations distribute heterogeneously over the genome at multiple levels of resolution. The involved mechanisms act in the context of genome sequence, in interaction with genome function and chromatin. This review addresses what we currently know about the genome distribution of oxidative DNA damage, repair intermediates, and mutations. It will specifically focus on the various methodologies to measure oxidative DNA damage distribution and discuss the mechanistic conclusions derived from the different approaches. It will also address the consequences of oxidative DNA damage, specifically how it gives rise to mutations, genome instability, and how it can act as an epigenetic mark.

AP-Seq: A Method to Measure Apurinic Sites and Small Base Adducts Genome-Wide

DNA is constantly challenged by chemical modification and spontaneous loss of its bases, which results in apurinic sites (AP-sites). In addition to the direct route, modified bases may be converted into AP-sites through enzymatic removal of the base as part of the base excision repair pathway. Here we present the method AP-seq, which allows enriching and sequencing AP-sites genome-wide. Quantification of DNA recovery (AP-quant) allows for relative quantification of global AP-sites, and AP-site pulldown followed by qPCR (AP-qPCR) allows for site-specific damage assessment. Taking advantage of glycosylases that specifically excise modified bases also in vitro, this method allows not only to address the genomic distribution of AP-sites but also to detect base modifications, e.g., 8-oxo-7,8-dihydroguanine (8-oxoG). AP-quant, AP-qPCR, and AP-seq can be applied to investigate quantitatively the relative amount and genome specificity of DNA damage and repair, effects of radiation, as well as multiple other questions around AP-sites and base modifications.

Quantitation of Apurinic/Apyrimidinic Sites in Isolated DNA and in Mammalian Tissue with a Reduced Level of Artifacts

The apurinic/apyrimidinic (AP) site is a common lesion of DNA damage. The levels of AP sites reported in the literature cover a wide range, which is primarily due to the artifactual generation or loss of AP sites during processing of the DNA. Herein, we have developed a method for quantitating AP sites with a largely reduced level of artifacts by derivatizing AP sites before DNA isolation. A rapid digestion of nuclear protein was performed to minimize enzymatic DNA repair, followed by direct derivatization of AP sites in the nuclear lysate with O-(pyridin-3-yl-methyl)hydroxylamine, yielding an oxime derivative that is stable through the subsequent DNA processing steps. Quantitation was done using highly selective and sensitive liquid chromatography-tandem mass spectrometry, with a limit of quantitation at 2.2 lesions per 10⁸ nucleotides (nts, 0.9 fmol on column). The method was applied in vivo to measure AP sites in rats undergoing oxidative stress [liver, 3.31 ± 0.47/10⁷ nts (dosed) vs 0.91 ± 0.06/10⁷ nts (control); kidney, 1.60 ± 0.07/10⁷ nts (dosed) vs 1.13 ± 0.12/10⁷ nts (control)]. The basal AP level was significantly lower than literature values. The method was also used to measure AP sites induced by the chemotherapeutic nitrogen mustard in vitro.

Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis

BACKGROUND

DNA is subject to constant chemical modification and damage, which eventually results in variable mutation rates throughout the genome. Although detailed molecular mechanisms of DNA damage and repair are well understood, damage impact and execution of repair across a genome remain poorly defined.

RESULTS

To bridge the gap between our understanding of DNA repair and mutation distributions, we developed a novel method, AP-seq, capable of mapping apurinic sites and 8-oxo-7,8-dihydroguanine bases at approximately 250-bp resolution on a genome-wide scale. We directly demonstrate that the accumulation rate of apurinic sites varies widely across the genome, with hot spots acquiring many times more damage than cold spots. Unlike single nucleotide variants (SNVs) in cancers, damage burden correlates with marks for open chromatin notably H3K9ac and H3K4me2. Apurinic sites and oxidative damage are also highly enriched in transposable elements and other repetitive sequences. In contrast, we observe a reduction at chromatin loop anchors with increased damage load towards inactive compartments. Less damage is found at promoters, exons, and termination sites, but not introns, in a seemingly transcription-independent but GC content-dependent manner. Leveraging cancer genomic data, we also find locally reduced SNV rates in promoters, coding sequence, and other functional elements.

CONCLUSIONS

Our study reveals that oxidative DNA damage accumulation and repair differ strongly across the genome, but culminate in a previously unappreciated mechanism that safeguards the regulatory and coding regions of genes from mutations.

Selective Labeling Aldehydes in DNA

A naphthalimide hydroxylamine probe has been designed and synthesized to selectively label the whole natural aldehydes present in DNAs including 5-formylcytosine, 5-formyluracil, and abasic sites. The fluorescence characteristics of the generated nucleosides have been examined in detail, and the reaction activities of hydroxylamine, amine groups toward aldehydes in DNA have been discussed with others, which will be a vital reference for designing chemicals for selective labeling of DNAs.

New method for estimating clustering of DNA lesions induced by physical/chemical mutagens using fluorescence anisotropy

We have developed a new method for estimating the localization of DNA damage such as apurinic/apyrimidinic sites (APs) on DNA using fluorescence anisotropy. This method is aimed at characterizing clustered DNA damage produced by DNA-damaging agents such as ionizing radiation and genotoxic chemicals. A fluorescent probe with an aminooxy group (AlexaFluor488) was used to label APs. We prepared a pUC19 plasmid with APs by heating under acidic conditions as a model for damaged DNA, and subsequently labeled the APs. We found that the observed fluorescence anisotropy (r_obs) decreases as averaged AP density (λ_AP: number of APs per base pair) increases due to homo-FRET, and that the APs were randomly distributed. We applied this method to three DNA-damaging agents, ⁶⁰Co γ-rays, methyl methanesulfonate (MMS), and neocarzinostatin (NCS). We found that r_obs-λ_AP relationships differed significantly between MMS and NCS. At low AP density (λ_AP < 0.001), the APs induced by MMS seemed to not be closely distributed, whereas those induced by NCS were remarkably clustered. In contrast, the AP clustering induced by ⁶⁰Co γ-rays was similar to, but potentially more likely to occur than, random distribution. This simple method can be used to estimate mutagenicity of ionizing radiation and genotoxic chemicals.

5-Formyl- and 5-Carboxydeoxycytidines Do Not Cause Accumulation of Harmful Repair Intermediates in Stem Cells

5-Formyl-dC (fdC) and 5-carboxy-dC (cadC) are newly discovered bases in the mammalian genome that are supposed to be substrates for base excision repair (BER) in the framework of active demethylation. The bases are recognized by the monofunctional thymine DNA glycosylase (Tdg), which cleaves the glycosidic bond of the bases to give potentially harmful abasic sites (AP-sites). Because of the turnover of fdC and cadC during cell state transitions, it is an open question to what extent such harmful AP-sites may accumulate during these processes. Here, we report the development of a new reagent that in combination with mass spectrometry (MS) allows us to quantify the levels of AP-sites. This combination also allowed the quantification of β-elimination (βE) products, which are repair intermediates of bifunctional DNA glycosylases. In combination with feeding of isotopically labeled nucleosides, we were able to trace the intermediates back to their original nucleobases. We show that, while the steady-state levels of fdC and cadC are substantially increased in Tdg-deficient cells, those of both AP- and βE-sites are unaltered. The levels of the detected BER intermediates are 1 and 2 orders of magnitude lower than those of cadC and fdC, respectively. Thus, neither the presence of fdC nor that of cadC in stem cells leads to the accumulation of harmful AP- and βE-site intermediates.

The colorimetric determination of selectively cleaved adenosines and guanosines in DNA oligomers using bicinchoninic acid and copper

Colorimetric methods combined with color-changing chemical probes are widely used as simple yet effective tools for identifying and quantifying a wide variety of molecules in solution. For nucleic acids (DNA and RNA), perhaps the most commonly used colorimetric probe is potassium permanganate, which can be used to identify single-stranded pyrimidines (thymine and cytosine) in polymers. Unfortunately, permanganate is not an effective probe for identifying purines (adenine and guanine), especially in the presence of the more reactive pyrimidines. Therefore, robust methods for discriminating between the purines remain elusive, thereby creating a barrier toward developing more complex colorimetric applications. In this proof-of-principle study, we demonstrate that bicinchoninic acid (BCA) and copper, when combined with purine-specific chemical cleavage reactions, can be a colorimetric probe for the identification and quantification of adenosines and/or guanosines in single-stranded DNA oligomers, even in the presence of pyrimidines. Furthermore, the reactions are stoichiometric, which allows for the quantification of the number of adenosines and/or guanosines in these oligomers. Because the BCA/copper reagent detects the reducing sugar, 2-deoxyribose, that results from the chemical cleavage of a given nucleotide's N-glycosidic bond, these colorimetric assays are effectively detecting apurinic sites in DNA oligomers, which are known to occur via DNA damage in biological systems. We demonstrate that simple digital analysis of the color-changing chromophore (BCA/copper) is all that is necessary to obtain quantifiable and reproducible data, which indicates that these assays should be broadly accessible.

A versatile new tool to quantify abasic sites in DNA and inhibit base excision repair

A number of endogenous and exogenous agents, and cellular processes create abasic (AP) sites in DNA. If unrepaired, AP sites cause mutations, strand breaks and cell death. Aldehyde-reactive agent methoxyamine reacts with AP sites and blocks their repair. Another alkoxyamine, ARP, tags AP sites with a biotin and is used to quantify these sites. We have combined both these abilities into one alkoxyamine, AA3, which reacts with AP sites with a better pH profile and reactivity than ARP. Additionally, AA3 contains an alkyne functionality for bioorthogonal click chemistry that can be used to link a wide variety of biochemical tags to AP sites. We used click chemistry to tag AP sites with biotin and a fluorescent molecule without the use of proteins or enzymes. AA3 has a better reactivity profile than ARP and gives much higher product yields at physiological pH than ARP. It is simpler to use than ARP and its use results in lower background and greater sensitivity for AP site detection. We also show that AA3 inhibits the first enzyme in the repair of abasic sites, APE-1, to about the same extent as methoxyamine. Furthermore, AA3 enhances the ability of an alkylating agent, methylmethane sulfonate, to kill human cells and is more effective in such combination chemotherapy than methoxyamine.

Recognition and repair of chemically heterogeneous structures at DNA ends

Exposure to environmental toxicants and stressors, radiation, pharmaceutical drugs, inflammation, cellular respiration, and routine DNA metabolism all lead to the production of cytotoxic DNA strand breaks. Akin to splintered wood, DNA breaks are not "clean." Rather, DNA breaks typically lack DNA 5'-phosphate and 3'-hydroxyl moieties required for DNA synthesis and DNA ligation. Failure to resolve damage at DNA ends can lead to abnormal DNA replication and repair, and is associated with genomic instability, mutagenesis, neurological disease, ageing and carcinogenesis. An array of chemically heterogeneous DNA termini arises from spontaneously generated DNA single-strand and double-strand breaks (SSBs and DSBs), and also from normal and/or inappropriate DNA metabolism by DNA polymerases, DNA ligases and topoisomerases. As a front line of defense to these genotoxic insults, eukaryotic cells have accrued an arsenal of enzymatic first responders that bind and protect damaged DNA termini, and enzymatically tailor DNA ends for DNA repair synthesis and ligation. These nucleic acid transactions employ direct damage reversal enzymes including Aprataxin (APTX), Polynucleotide kinase phosphatase (PNK), the tyrosyl DNA phosphodiesterases (TDP1 and TDP2), the Ku70/80 complex and DNA polymerase β (POLβ). Nucleolytic processing enzymes such as the MRE11/RAD50/NBS1/CtIP complex, Flap endonuclease (FEN1) and the apurinic endonucleases (APE1 and APE2) also act in the chemical "cleansing" of DNA breaks to prevent genomic instability and disease, and promote progression of DNA- and RNA-DNA damage response (DDR and RDDR) pathways. Here, we provide an overview of cellular first responders dedicated to the detection and repair of abnormal DNA termini.

Flap endonuclease 1

First discovered as a structure-specific endonuclease that evolved to cut at the base of single-stranded flaps, flap endonuclease (FEN1) is now recognized as a central component of cellular DNA metabolism. Substrate specificity allows FEN1 to process intermediates of Okazaki fragment maturation, long-patch base excision repair, telomere maintenance, and stalled replication fork rescue. For Okazaki fragments, the RNA primer is displaced into a 5' flap and then cleaved off. FEN1 binds to the flap base and then threads the 5' end of the flap through its helical arch and active site to create a configuration for cleavage. The threading requirement prevents this active nuclease from cutting the single-stranded template between Okazaki fragments. FEN1 efficiency and specificity are critical to the maintenance of genome fidelity. Overall, recent advances in our knowledge of FEN1 suggest that it was an ancient protein that has been fine-tuned over eons to coordinate many essential DNA transactions.

Combination of pentafluorophenylhydrazine derivatization and isotope dilution LC-MS/MS techniques for the quantification of apurinic/apyrimidinic sites in cellular DNA

Apurinic/apyrimidinic (AP) sites are common DNA lesions arising from spontaneous hydrolysis of the N-glycosidic bond and base-excision repair mechanisms of the modified bases. Due to the strong association of AP site formation with physically/chemically induced DNA damage, quantifying AP sites provides important information for risk assessment of exposure to genotoxins and oxidative stress. However, rigorous quantification of AP sites in DNA has been hampered by technical problems relating to the sensitivity and selectivity of existing analytical methods. We have developed a new isotope dilution liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) method for the rigorous quantification of AP sites in genomic DNA. The method entails enzymatic digestion of AP site-containing DNA by endo- and exonucleases, derivatization with pentafluorophenylhydrazine (PFPH), addition of an isotopically labeled PFPH derivative as internal standard, and quantification by LC-MS/MS. The combination of PFPH derivatization with LC-MS/MS analysis on a triple quadrupole mass spectrometer allows for sensitive and selective quantification of AP sites in DNA at a detection limit of 6.5 fmol, corresponding to 4 AP sites/10(9) nt in 5 μg of DNA, which is at least ten times more sensitive than existing analytical methods. The protocol was validated by AP site-containing oligonucleotides and applied in quantifying methyl methanesulfonate-induced formation of AP sites in cellular DNA.

A methodology for estimating localization of apurinic/apyrimidinic sites in DNA using fluorescence resonance energy transfer

We have developed a methodology for estimating localization of lesions on double-stranded DNA using fluorescence resonance energy transfer (FRET). We focused on apurinic/apyrimidinic (AP) sites, which are typical DNA lesions induced by radiation and chemicals and produced spontaneously under physiological conditions. Donor-acceptor fluorescent probes with O-amino groups (Alexa Fluor 350-Alexa Fluor 488 dye pair) were used for selectively labeling AP sites. pUC19 plasmid subjected to heat treatment (pH 5.2, 70 °C) was used as a model double-stranded DNA containing AP sites. The results of both FRET analysis and theoretical study enabled us to prove that AP sites induced by the heat treatment are distributed almost randomly along the DNA molecule. This methodology will be useful for estimating the risk of ionizing radiation and chemicals (e.g., pollutants and anticancer agents) based on the probability of producing "clustered DNA damage sites," which are considered to be less easily repairable and, therefore, more harmful to living systems.

Promotion of DNA repair by nuclear IKKβ phosphorylation of ATM in response to genotoxic stimuli

Ataxia-telangiectasia mutated (ATM) is one of the key molecules involved in the cellular response to DNA damage. A portion of activated ATM is exported from the nucleus into the cytoplasm, where it activates the I kappa B kinase/nuclear factor kappa B (IKK/NF-κB) signaling pathway. It has been thought that activated IKKβ, which is a critical kinase for NF-κB activation, generally resides in the cytoplasm and phosphorylates cytoplasmic downstream molecules, such as IκBα. Here, we identified a new role for IKKβ during the response to DNA damage. ATM phosphorylation in response to alkylating agents consisted of two phases: the early phase (up to 3 h) and late phase (after 6 h). A portion of the activated IKKβ generated during the DNA damage response was found to translocate into the nucleus and directly phosphorylate ATM in the late phase. Furthermore, the phosphorylation of ATM by nuclear IKKβ was suggested to promote DNA repair. In parallel, activated IKKβ induced classical NF-κB activation and was involved in anti-apoptosis. Our findings define the function of IKKβ during the response to DNA damage, which promotes cell survival and DNA repair, and maintains cellular homeostasis.

Templated synthesis of nylon nucleic acids and characterization by nuclease digestion

Nylon nucleic acids containing oligouridine nucleotides with pendent polyamide linkers and flanked by unmodified heteronucleotide sequences were prepared by DNA templated synthesis. Templation was more efficient than the single-stranded synthesis: Coupling step yields were as high as 99.2%, with up to 7 amide linkages formed in the synthesis of a molecule containing 8 modified nucleotides. Controlled digestion by calf spleen phosphodiesterase enabled the mapping of modified nucleotides in the sequences. A combination of complete degradation of nylon nucleic acids by snake venom phosphodiesterase and dephosphorylation of the resulting nucleotide fragments by bacterial alkaline phosphatase, followed by LCMS analysis, clarified the linear structure of the oligo-amide linkages. The templated synthesis strategy afforded nylon nucleic acids in the target structure and was compatible with the presence heteronucleotides. The complete digestion procedure produced a new species of DNA analogues, nylon ribonucleosides, which display nucleosides attached via a 2'-alkylthio linkage to each diamine and dicarboxylate repeat unit of the original nylon nucleic acids. The binding affinity of a nylon ribonucleoside octamer to the complementary DNA was evaluated by thermal denaturing experiments. The octamer was found to form stable duplexes with an inverse dependence on salt concentration, in contrast to the salt-dependent DNA control.

The impact of acute temperature stress on hemocytes of invasive and native mussels (Mytilus galloprovincialis and M. californianus): DNA damage, membrane integrity, apoptosis and signalling pathways

We investigated effects of acute heat- and cold stress on cell viability, lysosome membrane stability, double- and single-stranded DNA breakage, and signalling mechanisms involved in cellular homeostasis and apoptosis in hemocytes of native and invasive mussels, Mytilus californianus and M. galloprovincialis, respectively. Both heat stress (28ºC, 32ºC) and cold stress (2ºC, 6ºC) led to significant double- and single-stranded breaks in DNA. The types and extents of DNA damage were temperature- and time-dependent, as was caspase-3 activation, an indicator of apoptosis, which may occur in response to DNA damage. Hemocyte viability and lysosomal membrane stability decreased significantly under heat stress. Western blot analyses of hemocyte extracts with antibodies for proteins associated with cell signalling and stress responses [including members of the phospho-specific Mitogen Activated Protein Kinase (MAPK) family (c-JUN NH(2)-terminal kinase (JNK) and p38-MAPK) and apoptosis executor caspase-3] revealed that heat- and cold stress induced a time-dependent activation of JNK, p38-MAPK and caspase-3 and that these signalling and stress responses differed between species. Thermal limits for activation of cell signalling processes linked to repair of stress-induced damage may help determine cellular thermal tolerance limits. Our results show similarities in responses to cold- and heat stress and suggest causal linkages between levels of DNA damage at both extremes of temperature and downstream regulatory responses, including induction of apoptosis. Compared to M. californianus, M. galloprovincialis might have a wider temperature tolerance due to a lower amount of double-stranded DNA damage, faster signalling activation and transduction, and stronger repair ability against temperature stress.

Construction of highly reactive probes for abasic site detection by introduction of an aromatic and a guanidine residue into an aminooxy group

Abasic sites (AP sites) arise from hydrolysis of glycosidic bonds of DNA that is damaged by various external and internal processes; unrepaired AP sites give rise to genetic mutations. We have constructed highly reactive AP-site-detecting probes by introducing a hydrophobic and a hydrophilic residue in an aminooxy group. Synthesized probes containing either a naphthalene or a guanidine residue conjugate effectively with AP sites. In particular, a probe containing both functional groups shows the highest reaction rate, indicating that the hydrophobic and hydrophilic interactions act cooperatively in reaction with AP sites. The guanidine residue also contributes to the solubility of the molecules in aqueous media. The biotinylated probes provide much more sensitive detection of AP sites in genomic DNA than the conventional aldehyde-reactive probe.

Unambiguous structural elucidation of base-modified purine nucleosides using NMR

A general and unambiguous approach has been developed for structural elucidation of modified purine nucleosides using NMR spectroscopy. Systematic assignment of proton and carbon signals of modified nucleosides was firmly established by COSY and the anomerism of the glycosidic linkage of synthetic nucleosides clearly elucidated by NOESY experiments. Characteristic properties of 15N-isotopic labelling at specific positions of nucleosides were also employed for structural studies. The reported approach is applicable to other modified nucleosides and nucleotides, as well as nucleobases.

Limits of suspicion, recognition and confirmation as concepts that account for the confirmation transitions at the detection limit for quantification by liquid chromatography-tandem mass spectrometry

With the emergence of liquid chromatography coupled to tandem quadrupolar mass spectrometry (LC-QqQ) as a routine technique for quantitative analysis, analytical chemists claimed LC-QqQ to be the gold standard to reach the best compromise between versatility, high throughput, robustness, sensitivity and selectivity. In particular, a high selectivity is ensured when two or more transitions are monitored because not only the retention time and protonated molecule are controlled but also two or more product ions are. With the multiple-transition recording, the transition leading to the most intense signal is used for the quantification (quantifier), while the other one(s) is(are) aimed at confirming the detection of the analyte (qualifiers). The confirmation is based on the calculation of the relative intensity between the signal intensities of the quantifier and the qualifier(s). This useful approach raises the question of the validity of the limit of detection (LOD), initially employed for mono-channel detections such as HPLC combined with ultraviolet or fluorescence detection. Furthermore, it was shown that the multiple-transition recording leads to a confusing calculation of the decision limit (CCalpha) and detection capability (CCbeta). In the present article, the LOD is split in three concepts defined as the limit of suspicion (LOS), recognition (LOR), and confirmation (LOC). For these three limits, applications and drawbacks are shown, while determination methods are proposed.

Synthesis and site-specific incorporation of a simple fluorescent pyrimidine

We describe procedures for the synthesis of a fluorescent pyrimidine analog and its site-specific incorporation into a DNA oligomer. The 5'-protected and 3'-activated nucleoside 4 is synthesized in three steps with an overall yield of 40%. Site-specific incorporation into a DNA oligomer occurs with greater than 88% coupling efficiency. This isosteric fluorescent DNA analog can be used to monitor denaturation of DNA duplexes via fluorescence and can positively detect the presence of abasic sites in DNA duplexes. The total time for synthesis of the phosphoramidite 4 is about 75 h, whereas the total time for site-specific incorporation of nucleoside 2 into an oligonucleotide and purification of the corresponding oligonucleotide is about 114 hours.