DNA N6-methyl-2′-deoxyadenosine (6mdA) is an epigenetic modification in both eukaryotes and bacteria. Here we exploited stable isotope-labeled deoxynucleoside [15N5]-2′-deoxyadenosine ([15N5]-dA) as an initiation tracer and for the first time developed a metabolically differential tracing code for monitoring DNA 6mdA in human cells. We demonstrate that the initiation tracer [15N5]-dA undergoes a specific and efficient adenine deamination reaction leading to the loss the exocyclic amine 15N, and further utilizes the purine salvage pathway to generate mainly both [15N4]-dA and [15N4]-2′-deoxyguanosine ([15N4]-dG) in mammalian genomes. However, [15N5]-dA is largely retained in the genomes of mycoplasmas, which are often found in cultured cells and experimental animals. Consequently, the methylation of dA generates 6mdA with a consistent coding pattern, with a predominance of [15N4]-6mdA. Therefore, mammalian DNA 6mdA can be potentially discriminated from that generated by infecting mycoplasmas. Collectively, we show a promising approach for identification of authentic DNA 6mdA in human cells and determine if the human cells are contaminated with mycoplasmas.

DNA 5-hydroxymethylcytosine (5hmC) is an important epigenetic modification found in various mammalian cells. Immunofluorescence imaging analysis essentially provides visual pictures for the abundance and distribution of DNA 5hmC in single cells. However, nuclear DNA is usually wrapped around nucleosomes, packaged into chromatins, and further bound with many functional proteins. These physiologically relevant events would generate barriers to the anti-5hmC antibody to selectively recognize 5hmC in DNA. By taking advantage of these naturally generated barriers, here, we present a strategy to evaluate the accessibility of DNA 5hmC in chromatins in situ. We demonstrate that a few of the 5hmC sites in DNA are exposed or accessible to anti-5hmC antibody under nondenaturing conditions, suggesting that these 5hmC sites are not covered by functional DNA-binding proteins in mouse embryonic stem cells. Consistently, these 5hmC foci were distributed in open euchromatin regions as revealed by the 4′,6-diamidino-2-phenylindole (DAPI) staining. By overexpressing TET1 catalytic domain (responsible for oxidation 5mC to produce 5hmC) in human MCF-7 cells, we observed a significant increase in accessible 5hmC along with an increase in total 5hmC sites. Collectively, by the use of the nondenaturing immunofluorescence imaging approach, we could obtain a visual landscape on the accessibility of DNA 5hmC in chromatins.

Ten-eleven translocation (Tet) family proteins are Fe(II)- and 2-oxoglutarate-dependent dioxygenases that regulate the dynamics of DNA methylation by catalyzing the oxidation of DNA 5-methylcytosine (5mC). To exert physiologically important functions, redox-active iron chelated in the catalytic center of Tet proteins directly involves the oxidation of the multiple substrates. To understand the function and interaction network of Tet dioxygenases, it is interesting to obtain high affinity and a specific inhibitor. Surprisingly, here we found that natural Ni(II) ion can bind to the Fe(II)-chelating motif (HXD) with an affinity of 7.5-fold as high as Fe(II). Consistently, we further found that Ni(II) ion can displace the cofactor Fe(II) of Tet dioxygenases and inhibit Tet-mediated 5mC oxidation activity with an estimated IC50 of 1.2 μM. Essentially, Ni(II) can be used as a high affinity and selective inhibitor to explore the function and dynamics of Tet proteins.

•An UHPLC–MS/MS method was developed for accurate detection of 8-OHdG in leukocyte.•8-OHdG in leukocyte but urine can indicate oxidative DNA damage.•Higher levels of leukocyte 8-OHdG were found in cancer patients over health control.8-Hydroxydeoxyguanosine (8-OHdG) is a widely-used biomarker of oxidative DNA damages. 8-OHdG in peripheral blood leukocyte is associated with mutation and cancer risk. The level of 8-OHdG in peripheral blood leukocytes can indicate a long-term response to oxidative stress rather than that in urine. Accurate identification and quantification of leukocyte 8-OHdG are essential for understanding its mechanism of formation, repair, and biological consequences. In this study, a fast and accurate ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC–MS/MS) method was developed and validated to detect 8-OHdG in human peripheral leukocyte. DNA in blood samples were extracted and digested, then subjected onto UHPLC–MS/MS using an isocratic elution on a Zorbax Eclipse Plus C18 column (2.1 × 100 mm, 1.8 μm). Multiple reaction monitoring (MRM) mode was adopted by using [15N5]-8-OHdG as an internal standard. The assay was linear over the concentration range of 1.0–100 nM with R2 = 0.999. The accuracy for spiked samples was 90.9%–94.8%, and the intra-day precision was within 3.7%. The limit of detection (LOD) is 0.30 nM and limit of quantification (LOQ) is 1.0 nM with 5 μl of sample injection. By the analysis of human leukocyte 8-OHdG (n = 121) using the developed UHPLC–MS/MS method, it demonstrates that the level of leukocyte 8-OHdG of the cancer patients group (n = 46) is significantly higher than that of the health control (n = 75).

Structure-based DNA modification analysis provides accurate and important information on genomic DNA changes from epigenetic modifications to various DNA lesions. However, genomic DNA strands are often required to be efficiently digested into single nucleosides. It is an arduous task because of the involvement of multiple enzymes with different catalytic acitivities. Here we constructed a three-enzyme cascade capillary monolithic bioreactor that consists of immobilized deoxyribonuclease I (DNase I), snake venom phosphodiesterase (SVP), and alkaline phosphatase (ALPase). By the use of this cascade capillary bioreactor, genomic DNA can be efficiently digested into single nucleosides with an increasing rate of ∼20 folds. The improvement is mainly attributed to dramatically increase enzymatic capacity and activity. With a designed macro-porous structure, genomic DNA of 5–30 Kb (∼1.6–10 million Daltons) can be directly passed through the bioreactor simply by hand pushing or a low-pressure microinjection pump. By coupling with liquid chromatography-tandem mass spectrometry (LC-MS/MS), we further developed a sensitive assay for detection of an oxidative stress biomarker 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) in DNA. The proposed three-enzyme cascade bioreactor is also potentially applicable for fast identification and quantitative detection of other lesions and modifications in genomic DNA.

The formation of a highly adapted high-E zone is critical to isotachophoresis separation and focusing. Recently, we discovered that the high-E zone is present only in a small portion of electrophoresis channel in the presence of EOF (Liu, S. Q. et al. J. Am. Chem. Soc. 2013, 135, 4644–4647). Accordingly, a much narrower high-E zone is presumably present in t-ITP. If so, it is hard to achieve efficient t-ITP focusing. Indeed, by online coupling t-ITP with CE-LIF immunoassay, the immunocomplexes of carcinogenic BPDE-dG adducts are not efficiently focused using a freshly prepared background electrolyte. Intriguingly, we observed that 20-day stored background electrolyte displays a 10-fold better focusing efficiency. We hypothesize that the unexpected phenomenon is associated with the dissolution of aerial carbon dioxide, which is mainly converted to ionic HCO3– in the weak alkaline background electrolyte. Consequently, HCO3– of high electrophoretic mobility will be continuously injected into the capillary along with the background electrolyte and act as an alternative leading ion to improve the focusing. By addition of dry ice (without causing significant pH decrease, ΔpH < 0.4) to freshly prepared background electrolytes, we immediately observed the enhanced focusing of immunocomplexes of the DNA adducts. NH4HCO3 and Na2CO3, included in the background electrolyte, also improve the focusing efficiency and reproducibility. All these consistently support our hypothesis. To understand the underlying mechanism, an advanced CE-SMFI was exploited to monitor in real time the motion of single DNA molecules and the E change throughout t-ITP. We uncovered that t-ITP can induce a local high-E zone, but the presence of HCO3– in the background electrolyte could greatly increase the E value in the high-E zone, which allows more DNA molecules to rapidly move backward and to be efficiently stacked at LE/TE boundary. This study provides new insight into nonuniform electric field-induced electrophoresis focusing.

The sixth DNA base 5-hydroxymethylcytosine (5hmC) is the major oxidation product of the epigenetic modification 5-methylcytosine (5mC), mediating DNA demethylation in mammals. Reduced 5hmC levels are found to be linked with various tumors and neurological diseases; therefore, 5hmC is an emerging biomarker for disease diagnosis, treatment, and prognosis. Due to its advantages of being sterile, easily accessible in large volumes, and noninvasive to patients, urine is a favored diagnostic biofluid for 5hmC analysis. Here we developed an accurate, sensitive, and specific assay for quantification of 5mC, 5hmC, and other DNA demethylation intermediates in human urine. The urinary samples were desalted and enriched using off-line solid-phase extraction, followed by stable isotope dilution HPLC-MS/MS analysis for 5hmC and 5mC. By the use of ammonium bicarbonate (NH4HCO3) as an additive to the mobile phase, we improved the online-coupled MS/MS detection of 5mC, 5hmC, and 5-formylcytosine (5fC) by 1.8–14.3 times. The recovery of the method is approximately 100% for 5hmC, and 70–90% for 5mC. The relative standard deviation (RSD) of the interday precision is about 2.9–10.6%, and that of the intraday precision is about 1.4–7.7%. By the analysis of 13 volunteers using the developed method, we for the first time demonstrate the presence of 5hmC in human urine. Unexpectedly, we observed that the level of 5hmC (22.6 ± 13.7 nmol/L) is comparable to that of its precursor 5mC (52.4 ± 50.2 nmol/L) in human urine. Since the abundance of 5hmC (as a rare DNA base) is 1 or 2 orders of magnitude lower than 5mC in genomic DNA, our finding probably implicates a much higher turnover of 5hmC than 5mC in mammalian genomic DNA and underscores the importance of DNA demethylation in daily life.

Fluorescence anisotropy is a homogeneous, sensitive, ratiometric, and real-time analytical technology. However, it is a great challenge to produce a large fluorescence anisotropy change upon the presence of target small molecules without nanoparticles-dependent amplification. This work reports a nanoparticle-free and multiple G-enhanced fluorescence anisotropy assay for detection of DNAzyme activity. A Pb2+-dependent GR-5 DNAzyme was used as a model. We hybridized the rA-cleavable substrate strand containing a TMR label at the 5′-end with the DNAzyme strand containing an extended three G bases at the 3′-end. By this design, we demonstrate that both fluorescence quenching and the enhanced DNAzyme activity contribute to a Pb2+-induced large fluorescence anisotropy change (|Δr| = 0.168). The limit of detection for Pb2+ is estimated to be about 100 pM with a dynamic range from 200 pM to 100 nM. The interference from the other nine divalent metal ions of 1000-times excess amount is negligible. Moreover, we show an extended assay for evaluation of the interactions of Pb2+ with cysteine and glutathione by the detection of GR5 DNAzyme activity. Collectively, we developed a novel fluorescence anisotropy amplification assay, enabling us to detect DNAzyme activity and associated cofactors and inhibitors and to characterize the Pb2+-chelation capability of free thiols.

Human beings do not produce ascorbic acid (AA) and acquire AA through the sodium vitamin C transporters (SVCTs). Changes in the expression or function of SVCT proteins may be associated with human diseases. In this regard, imaging of SVCTs in living cells is important. However, the options for live-cell labelling of SVCTs were very limited. In this work, we synthesized a new small-molecule fluorescent probe RB–A–Vc, and demonstrated its application in selectively visualizing SVCTs in living cells. This probe features visible excitation and emission profiles, can easily enter into membranes, has high selectivity for SVCTs, and can monitor up-regulation or down-regulation of SVCT expression in living cells. We emphasize that this small-molecule probe is suitable for subcellular localization of SVCTs in living cells. This study provides a useful tool for simultaneously monitoring the level and distribution of intracellular SVCTs, which is probably more useful for evaluating the changes induced by external stimulations. We propose that this probe for SVCT imaging and the corresponding method could be applied to other cell lines, tissues, and species.

The methyl-CpG binding domain (MBD) family proteins can specifically bind methylated DNA sequences and thereby mediate gene transcription. In this study, we used neutral capillary electrophoresis coupled with laser-induced fluorescence to investigate the interactions of DNA and MBD2b, a model MBD family protein with the highest affinity. For this purpose, we synthesized 13 double-stranded oligonucleotides of varying length (20 bp to 80 bp) and of varying methylation density. The sequences of these oligonucleotides were adapted from a frequently methylated promoter region of human p16 INK4a gene. We demonstrate that multiple MBD2b proteins can bind to one DNA molecule with a DNA length-dependent binding stoichiometry. Each MBD2b protein can occupy 20 nucleotides in a bound DNA molecule regardless of the methylation status of DNA. By binding multiple MBD2b proteins (up to four protein molecules) to one dsDNA molecule (80 bp), methylated and unmethylated DNA were bound at similar percentages. Although the total amount of the DNA–MBD2b complexes increases with increasing DNA length for both unmethylated and methylated DNA, the DNA–MBD2b complexes of 1:1 display more than 10-fold higher affinity for methylated DNA (e.g., 40 bp DNA) accompanying a 20-fold lower dissociation rate constant. Hence, our study clarifies for the first time that the specificity of MBD2b to methylated DNA decreases as more MBD2b monomers binding to the same region of DNA. Additionally, this study opens a new venue to improve MBD protein-based assays for detecting DNA methylation.

•A fluorescence anisotropy approach for detection of Pb2+ was developed.•The strategy was based on binding-induced allosteric conformational change of aptamer probe.•The sensing mechanism was established by testing the photoinduced electron transfer interaction.Sensitive and selective detection of Pb2+ is of great importance to both human health and environmental protection. Here we propose a novel fluorescence anisotropy (FA) approach for sensing Pb2+ in homogeneous solution by a G-rich thrombin binding aptamer (TBA). The TBA labeled with 6-carboxytetramethylrhodamine (TMR) at the seventh thymine nucleotide was used as a fluorescent probe for signaling Pb2+. It was found that the aptamer probe had a high FA in the absence of Pb2+. This is because the rotation of TMR is restricted by intramolecular interaction with the adjacent guanine bases, which results in photoinduced electron transfer (PET). When the aptamer probe binds to Pb2+ to form G-quadruplex, the intramolecular interaction should be eliminated, resulting in faster rotation of the fluorophore TMR in solution. Therefore, FA of aptamer probe is expected to decrease significantly upon binding to Pb2+. Indeed, we observed a decrease in FA of aptamer probe upon Pb2+ binding. Circular dichroism, fluorescence spectra, and fluorescence lifetime measurement were used to verify the reliability and reasonability of the sensing mechanism. By monitoring the FA change of the aptamer probe, we were able to real-time detect binding between the TBA probe and Pb2+. Moreover, the aptamer probe was exploited as a recognition element for quantification of Pb2+ in homogeneous solution. The change in FA showed a linear response to Pb2+ from 10 nM to 2.0 μM, with 1.0 nM limit of detection. In addition, this sensing system exhibited good selectivity for Pb2+ over other metal ions. The method is simple, quick and inherits the advantages of aptamer and FA.

Methyl-CpG-binding domain (MBD) proteins can specifically recognize and bind methylated CpG sites of DNA, thus repress gene transcription. In this study, we designed and expressed two recombinant proteins, MBD2b and SNAP-MBD2b, in E. coli. An optimized protocol was developed to purify the proteins using Ni-NTA affinity cartridge and cation exchange resin. The engineered proteins purified by this method exhibited more than 93% purity and high binding avidity. We found that both SNAP-MBD2b and MBD2b were prone to aggregate during dialysis. However, this could be prevented by the use of 0.3 mol/L NaCl. The fusion of SNAP-tag with MBD2b significantly enhanced the expression of MBD2b protein in E. coli and reduced the adsorption of MBD2b on solid interfaces involved in protein purification and immobilization. The engineered proteins can be used for the study of interaction with methylated DNA and the assays for DNA methylation.

The nonuniform motion of charged species in a varying electric field may provide unique separation and focusing power for chemical, biochemical, and nanoscale studies. We imaged in real time the nonuniform motion of single DNA molecules under varying-field isotachophoresis (ITP) conditions. From the trajectories of single molecules, we obtained the time- and position-dependent electric field strength (E) and revealed the behavior of adaption barriers within electro-osmotic flow (EOF)-driven and EOF-independent ITP. We found that the initial terminating electrolyte zone of constant E is split into two zones: a highly adapted high-E zone and a low-E zone of gradually adapting electric field. The formation of the two unique zones is associated with the rate-limiting mass transfer barrier in EOF-driven ITP. As a result of the unique E distribution, DNA molecules first slow to a stop and then rapidly move backward to the leading electrolyte/terminating electrolyte boundary. This provides a novel mechanism for selective focusing of target molecules in dilute solutions of large volume. We show that the ITP focusing can improve the detection of single DNA molecules (limit of detection = 4 × 10–17 mol/L), which are stochastically distributed at extremely low concentrations. The ITP strategy focuses individual molecules into a small volume that is matched with the focal point of single-molecule imaging.

DNA hydroxymethylation and its mediated DNA demethylation are critical for multiple cellular processes, for example, nuclear reprogramming, embryonic development, and many diseases. Here, we demonstrate that a vital nutrient ascorbic acid (AA), or vitamin C (Vc), can directly enhance the catalytic activity of Tet dioxygenases for the oxidation of 5-methylcytosine (5mC). As evidenced by changes in intrinsic fluorescence and catalytic activity of Tet2 protein caused by AA and its oxidation-resistant derivatives, we further show that AA can uniquely interact with the C-terminal catalytic domain of Tet enzymes, which probably promotes their folding and/or recycling of the cofactor Fe2+. Other strong reducing chemicals do not have a similar effect. These results suggest that AA also acts as a cofactor of Tet enzymes. In mouse embryonic stem cells, AA significantly increases the levels of all 5mC oxidation products, particularly 5-formylcytosine and 5-carboxylcytosine (by more than an order of magnitude), leading to a global loss of 5mC (∼40%). In cells deleted of the Tet1 and Tet2 genes, AA alters neither 5mC oxidation nor the overall level of 5mC. The AA effects are however restored when Tet2 is re-expressed in the Tet-deficient cells. The enhancing effects of AA on 5mC oxidation and DNA demethylation are also observed in a mouse model deficient in AA synthesis. Our data establish a direct link among AA, Tet, and DNA methylation, thus revealing a role of AA in the regulation of DNA modifications.

Acrolein (Acr), a ubiquitous environmental pollutant, can react directly with genomic DNA to form mutagenic adducts without undergoing metabolic activation. To sensitively and accurately quantify Acr–DNA adducts (including structural isomers and stereoisomers) in human leukocytes, we developed an enhanced stable isotope dilution ultrahigh performance liquid chromatography (UHPLC)–tandem mass spectrometry (MS/MS) method using ammonium bicarbonate (NH4HCO3), which is thermally unstable and degrades readily to carbon dioxide and ammonia in heated gas phase. Interestingly, ammonium bicarbonate (as an additive to the mobile phase) not only improves the protonation of AcrdG adducts but also suppresses the formation of MS signal-deteriorating metal–AcrdG complexes during electrospray ionization, leading to the enhancement of their MS detection by 2.3–8.7 times. In contrast, routinely used ammonium salts (ammonium acetate and ammonium formate) and formic acid do not show similar enhancement. The developed method is potentially useful for enhancing ESI-MS detection of other modified 2′-deoxyribonucleosides that have difficulty in protonation and may form excess metal complexes during electrospray ionization. The limits of detection (LODs, S/N = 3) are estimated to be about 40–80 amol. By the use of the developed method, we found that the Acr adducts of three nucleotides (dG, dA, and dC) can be detected in human leukocytes. In addition to the known γ-AcrdG, α-AcrdA is also identified as an Acr-adduct of high abundance (2.5–20 adducts per108 nts).

Polyvinyl pyrrolidone polymer (PVP) has been widely applied in biological and medical fields. A few in vitro studies indicated that PVP might cause toxicity. However, the underlying mechanism is poorly understood. In this work, we found that PVP directly induced strand breakages of various DNA molecules, implicating a cleavage activity. Moreover, reactive oxygen species (ROS) scavenging analysis shows that DNA cleavage activity of PVP is not related to ROS-induced oxidation. As revealed by gel electrophoresis and liquid chromatography/mass spectrometry analysis, the major cleavage products of DNA were identified as two purine bases, guanine and adenine, suggesting that PVPs have a novel depurination activity. The selective depurination and DNA cleavage activity of PVPs were further confirmed by studying the interaction of PVP with four nucleosides and four well-designed oligodeoxynucleotides probes containing specific nucleotides. This study may provide insights into PVP-DNA interactions and resultant genotoxicity and may also open a new way for DNA study.

Exogenous and endogenous genotoxic carcinogens and their in vivo metabolites may result in DNA damage and cause adverse health effects. It is very difficult to specifically detect trace DNA damage in the presence of a large excess of unmodified nucleosides. Here we report a molecularly imprinted polymer (MIP) nanocomposite, namely nanoMIP, which can be used as a “plastic antibody” for specific recognition of benzo[a]pyrene diol epoxide (BPDE)–DNA adduct. Enhanced binding affinity (880 nM) of nanoMIPs was achieved by using two tailor-made functional monomers. The property of binding kinetics was greatly improved in virtue of the well-defined nanostructure, which was fabricated by initiators for continuous activator regeneration-atom transfer radical polymerization (ICAR-ATRP). The BPDE-adducted DNA can be specifically captured by synthetic nanoMIP. By taking advantage of this antibody-mimicking behavior, we further developed a fluorescently imaged particle counting immunoassay (FIPCIA) method for ultrasensitive detection of BPDE–ssDNA adducts using a laser scanning confocal microscope (LSCM). The number of countable fluorescent dots is proportional to the content of BPDE–ssDNA adducts in the DNA sample. The proposed plastic antibody-based FIPCIA method can detect traces of BPDE–DNA adducts as low as 18 pM in human lung carcinoma A549 cells. This highly-sensitive detection of DNA lesions offers a promising alternative to immunogenic antibody-based immunoassays for genomics and DNA modification analysis.

A capillary monolithic bioreactor of snake venom phosphodiesterase (SVP) was constructed to generate different single-nucleotide mass ladders of oligodeoxynucleotides for mass spectrometry (MS)-based sequencing by immobilization. The immobilization of SVP in the porous silica monolith significantly enhances its stability for prolonged and repeated applications. The constructed capillary bioreactor has the advantages of handling (sub)microliter DNA samples and having good permeability. Benefiting from its good permeability, DNA solutions can be directly injected into the sequential digestion bioreactor simply by hand pushing or a low-pressure microinjection pump. Moreover, the immobilization of SVP facilitates the elimination or repression of the metal adducts of oligodeoxynucleotides, improving the analytical performance of MS sequencing. By the application of capillary bioreactor of immobilized SVP, the sequence-specific modification of single-stranded oligodeoxynucleotide induced by a ubiquitous pollutant acrolein (Acr) was identified, demonstrating its promising applications in identification of sequence-specific damage, which may further our understanding of DNA damage caused mutagenesis.

Fluorescence anisotropy (FA) is a homogeneous, ratiometric, and real-time analytical technology. By selective labeling of a guanine (G)-quadruplex motif with tetramethylrhodamine (TMR), here, it is established that a large reduction in FA response can be specifically associated with the unfolding → folding transition of G-quadruplex structures. On the basis of fluorescence intensity, polarization and lifetime analysis, and molecular docking simulation, the mechanism was found to be that the labeled fluorophore (TMR) can intramolecularly interact with adjacent G bases in an unfolded G-quadruplex motif, which allows for the photoinduced electron transfer (PET) occurring between the fluorophore and G bases, leading to a short fluorescence lifetime. Upon the folding of the motif to form a stable G-quadruplex structure, the intramolecular interactions and the concomitant PET could be eliminated with an increased fluorescence lifetime, leading to a large reduction in the FA response. On the basis of this mechanism, a novel, specific, and sensitive FA approach was developed for the detection of biologically and functionally important G-quadruplex structures. The approach is examined and validated using one normal G-quadruplex motif, five mutants, and six small cations and is potentially applicable to the study of G-quadruplexes at single molecule level, ligand screening, profiling of highly ordered DNA nanostructures, and biosensing.

Real time protein signaling in a complex medium may provide a promising way for high-throughput protein analysis, but it is largely unmet due to the challenge of signal transduction and the interferences of nonspecific binding and high background. Our recent work indicates that a fluorescent aptamer can display a protein binding-induced reduction of fluorescence anisotropy (FA) (Zhang, D.; Lu, M.; Wang, H. J. Am. Chem. Soc.2011, 133, 9188–9191), which is exclusively different from a traditionally simplified concept hinting a molecular size increase-induced FA increase. Inspired by this unexpected observation, we describe a novel FA reduction approach for protein signaling. The feasibility of this approach is demonstrated through the assays of a blood protein human α-thrombin and an oncoprotein human platelet-derived growth factor B-chain (PDGF-BB) using two screened fluorescent aptamers, respectively. By the developed FA reduction method, the spiked human α-thrombin in diluted serum can be detected at the concentration as low as 250 pM. In contrast, in a traditional molecular size-dependent FA assay, the thrombin spiked in diluted serum cannot induce reliable FA change even at a 256-fold higher concentration (64 nM). The results clearly show that the FA reduction approach has a dramatically enhanced specificity against target protein and high sensitivity in complex medium and is applicable to the no-separation based detection of proteins in biological matrixes.

The toxicity of NPs is not well characterized in terms of their size. In particular, the size-based toxicity of fullerene (C60) remains an issue because of a lack of C60 NPs with a well-controlled size. In this work, six fractions of the nano-C60 aggregates (nC60) with different size distribution were prepared by a simple differential centrifugation. By using these nC60 fractions, we demonstrate the size-dependent inhibition of DNA polymerase and reduced-size enhanced cytotoxicity. Above all, we found that nC60 NPs with smaller size may have higher toxicity potency. These size-dependent effects were observed at the high exposure doses (4–6 mg/L). Interestingly, at 20-times lower and noncytotoxic doses, the size-dependent effect can be indicated by apoptosis-related fluorescent protein fused Bax translocation. Considering the toxicity of NPs is often ignored in the traditional end-point analysis for cytotoxicity when the exposure dose is low, the findings presented here will assist in the evaluation of the size-dependent cytotoxicity and dose–response relationships of toxicity mediated by nC60 NPs at low doses.

A DNA aptamer based high-performance affinity chromatography is developed for selective extraction and screening of a basic protein lysozyme. First, a poly(glycidyl methacrylate-co-ethylene dimethacrylate) monolithic column was synthesized in situ by thermally initiated radical polymerization, and then an anti-lysozyme DNA aptamer was covalently immobilized on the surface of the monolith through a 16-atom spacer arm. The target protein lysozyme but non-target proteins can be trapped by the immobilized anti-lysozyme DNA aptamer. In contrast, lysozyme cannot be trapped by the immobilized oligodeoxynucleotide that does not contain the sequence of the anti-lysozyme DNA aptamer. The study clearly demonstrates the trapping of lysozyme by the immobilized anti-lysozyme DNA aptamer is mainly due to specific recognition rather than simple electrostatic interaction of positively charged protein and the negatively charged DNA. The inter-day precision was determined as 0.8% for migration time and 4.2% for peak area, respectively. By the use of aptamer affinity monolith, a screening strategy is developed to selectively extract lysozyme from chicken egg white, showing the advantages of high efficiency, low cost and ease-of-operation.Highlights► Anti-lysozyme DNA aptamer affinity chromatography column was prepared for HPLC. ► DNA aptamers were covalently immobilized on the surface of monolithic column. ► Lysozyme was extracted in a single step by the aptamer monolithic column.

A number of known and potential chemicals may cause substantial damage to genomic DNA, further inducing mutagenesis and carcinogenesis. To screen potentially genotoxic compounds from a multitude of chemicals, fast and senstive bioanalytical technologies are desirable. By taking advantage of the DNA damage-dependent SOS response (a regulatory signal initiated by damage to DNA or the physiological consequences of such damage in prokaryotes) in reactive oxygen species (ROS)-sensitive bacterium and the enhanced green fluorescent protein reporter, we constructed a composite bacterial biosensor for detection of DNA damage agents. The sensitivity of the bacterium to ROS induced DNA damage is 10−20-times enhanced by the knockout of one alkyl hydroperoxide reductase gene and two catalase genes. This biosensor can be used for fast and sensitive detection of DNA damaging agents among which some cannot be detected by previous bacterial biosensors, demonstrating the potential and promising applications for evaluation of DNA damage and for screening of DNA damaging agents in large scale.

Bisphenols (BPs) are potential endocrine-disrupting chemicals that may adversely affect human health and wildlife. The complexity of matrix encountered in real-world samples renders screening of trace BPs a formidable challenge. The present study highlighted the potential of molecularly imprinted solid-phase extraction (MISPE) for selective detection of trace bisphenols and their halogenated analogues in surface water. The template bleeding was observed at parts-per-billion levels, deteriorating the accuracy and precision of BPs quantification. To surmount this problem, a dummy MISPE strategy was proposed, in which bisphenol E (BPE) was selected as a dummy template for molecularly imprinted polymer (MIP) synthesis. Coupling this MISPE strategy with chromatographic analysis, a dummy MISPE-HPLC method was established. The linearity, precision, limit of detection (LOD) and recovery were then validated. The linearity of the calibration curve for each BP was observed over the range of 20–2000 ng L−1 (r > 0.998). LOD for each bisphenol was measured as low as 2.5–5.0 ng L−1. This technique was applied to simultaneous screening of BPs in the Qinghe River, and five bisphenols were found within the concentration range of 0–224 ng L−1 in river samples. The designed dummy MIP was superior to the commercial sorbents with regard to the selectivity, cross-reactivity, matrix removal efficiency and reusability. These merits enabled the applications of dummy MISPE for selective extraction and sensitive screening of BPs in environmental water samples. This method also provided a promising tool for monitoring the occurrence, distribution and fate of BPs in surface water.

Aberrant DNA methylation in human sperms has been proposed to be a possible mechanism associated with male infertility. We developed an ultra-performance liquid chromatography/tandem mass spectrometry (UPLC–MS/MS) method for rapid, sensitive, and specific detection of global DNA methylation level in human sperms. Multiple-reaction monitoring (MRM) mode was used in MS/MS detection for accurate quantification of DNA methylation. The intra-day and inter-day precision values of this method were within 1.50–5.70%. By using 2-deoxyguanosine as an internal standard, UPLC–MS/MS method was applied for the detection of global DNA methylation levels in three cultured cell lines. DNA methyltransferases inhibitor 5-aza-2′-deoxycytidine can significantly reduce global DNA methylation levels in treated cell lines, showing the reliability of our method. We further examined global DNA methylation levels in human sperms, and found that global methylation values varied from 3.79% to 4.65%. The average global DNA methylation level of sperm samples washed only by PBS (4.03%) was relatively lower than that of sperm samples in which abnormal and dead sperm cells were removed by density gradient centrifugation (4.25%), indicating the possible aberrant DNA methylation level in abnormal sperm cells. Clinical application of UPLC–MS/MS method in global DNA methylation detection of human sperms will be useful in human sperm quality evaluation and the study of epigenetic mechanisms responsible for male infertility.

Pristine fullerene nanoparticles are capable of adsorbing polymerase and significantly inhibiting its biologically important replication activity; however, the inhibition can be partially mitigated by abundant proteins through competitive binding.

Nucleic acid electrophoresis separation heavily depends upon gel or nongel sieving matrix. Here we propose a metal ion mediated-capillary electrophoresis (MCE-CE) by utilizing the nonspecific interactions of Mg2+ and Ca2+ and demonstrate the size, conformation, or sequence based separation and characterization of versatile nucleic acid molecules in free solution. Mg2+ and Ca2+ can induce DNA separation at the concentrations as low as 100 and 50 μM, respectively. Noteworthy, the two naturally occurring polymorphisms of one base substitution that may change the secondary folding structure or base stacking can be discriminated by MCM-CE, showing its unique capability of resolving length-identical but conformation-different ssDNA. Benefiting from the achieved separation, we further demonstrate that the folding conformation of oligomers and its change caused by single base substitution can be promptly sensed by online coupled fluorescence polarization. We anticipate that this method will be applicable in length polymorphism analysis, single-strand polymorphism analysis, hybridization analysis, microRNA analysis, and study of protein−nucleic acid interactions and the conformation−function relationship.

Modifications of genomic DNA may change gene expression and cause adverse health effects. Here we for the first time demonstrate a particle counting immunoassay for rapid and sensitive detection of DNA modifications using benzo[a]pyrenediol epoxide (BPDE)−DNA adducts as an example. The BPDE-adducted DNA is specifically captured by immunomagnetic particles and then isolated from unmodified DNA by applying an external magnetic field. By taking advantage of the fluorescence signal amplification through multiple labeling of captured DNA by OliGreen dye, the captured BPDE−DNA adducts can be quantified by particle counting from fluorescence imaging. This clearly demonstrates that the number of fluorescently countable particles is proportional to the modification content in genomic DNA. It is interesting to note that the background fluorescence signal caused by nonspecific adsorption of OliGreen dye can be more effectively quenched than that induced by the binding of OliGreen dye to ssDNA, allowing for significant reduction in the background fluorescence and further enhancing the detection sensitivity. The developed method can detect trace BPDE−DNA adducts as low as 180 fM in the presence of 1 billion times more normal nucleotides in genomic DNA and has a dynamic range over 4 orders of magnitude. By using anti-5-methylcytosine antibody, the method is extended to the detection of global DNA methylation. With high sensitivity and specificity, this rapid and easy-to-perform analytical method for DNA modifications shows a broad spectrum of potential applications in genotoxical and epigenetic analysis.

To assess the potential risks associated with the environmental exposure of β-lactam antibiotics (BLAs), the monitoring of the occurrence, distribution, and fate of these emerging contaminants in the environment is required. Herein, we demonstrate a molecularly imprinted solid-phase extraction (MISPE) method for selective and reliable screening of trace BLAs in river and tap water. By developing a low-temperature photopolymerization, highly selective molecularly imprinted polymers (MIPs) for five BLAs (penicillin G, amoxicillin, ampicillin, nafcillin and mezlocillin) were synthesized. Nafcillin was chosen as a pseudo template to make the MIP sorbent (Nafc-MIP), which was used in pseudo-template MISPE for preconcentration of the other four BLAs from river and tap water. The application of pseudo-template MISPE overcomes the template bleeding, which significantly elevates the sample background and restricts the application of MIP for detection of the target BLA below 2 μg/L. The average recoveries of BLAs are in the range of 60–90% when Nafc-MIP was adopted as the selective MISPE sorbent. The developed method was validated, and applied to the screening of trace β-lactam antibiotics in river and tap water. The linearity of the calibration curve for each BLA was observed over the range of 0.1–20 μg/L (r > 0.998). The β-lactam antibiotics were found within the range of 0–9.56 μg/L in river water at the downstream of antibiotics manufacturers, and none were detected in the tap water.

The stereospecific binding of monoclonal antibody (mAb) 8E11 to anti-benzo(a)pyrene diol epoxide (BPDE)-dG adducts in single nucleoside, long oligonucleotide, and genomic DNA were quantitatively evaluated using noncompetitive and competitive capillary electrophoresis (CE) immunoassays. Two single-stranded TMR-BPDE-90mers containing a single anti-BPDE-dG adduct with defined stereochemistry and a fluorescent label at 5′-end were used as fluorescent probes for competitive CE immunoassay. To quantitatively evaluate the binding affinity through competitive CE immunoassays, a series of equations were derived according to the binding stoichiometry. The binding of mAb 8E11 to trans-(+)-anti-BPDE-dG displays strongest affinity (Kb: 3.57 × 108 M−1) among all four investigated anti-BPDE-dG mononucleoside adducts, and the cis-(−)-anti-BPDE-dG displays lowest affinity (Kb: 1.14 ×107 M−1). The binding of monoclonal antibody (mAb) 8E11 to BPDE-dG adducts in long DNA (90mer) preferentially forms the complex with a stoichiometry of 1:1, and that mAb 8E11 displays a slightly higher affinity with trans-(+)-anti-BPDE-90mers (Kb: 6.36 ± 0.54 × 108 M−1) than trans-(−)-anti-BPDE-90mers (Kb: 4.52 ± 0.52 × 108 M−1). The mAb 8E11 also displays high affinity with BPDE-dG adducts in genomic DNA (Kb: 3.74 × 108 M−1), indicating its promising applications for sensitive immuno-detection of BPDE-DNA adducts in genomic DNA.

An organic osmolyte mediated kinetic capillary electrophoresis is developed and applied to study the binding of Escherichia coli RecA protein to single-stranded (ss) DNA. The complex of RecA and ssDNA can be significantly enhanced and stabilized by 20% glycerol over 5.6 times. Kinetic capillary electrophoresis study reveals that glycerol may function in the preservation of RecA native conformation, enhancement of specific binding affinity (20 times), and decrease in dissociation rate constant (1 time). The combined laser-induced fluorescence polarization (LIFP) study further indicates a tightened assembly of RecA on ssDNA induced by glycerol. The binding of RecA to ssDNA was also enhanced by two additional protecting organic osmolytes, sucrose and PEG 400. In contrast, a denaturing organic osmolyte, urea, even at a concentration of 110 mM can prevent the formation of the RecA−ssDNA complexes. The detection of the binding of E. coli single-stranded binding protein (SSBP) to ssDNA was also improved by the same method. By combining the protection of organic osmolytes with low-temperature storage, a method for preservation of protein−DNA complex up to 43 h is further demonstrated. By use of a long capillary and protecting glycerol together an enhanced kinetic CE analysis was also developed, providing a better separation and analysis of the undissociated complex, the dissociated complex, and the unbound probe. The results demonstrate the wide applicability of the method to the study of various protein−DNA binding.

Genomic DNA hypomethylation is epigenetically associated with aberrant gene expression and chromosome instability. Here we describe a method for rapid and sensitive detection of genomic DNA methylation without the need for bisulfite conversion, enzymatic digestion, or PCR amplification. The methylated DNA is first specifically recognized by an anti-5-methylcytosine IgG1 antibody and noncovalently labeled by a monovalent, fluorescently labeled, Fc-specific anti-IgG1 Fab fragment (secondary antibody). The formed immuno-complex of methylated DNA can be efficiently focused and separated from the DNA unbound secondary antibody by capillary electrophoresis (CE). The free fluorescent dye comigrates with the immuno-complex. However, by taking advantage of online laser-induced fluorescence polarization detection (LIFP), the target immuno-complex can be distinguished and accurately measured from the overlapped dye without further separation. The developed method is highly sensitive with a LOD of 0.3 nM and is highly specific for the detection of methylated DNA. Moreover, the CE−LIFP immunoassay is rapid (1.2 min for one analysis) and only consumes less than 0.1 ng of genomic DNA. The method was validated by examining human cell lines treated by methyltransferase inhibitor 5-aza-2′-deoxycytidine at low doses (10 nM−10 μM). Because of its sensitivity and speed, our method will be applicable for rapid epigenetic evaluation and for the study of tumorigenesis and chemical−cell interactions.

Here we demonstrate that quantum dots (QD) can greatly improve the ultrasensitive capillary electrophoresis-laser induced fluorescence immunoassay of trace anti-benzo(a)pyrene diol epoxide (BPDE)−DNA adducts from sensitivity to separation. We for the first time show that the target QD−antibody−DNA complex is not only effectively separated but also effectively focused by capillary electrophoresis. With the online laser-induced fluorescence detection coupled, the low limits of detection of 6.6 × 10−21 mol in mass and 120 fM in concentration are achieved for BPDE−DNA adducts. The achieved ultrasensitivity allows for human exposure biomonitoring and shows promising applications of QD in various DNA analyses, including DNA damage.

The detection and quantification of disease-related proteins play critical roles in clinical practice and diagnostic assays. We present an affinity probe capillary electrophoresis/laser-induced fluorescence polarization (APCE/LIFP) assay for detection of human thrombin using a specific aptamer as probe. In the APCE/LIFP assay, the mobility and fluorescence polarization of complex are measured simultaneously during CE analysis. The affinity complex of human thrombin can be well separated from unbound aptamer on CE and clearly identified on the basis of its fluorescence polarization and migration. Because of the binding favorable G-quartet conformation potentially involved in the specific aptamer, it was assumed that monovalent and bivalent cations promoting the formation of a stable G quadruplex conformation in the aptamer may enhance the binding of the aptamer and thrombin. Therefore, we investigated the effects of various metal cations on the binding of human thrombin and the aptamer. Our results show that cations like K+ and Mg2+ could not stabilize the affinity complex. Without the use of typical cations, a highly sensitive assay of human thrombin was developed with the corresponding detection limits of 4.38 × 10−19 and 2.94 × 10−19 mol in mass for standard solution and human serum, respectively.

We present a comprehensive study of synthesis and characterization of DNA probes containing covalently bound benzo[a]pyrene diol epoxide (BPDE) isomers at a defined site. Short oligonucleotides of 16mers containing a single trans-(+)- or trans-(−)-anti-BPDE-N2-guanine adducts (BPDE-16mer) were first synthesized and then ligated with a fluorescently labeled single-stranded oligonucleotide. The ligation products (double-stranded or single-stranded 90mers) contained a single BPDE adduct of defined stereochemistry and a fluorescent label. The BPDE adduct could be recognized by a specific antibody, and the fluorescent label was useful for highly sensitive laser-induced fluorescence detection. The incorporation of single BPDE in the 16mers was validated by liquid chromatography, UV spectroscopy, and tandem mass spectrometry analysis. The stereochemistry of the single BPDE adducts in the 16mers was further identified by enzyme digestion-coupled stereoselective chromatography analysis. The ligation of BPDE-16mer with normal oligonucleotides for the synthesis of tetramethylrhodamine (TMR)-BPDE-90mers was evaluated. It was found that the modification of the 16mer by anti-BPDE could significantly reduce the ligation yield of ds90mer and lead to the formation of gapped DNA. The incorporation of a single anti-BPDE adduct in ligated ds90mers was confirmed using an antibody specific to the anti-BPDE-dG and affinity capillary electrophoresis. The detection limits of the TMR-BPDE-90mers by capillary electrophoresis coupled with laser-induced fluorescence are below 4 × 10−19 mol.

An ultra-performance liquid chromatography tandem mass spectrometry with multiple reaction monitoring method (UPLC-MRM/MS) is developed for fast and sensitive analysis of four genotoxic stereoisomers of anti-benzo[a]pyrene diol epoxide (BPDE)–N2dG adducts (trans-(+), trans-(−), cis-(+) and cis-(−)), which result from environmental exposure to ubiquitous pollutant benzo[a]pyrene (B[a]P). The developed method displays a low limit of detection of <0.7 fmol (S/N = 3) for the four stereoisomers of anti-BPDE–N2dG, a dynamic range of 2 orders of magnitude (2.3–630 fmol, R2 ≥ 0.997), and one separation of 2–4 min. The developed method enables us to use the stereoisomers of anti-BPDE–N2dG as a biomarker and to study the stereoselectivity of metabolic activation of B[a]P in human lung A549 cells. The UPLC-MRM/MS analysis of cellular DNA exposed to B[a]P show that activation of B[a]P in A549 cells predominantly induces trans-(+)-anti-BPDE–N2dG with cis-(+)-anti-BPDE–N2dG and one syn-BPDE–N2dG as two minorities, while trans-(−)-anti-BPDE–N2dG and cis-(−)-anti-BPDE–N2dG are absent. The observed preferential formation of trans-(+)-anti-BPDE–N2dG in B[a]P treated A549 cells may result from combined stereoselectivity of the metabolic activation of B[a]P and the reaction of anti-BPDE with dsDNA. The results also suggest that a number of key optical intermediates are formed during activation of B[a]P in A549 cells, including trans-(+)-B[a]P-7,8-dihydrodiol and trans-(−)-B[a]P-7,8-dihydrodiol and their corresponding downstream metabolites (+)-anti-BPDE and (+)-syn-BPDE.

Pentachlorophenol (PCP) is a widespread, persistent environmental contaminant, and it is enzymatically activated to form a reactive metabolite, tetrachloro-1,4-benzoquinone (TCBQ). To our knowledge, there is no information about TCBQ toxicity on embryonic stem cells. Here, we demonstrated that TCBQ induced significantly apoptosis of mouse embryonic stem cells in a concentration-dependent manner. We also showed that TCBQ elevated genomic 5-hydroxymethylcytosine (5hmC) by affecting ten-eleven translocation (Tet) dioxygenases in mouse embryonic stem cells. We further investigated whether Tet dioxygenases were implicated in TCBQ-induced apoptosis. By depleting all three dioxygenases (Tet1-3), we found that Tet dioxygenases slightly inhibited both early and late apoptosis induced by TCBQ at a low concentration (30 μmol/L). Meanwhile, treated by TCBQ at higher concentrations (40 and 50 μmol/L), the total percentage of apoptotic cells was not affected by Tet dioxygenases. However, Tet dioxygenases tended to arrest mouse ES cells to be at early apoptotic stage and to reduce the cells to enter later apoptotic stage. These results indicate that Tet dioxygenases play a role in shaping TCBQ-induced apoptosis in mouse embryonic stem cells. Our study provides new insights into the toxicology of PCP and its reactive metabolite TCBQ.Download high-res image (123KB)Download full-size image

Structural characterization of aptamer–protein interactions is challenging and limited despite the tremendous applications of aptamers. Here we for the first time report a fluorescence anisotropy (FA) approach for mapping the interaction of an aptamer and its protein target at the single nucleotide level. Nine fluorescently labeled aptamers, each conjugated to a single tetramethylrhodamine at a specified nucleotide in the aptamer, were used to study their interactions with thrombin. Simultaneous monitoring of both fluorescence anisotropy changes and electrophoretic mobility shifts upon binding of the fluorescently modified aptamer to the protein provides unique information on the specific nucleotide site of binding. T25, T20, T7 and the 3′-end were identified as the close contact sites, and T3, C15T, and the 5′-end were identified as the sites distant from the binding. This approach is highly sensitive and does not require cross-linking reactions. Studies of aptamer–protein interactions using this technique are potentially useful for design, evolution, and modification of functional aptamers for a range of bioanalytical, diagnostic, and therapeutic applications.

Human beings do not produce ascorbic acid (AA) and acquire AA through the sodium vitamin C transporters (SVCTs). Changes in the expression or function of SVCT proteins may be associated with human diseases. In this regard, imaging of SVCTs in living cells is important. However, the options for live-cell labelling of SVCTs were very limited. In this work, we synthesized a new small-molecule fluorescent probe RB–A–Vc, and demonstrated its application in selectively visualizing SVCTs in living cells. This probe features visible excitation and emission profiles, can easily enter into membranes, has high selectivity for SVCTs, and can monitor up-regulation or down-regulation of SVCT expression in living cells. We emphasize that this small-molecule probe is suitable for subcellular localization of SVCTs in living cells. This study provides a useful tool for simultaneously monitoring the level and distribution of intracellular SVCTs, which is probably more useful for evaluating the changes induced by external stimulations. We propose that this probe for SVCT imaging and the corresponding method could be applied to other cell lines, tissues, and species.

Pristine fullerene nanoparticles are capable of adsorbing polymerase and significantly inhibiting its biologically important replication activity; however, the inhibition can be partially mitigated by abundant proteins through competitive binding.