RESUMO
Genetic drivers of cancer can be dysregulated through epigenetic modifications of DNA. Although the critical role of DNA 5-methylcytosine (5mC) in the regulation of transcription is recognized, the functions of other non-canonical DNA modifications remain obscure. Here, we report the identification of novel N6-methyladenine (N6-mA) DNA modifications in human tissues and implicate this epigenetic mark in human disease, specifically the highly malignant brain cancer glioblastoma. Glioblastoma markedly upregulated N6-mA levels, which co-localized with heterochromatic histone modifications, predominantly H3K9me3. N6-mA levels were dynamically regulated by the DNA demethylase ALKBH1, depletion of which led to transcriptional silencing of oncogenic pathways through decreasing chromatin accessibility. Targeting the N6-mA regulator ALKBH1 in patient-derived human glioblastoma models inhibited tumor cell proliferation and extended the survival of tumor-bearing mice, supporting this novel DNA modification as a potential therapeutic target for glioblastoma. Collectively, our results uncover a novel epigenetic node in cancer through the DNA modification N6-mA.
Assuntos
Adenina/análogos & derivados , Neoplasias Encefálicas/patologia , Metilação de DNA , Glioblastoma/patologia , Adenina/análise , Adenina/química , Adulto , Idoso , Homólogo AlkB 1 da Histona H2a Dioxigenase/antagonistas & inibidores , Homólogo AlkB 1 da Histona H2a Dioxigenase/genética , Homólogo AlkB 1 da Histona H2a Dioxigenase/metabolismo , Animais , Astrócitos/citologia , Astrócitos/metabolismo , Neoplasias Encefálicas/metabolismo , Neoplasias Encefálicas/mortalidade , Hipóxia Celular , Criança , Epigenômica , Feminino , Glioblastoma/metabolismo , Glioblastoma/mortalidade , Heterocromatina/metabolismo , Histonas/metabolismo , Humanos , Estimativa de Kaplan-Meier , Masculino , Camundongos , Pessoa de Meia-Idade , Células-Tronco Neoplásicas/citologia , Células-Tronco Neoplásicas/metabolismo , Interferência de RNA , RNA Interferente Pequeno/metabolismo , Proteína Supressora de Tumor p53/metabolismoRESUMO
DNA N6-methyladenine (6mA) protects against restriction enzymes in bacteria. However, isolated reports have suggested additional activities and its presence in other organisms, such as unicellular eukaryotes. New data now find that 6mA may have a gene regulatory function in green alga, worm, and fly, suggesting m6A as a potential "epigenetic" mark.
Assuntos
Adenina/análogos & derivados , Metilação de DNA , Epigênese Genética , Adenina/análise , Adenina/metabolismo , Animais , Bactérias/genética , Regulação da Expressão Gênica , Análise de Sequência de DNARESUMO
Surface-enhanced Raman scattering (SERS) is a highly sensitive technique used in diverse biomedical applications including rapid antibiotic susceptibility testing (AST). However, signal fluctuation in SERS, particularly the widespread of signals measured from different batches of SERS substrates, compromises its reliability and introduces potential errors in SERS-AST. In this study, we investigate the use of purine as an internal standard (IS) to recalibrate SERS signals and quantify the concentrations of two important purine derivatives, adenine and hypoxanthine, which are the most important biomarkers used in SERS-AST. Our findings demonstrate that purine IS effectively mitigates SERS signal fluctuations and enables accurate prediction of adenine and hypoxanthine concentrations across a wide range (5 orders of magnitude). Calibrations with purine as an IS outperform those without, exhibiting a 10-fold increase in predictive accuracy. Additionally, the calibration curve obtained from the first batch of SERS substrates remains effective for 64 additional substrates fabricated over a half-year period. Measurements of adenine and hypoxanthine concentrations in bacterial supernatants using SERS with purine IS closely align with the liquid chromatography-mass spectrometry results. The use of purine as an IS offers a simple and robust platform to enhance the speed and accuracy of SERS-AST, while also paving the way for in situ SERS quantification of purine derivatives released by bacteria under various stress conditions.
Assuntos
Adenina , Purinas , Reprodutibilidade dos Testes , Adenina/análise , Bactérias , Análise Espectral Raman/métodos , HipoxantinasRESUMO
Traditional epitranscriptomics relies on capturing a single RNA modification by antibody or chemical treatment, combined with short-read sequencing to identify its transcriptomic location. This approach is labor-intensive and may introduce experimental artifacts. Direct sequencing of native RNA using Oxford Nanopore Technologies (ONT) can allow for directly detecting the RNA base modifications, although these modifications might appear as sequencing errors. The percent Error of Specific Bases (%ESB) was higher for native RNA than unmodified RNA, which enabled the detection of ribonucleotide modification sites. Based on the %ESB differences, we developed a bioinformatic tool, epitranscriptional landscape inferring from glitches of ONT signals (ELIGOS), that is based on various types of synthetic modified RNA and applied to rRNA and mRNA. ELIGOS is able to accurately predict known classes of RNA methylation sites (AUC > 0.93) in rRNAs from Escherichiacoli, yeast, and human cells, using either unmodified in vitro transcription RNA or a background error model, which mimics the systematic error of direct RNA sequencing as the reference. The well-known DRACH/RRACH motif was localized and identified, consistent with previous studies, using differential analysis of ELIGOS to study the impact of RNA m6A methyltransferase by comparing wild type and knockouts in yeast and mouse cells. Lastly, the DRACH motif could also be identified in the mRNA of three human cell lines. The mRNA modification identified by ELIGOS is at the level of individual base resolution. In summary, we have developed a bioinformatic software package to uncover native RNA modifications.
Assuntos
Biologia Computacional/métodos , Sequenciamento de Nucleotídeos em Larga Escala , Processamento Pós-Transcricional do RNA , RNA-Seq , Erro Científico Experimental , Software , Adenina/análogos & derivados , Adenina/análise , Animais , Linhagem Celular , Escherichia coli/genética , Humanos , Meiose , Metiltransferases/deficiência , Metiltransferases/metabolismo , Camundongos , Camundongos Knockout , Motivos de Nucleotídeos , RNA Bacteriano/genética , RNA Fúngico/genética , RNA Mensageiro/genética , RNA Ribossômico/genética , Curva ROC , Saccharomyces cerevisiae/genética , Análise de Sequência de DNA , Moldes Genéticos , Transcrição GênicaRESUMO
Thin-layer chromatography (TLC) is widely used in various branches of chemical science to separate components in complex mixtures because of its simplicity. In most cases, analyte spots are visually detected by fluorescence, and the retention factor (Rf) is determined from the distance traveled by the analyte. Further characterizations are often necessary to identify separated chemicals because molecular information other than Rf is not available. Surface-enhanced Raman scattering (SERS) has been coupled with TLC to complement molecular information. In previously reported TLC-SERS, metal nanoparticle suspension was dropped onto analyte spots to obtain SERS spectra. This approach is simple and efficient for SERS measurements on the TLC plate but has limited sensitivity for several reasons, such as the low solubility of analytes in the dropped solution, difficult control of nanoparticle aggregation, and interference from the stationary phase. We recently showed that freezing enhances SERS sensitivity by a factor of â¼103. Freezing simultaneously concentrates analytes and silver nanoparticles (AgNPs) in a freeze concentrated solution, where aggregation of AgNPs is facilitated, allowing sensitive freeze SERS (FSERS) measurements. Here, we discuss FSERS measurements on TLC plates to demonstrate the superiority of this combination, i.e. TLC-FSERS. Freezing enhances SERS sensitivity by freeze concentration and facilitated aggregation of AgNPs and, in addition, eliminates interference from the stationary phase. Under the optimized condition, TLC-FSERS enables the on-site detection of pesticides at the nM level. The use of the SERS signal from adenine added as the internal standard allows us to quantify pesticides. Applications to a commercial green tea beverage are also demonstrated.
Assuntos
Nanopartículas Metálicas , Praguicidas , Adenina/análise , Cromatografia em Camada Fina/métodos , Congelamento , Nanopartículas Metálicas/química , Praguicidas/análise , Prata/química , Análise Espectral Raman/métodos , CháRESUMO
Riboswitches are natural biosensors that can regulate gene expression by sensing small molecules. Knowledge of the structural dynamics of riboswitches is crucial to elucidate their regulatory mechanism and develop RNA biosensors. In this work, we incorporated the fluorophore, Cy3, and its quencher, TQ3, into a full-length adenine riboswitch RNA and its isolated aptamer domain to monitor the dynamics of the RNAs in vitro and in cell. The adenine riboswitch was sensitive to Mg2+ concentrations and could be used as a biosensor to measure cellular Mg2+ concentrations. Additionally, the TQ3/Cy3-labeled adenine riboswitch yielded a Mg2+ concentration that was similar to that measured using a commercial assay kit. Furthermore, the fluorescence response to the adenine of the TQ3/Cy3-labeled riboswitch RNA was applied to determine the proportions of multiple RNA conformational changes in cells. The strategy developed in this work can be used to probe the dynamics of other RNAs in cells and may facilitate the developments of RNA biosensors, drugs and engineering.
Assuntos
Adenina/análise , Técnicas Biossensoriais , Transferência Ressonante de Energia de Fluorescência , Dobramento de RNA , Riboswitch , Adenina/químicaRESUMO
Porphyrins absorb strongly in the visible region and are also excellent fluorophores that emit in the visible region that make them excellent candidates for fluorescence sensing and in vivo imaging. This work describes the fluorescence determination of adenine using cobalt complex of a simple porphyrin. Tetraphenylporphyrin (TPP) and tetraphenylpophyrinatocobalt(II) (CoTPP) were synthesized and characterised. TPP on metallation with cobalt resulted in the red shift of fluorescence emission in the region 652 nm and 716 nm and showed an enhancement in the emission peaks with the addition of the nucleobase, adenine. CoTPP is found to be an efficient fluorescent sensor for adenine in DMF solvent. The fluorescence enhancement is due to the formation of the ground state complex formation between adenine and CoTPP, which is supported by experimental evidences from UV- visible spectra, time resolved fluorescence life time measurements etc. The detection limit of adenine was found to be 4.2 µM using the CoTPP fluorescent probe. The proposed sensor is found to be highly selective for adenine in presence of other nitrogen bases like guanine, cytosine, uracil, thymine, alanine, histidine etc. in 1:1 concentration.
Assuntos
Adenina/análise , Cobalto/química , Complexos de Coordenação/química , Porfirinas/química , Complexos de Coordenação/síntese química , Estrutura Molecular , Espectrometria de Fluorescência , Espectrofotometria UltravioletaRESUMO
Knowledge of the structure and dynamics of RNA molecules is critical to understanding their many biological functions. Furthermore, synthetic RNAs have applications as therapeutics and molecular sensors. Both research and technological applications of RNA would be dramatically enhanced by methods that enable incorporation of modified or labelled nucleotides into specifically designated positions or regions of RNA. However, the synthesis of tens of milligrams of such RNAs using existing methods has been impossible. Here we develop a hybrid solid-liquid phase transcription method and automated robotic platform for the synthesis of RNAs with position-selective labelling. We demonstrate its use by successfully preparing various isotope- or fluorescently labelled versions of the 71-nucleotide aptamer domain of an adenine riboswitch for nuclear magnetic resonance spectroscopy or single-molecule Förster resonance energy transfer, respectively. Those RNAs include molecules that were selectively isotope-labelled in specific loops, linkers, a helix, several discrete positions, or a single internal position, as well as RNA molecules that were fluorescently labelled in and near kissing loops. These selectively labelled RNAs have the same fold as those transcribed using conventional methods, but they greatly simplify the interpretation of NMR spectra. The single-position isotope- and fluorescently labelled RNA samples reveal multiple conformational states of the adenine riboswitch. Lastly, we describe a robotic platform and the operation that automates this technology. Our selective labelling method may be useful for studying RNA structure and dynamics and for making RNA sensors for a variety of applications including cell-biological studies, substance detection, and disease diagnostics.
Assuntos
Fluorescência , Marcação por Isótopo/métodos , RNA/química , RNA/síntese química , Adenina/análise , Adenina/química , Adenina/metabolismo , Aptâmeros de Nucleotídeos/análise , Aptâmeros de Nucleotídeos/química , Aptâmeros de Nucleotídeos/metabolismo , Automação/métodos , Sequência de Bases , Técnicas Biossensoriais , DNA/genética , DNA/metabolismo , Transferência Ressonante de Energia de Fluorescência , Técnicas In Vitro , Espectroscopia de Ressonância Magnética , Dados de Sequência Molecular , Conformação de Ácido Nucleico , RNA/análise , RNA/genética , Riboswitch/genética , Robótica , Moldes Genéticos , Transcrição GênicaRESUMO
In this study, a novel electrochemical biosensor was constructed for ultrasensitive and locus-specific detection of N6-Methyladenine (m6A) in DNA using double-hindered replication and nucleic acid-coated methylene blue (MB)@Zr-MOF. Based on the combination of m6A-impeded replication and AgI-mediated mismatch replication, this mode could effectively stop the extension of the strand once DNA polymerase encountered m6A site, which specifically distinguish the m6A site from natural A site in DNA. Also, Zr-MOF with high porosity and negative surface potential features was carefully chose to load cationic MB, resulting a stable and robust MB@Zr-MOF electrochemical tag. As a result, the developed biosensor exhibited a wide linear range from 1 fM to 1 nM with detection limit down to 0.89 fM. Profiting from the high sensitivity and selectivity, the biosensing strategy revealed good applicability, which had been demonstrated by quantitating m6A DNA at specific site in biological matrix. Thus, the biosensor provides a promising platform for locus-specific m6A DNA analysis.
Assuntos
Adenina/análogos & derivados , Técnicas Biossensoriais/métodos , DNA/química , Estruturas Metalorgânicas/química , Azul de Metileno/química , Adenina/análise , Adenina/química , Limite de Detecção , Nanotecnologia , Análise de Sequência de DNA , Zircônio/químicaRESUMO
Raman spectroscopy is a powerful method to characterize molecules in various media. Although surface-enhanced Raman scattering (SERS) is often employed to compensate for the intrinsically poor sensitivity of Raman spectroscopy, there remain serious tasks, such as simple preparations of SERS substrates, sensitivity control, and reproducible measurements. Here, we propose freezing as an efficient way to overcome these problems in SERS measurements using DNA bases as model targets. Solutes are expelled from ice crystals and concentrated in the liquid phase upon freezing. Silver nanoparticles (AgNPs) are also concentrated in the liquid phase to aggregate with Raman target analytes. The SERS signal intensity is maximized when the AgNP concentration exceeds the critical aggregation value. Freezing allows up to 5000 times enhancements of the SERS signal. Thus, an efficient SERS platform is prepared by simple freezing. The simultaneous detection of four DNA bases effectively eliminates variations of signal intensities and allows the reliable determination of concentration ratios.
Assuntos
Adenina/análise , Citosina/análise , Guanina/análise , Nanopartículas Metálicas/química , Timidina/análise , Cerveja/análise , Crioprotetores/química , Congelamento , Glicerol/química , Limite de Detecção , Prata/química , Análise Espectral Raman/métodos , Sacarose/químicaRESUMO
A rapid and sensitive electrochemical sensing platform is reported based on bimetallic gold-platinum nanoclusters (AuPtNCs) dispersed on reduced graphene oxide (rGO) for the simultaneous detection of guanine and adenine using square wave voltammetry (SWV). The synthesis of AuPtNCs-rGO nanocomposite was achieved by a simultaneous reduction of graphene oxide (GO) and metal ions (Au3+ and Pt4+) in an aqueous solution. The developed AuPtNCs-rGO electrochemical sensor with the optimized 50:50 bimetallic (Au:Pt) nanoclusters exhibited an outstanding electrocatalytic performance towards the simultaneous oxidation of guanine and adenine without the aid of any enzymes or mediators in physiological pH. The electrochemical sensor platform showed low detection limits of 60 nM and 100 nM (S/N = 3) for guanine and adenine, respectively, with high sensitivity and an extensive linear range from 1.0 µM to 0.2 mM for both guanine and adenine. The interference from the most common electrochemically active interferents, including ascorbic acid, uric acid, and dopamine, was almost negligible. The simultaneous sensing of guanine and adenine in denatured Salmon Sperm DNA sample was successfully achieved using the proposed platform, showing that the AuPtNCs-rGO nanocomposite could provide auspicious clinical diagnosis and biomedical applications.
Assuntos
Adenina/análise , Ligas/química , Grafite/química , Guanina/análise , Nanopartículas Metálicas/química , Nanocompostos/química , Animais , Ácido Ascórbico/química , Técnicas Biossensoriais , DNA/análise , Dopamina/química , Técnicas Eletroquímicas , Eletrodos , Ouro/química , Limite de Detecção , Masculino , Oxirredução , Platina/química , Salmão , Espermatozoides/química , Ácido Úrico/químicaRESUMO
A promising electrochemical strategy for assay of N6-methyladenosine (m6A)/N6-methyladenine (6mA) in RNA/DNA is proposed. The key of this strategy is the end-labeling of nucleic acid, which makes it possible to detect methylation level in unknown sequence. Firstly, the end of m6A-RNA or 6mA-DNA was labeled with sulfhydryl group through T4 polynucleotide kinase (T4 PNK) and then directly assembled on a gold nanoparticle-modified glassy carbon electrode (AuNPs/GCE). Secondly, methylation sites in RNA/DNA were specifically recognized by anti-m6A-antibody, and then, horseradish peroxidase-labeled goat anti-rabbit IgG (HRP-IgG) was further conjugated on the antibody. Thirdly, HRP-IgG catalyzed the hydroquinone oxidation reaction to generate amplified current signal which correlates with the amount of m6A/6mA in nucleic acid. This method showed a wide linear range from 0.0001 to 10 nM for m6A-RNA, 0.001 to 100 nM for 6mA-dsDNA, and 0.0001 to 10 nM for 6mA-ssDNA. The method was successfully applied to detection of m6A/6mA in RNA/DNA from HeLa cells and E. coli cells and validation of the decrease of m6A-RNA in HeLa cells after treatment with FTO protein.
Assuntos
Adenina/análogos & derivados , Adenosina/análogos & derivados , DNA/química , Técnicas Eletroquímicas/métodos , RNA/química , Adenina/análise , Adenina/imunologia , Adenosina/análise , Adenosina/imunologia , Anticorpos Monoclonais/imunologia , Armoracia/enzimologia , Escherichia coli/química , Ouro/química , Células HeLa , Peroxidase do Rábano Silvestre/química , Humanos , Ácidos Nucleicos Imobilizados/química , Imunoglobulina G/química , Limite de Detecção , Nanopartículas Metálicas/química , Metilação , Reprodutibilidade dos TestesRESUMO
A simple and easy-operation electrode modification strategy was proposed using Cu-MOF/GO nanohybrids for physiologists and pathologists for the feasible and reliable simultaneous electrochemical detections of DNA bases, namely guanine and adenine. The nanohybrids were prepared via a simple ultrasonic method and were employed for the fabrication of a sensing interface. SEM, TEM, XRD, FT-IR, and electrochemical characterizations were used to characterize the general morphology and structure of the nonohybrids. The proposed Cu-MOF/ERGO/GCE exhibited ultra-stable and high-sensitivity performance in the simultaneous electrochemical detection of guanine and adenine. The recorded DPV curves revealed a linear increase in the faradaic signals with increase in the concentrations of guanine and adenine in the range of 0.02-10 µM and 20-100 µM for guanine, and 0.005-20 µM and 40-200 µM for adenine. The relative standard deviation of guanine and adenine for 50 consecutive detections is 1.37% and 1.92%, respectively. It was proved that the proposed Cu-MOF/ERGO/GCE can be performed for the detection of guanine and adenine in real samples, such as Herring sperm DNA, and satisfactory results were obtained. This strategy does not require complicated modification procedures, professional modification techniques, or sophisticated instruments, but it can provide a highly sensitive and stable detection method, which is expected to expand and deepen the applications of electrochemical detection in life science research.
Assuntos
Adenina/análise , Cobre/química , DNA/análise , Grafite/química , Guanina/análise , Estruturas Metalorgânicas/química , Nanocompostos/química , Animais , Técnicas Biossensoriais , Técnicas Eletroquímicas/métodos , Eletrodos , Peixes , Masculino , Espermatozoides/metabolismoRESUMO
Detection and sequencing of various nucleobases are of immense usefulness that can revolutionise future medical diagnostics procedures. In this regard, the newly discovered 2D material, C3N, has demonstrated supreme potential for future nanoelectronic and spintronic developments due to its unique sets of electronic properties and structural similarity to graphene. Herein, we have investigated the effect of various nucleobases in the close vicinity of a C3N nanoribbon. Our extensive calculations revealed significant changes in the transport behaviour in the presence of DNA/RNA molecules. The transport response can be further modified through the (i) incorporation of doping, (ii) presence of defects, (iii) concentration of the adsorbed molecule, etc. Furthermore, in the presence of a gate voltage in a field-effect transistor (FET) geometry, the conductivity response can be improved significantly with an â¼100% change in the presence of an adsorbed molecule. The observation of a negative differential resistance (NDR) in the C3N system has also been reported here for the first time. Our current observation demonstrates the usefulness of the C3N system as a next generation bio-sensor for the sequencing of various nucleobases, offering new leads for future developments in bioelectronics, superior sensing architectures and sustainable designs.
Assuntos
Nanotubos de Carbono/química , Nitrilas/química , Adenina/análise , Adenina/química , Adsorção , Técnicas Biossensoriais/métodos , Citosina/análise , Citosina/química , Teoria da Densidade Funcional , Guanina/análise , Guanina/química , Modelos Químicos , Timina/análise , Timina/química , Uracila/análise , Uracila/químicaRESUMO
OBJECTIVE: To analyze the compositions of upper urinary tract stones and investigate their distributions in different gender and age groups. MATERIALS AND METHODS: Patients diagnosed with upper urinary tract stone disease between December 2014 and March 2018 were retrospectively reviewed. Patient's age, gender, BMI, comorbidities, stone event characteristics, and compositions were collected, and proportions of stone components in different gender and age groups were analyzed. RESULTS: A total of 1532 stone analyses were performed (992 from males and 540 from females). The mean age was younger in males (p<0.001). Males included more cases with larger BMI, hyperuricemia, and obesity, while females had more urinary tract infections. Multiple components were present in 61.8% of stones. Calcium oxalate (CaOx) (67.0%) was the most common component, followed by uric acid (UA) (11.8%), infection stone (11.4%), calcium phosphate (CaP) (8.0%), cystine (1.1%), brushite (0.4%), and 2,8-dihydroxyadenine (0.2%). Men contributed with more CaOx stones than women at age 30-49 years (all p<0.01) and more UA stones at 30-59 years (all p<0.05). Women contributed with more infection stones than men in age groups 30-49 and 60-69 years (all p<0.05), and more CaP stones at 30-49 years. The prevalence peak was 50-59 years in men and 60-69 years in women. Both genders had the lowest prevalence in adolescence. Prevalence of UA stones increased while that of infection stones decreased with aging in both genders. CONCLUSIONS: Age and sex had a strong association with distribution of stone compositions in this Chinese cohort.
Assuntos
Cálculos Urinários/química , Cálculos Urinários/epidemiologia , Adenina/análogos & derivados , Adenina/análise , Adulto , Distribuição por Idade , Fatores Etários , Oxalato de Cálcio/análise , Fosfatos de Cálcio/análise , China/epidemiologia , Feminino , Humanos , Modelos Logísticos , Masculino , Pessoa de Meia-Idade , Prevalência , Estudos Retrospectivos , Fatores de Risco , Distribuição por Sexo , Fatores Sexuais , Ácido Úrico/análise , Cálculos Urinários/etiologiaRESUMO
BACKGROUND: Directed DNA methylation on N6-adenine (6mA), N4-cytosine (4mC), and C5-cytosine (5mC) can potentially increase DNA coding capacity and regulate a variety of biological functions. These modifications are relatively abundant in bacteria, occurring in about a percent of all bases of most bacteria. Until recently, 5mC and its oxidized derivatives were thought to be the only directed DNA methylation events in metazoa. New and more sensitive detection techniques (ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-ms/ms) and single molecule real-time sequencing (SMRTseq)) have suggested that 6mA and 4mC modifications could be present in a variety of metazoa. RESULTS: Here, we find that both of these techniques are prone to inaccuracies, which overestimate DNA methylation concentrations in metazoan genomic DNA. Artifacts can arise from methylated bacterial DNA contamination of enzyme preparations used to digest DNA and contaminating bacterial DNA in eukaryotic DNA preparations. Moreover, DNA sonication introduces a novel modified base from 5mC that has a retention time near 4mC that can be confused with 4mC. Our analyses also suggest that SMRTseq systematically overestimates 4mC in prokaryotic and eukaryotic DNA and 6mA in DNA samples in which it is rare. Using UHPLC-ms/ms designed to minimize and subtract artifacts, we find low to undetectable levels of 4mC and 6mA in genomes of representative worms, insects, amphibians, birds, rodents and primates under normal growth conditions. We also find that mammalian cells incorporate exogenous methylated nucleosides into their genome, suggesting that a portion of 6mA modifications could derive from incorporation of nucleosides from bacteria in food or microbiota. However, gDNA samples from gnotobiotic mouse tissues found rare (0.9-3.7 ppm) 6mA modifications above background. CONCLUSIONS: Altogether these data demonstrate that 6mA and 4mC are rarer in metazoa than previously reported, and highlight the importance of careful sample preparation and measurement, and need for more accurate sequencing techniques.
Assuntos
Adenina/análogos & derivados , Artefatos , Citosina/análogos & derivados , Metilação de DNA , DNA/genética , Eucariotos/genética , Genoma , Adenina/análise , Adenina/metabolismo , Animais , Células Cultivadas , Citosina/análise , Citosina/metabolismo , Genômica , Humanos , Camundongos , Mioblastos/citologia , Mioblastos/metabolismoRESUMO
Research about DNA composition has been concentrated on DNA damage in the past few decades. However, it still remains a great challenge to construct a rapid, facile, and accurate approach for simultaneously monitoring four DNA bases, guanine (G), adenine (A), thymine (T), and cytosine (C). Herein, a novel electrochemical sensor based on phenanthroimidazole derivative, 2-(4-bromophenyl)-1-phenyl-1H-phenanthro[9,10-d]-imidazole (PPI), is successfully fabricated by a simple electrochemical method. The bromophenyl group in PI could expand their aromatic plane, induce the π-conjugated extension, and enhance the charge transfer and π-π interaction. The phenyl group at N1 position could regulate the intermolecular interaction, which could promote the possibility of intermolecular connection. The PPI polymer (poly(PPI)) with π-electron enriched conjugation architecture has been applied in simultaneous determination of G, A, T, and C in neutral solution by square wave voltammetry (SWV) method with well-separated peak potentials at 0.714, 1.004, 1.177, and 1.353 V, respectively. The sensor functionalized with poly(PPI) exhibits wide linear response for G, A, T, and C in the concentration ranges of 3-300, 1-300, 30-800, and 20-750 µM, respectively. With favorable selectivity, stability, and reproducibility, the sensor is successfully utilized to monitor four DNA bases in real samples, displaying a promising prospect for electrochemical sensing devices.
Assuntos
Adenina/análise , Citosina/análise , Guanina/análise , Fenantrolinas/química , Timina/análise , Técnicas Biossensoriais , Catálise , Técnicas EletroquímicasRESUMO
Developing a convenient method to discriminate among different types of DNA nucleotides within a target sequence of the human genome is extremely challenging. We herein report an artificial ferrocene-base (Fe-base) that was synthesized and incorporated into different loci of a DNA strand. The Fe-base replacement on a nucleobase can interact with DNA bases and efficiently discriminate among A, T, G, and C DNA bases of the complementary locus on the basis of interacting electrochemical properties. Furthermore, cyclic-voltammetry (CV) studies demonstrated the electrochemical stability of DNA strands incorporated with Fe-bases and the reversibility of the incorporation. Square-wave voltammetry (SWV) was performed to measure current changes between Fe-bases and bases of interest in the DNA duplex. The changes in the charge-transfer rates appeared to be correlated with the position of the Fe-base in the DNA strand, allowing rapid and efficient sensing of single-nucleobase changes in DNA and showing promise for the design of Fe-oligomer chip technology as a tool for DNA sequencing.
Assuntos
Adenina/análise , Citosina/análise , DNA/química , Técnicas Eletroquímicas , Guanina/análise , Timina/análiseRESUMO
BACKGROUND: Tenofovir monoester is a relatively lipophilic intermediate formed during the hydrolysis of tenofovir disoproxil to tenofovir. Its clinical pharmacokinetic profile and influence on the cellular pharmacology of tenofovir diphosphate have not been reported. METHODS: Plasma, PBMC and dried blood spots (DBS) were obtained from HIV-uninfected adults participating in a randomized, cross-over bioequivalence study of single-dose tenofovir disoproxil fumarate (TDF)/emtricitabine unencapsulated or encapsulated with a Proteus® ingestible sensor. Plasma pharmacokinetics of tenofovir monoester and tenofovir were characterized using non-compartmental methods. Relationships with tenofovir diphosphate in DBS and PBMC were examined using mixed-effects models. RESULTS: Samples were available from 24 participants (13 female; 19 white, 3 black, 2 Hispanic). Tenofovir monoester appeared rapidly with a median (range) Tmax of 0.5 h (0.25-2) followed by a rapid monophasic decline with a geometric mean (coefficient of variation) t½ of 26 min (31.0%). Tenofovir monoester Cmax was 131.6 ng/mL (69.8%) and AUC0-4 was 93.3 ng·h/mL (47.9%). The corresponding values for plasma tenofovir were 222.2 ng/mL (37.1%) and 448.1 ng·h/mL (30.0%). Tenofovir monoester AUC0-∞ (but not tenofovir AUC0-∞) was a significant predictor of tenofovir diphosphate in both PBMC (Pâ=â0.015) and DBS (Pâ=â0.005), increasing by 3.8% (95% CI 0.8%-6.8%) and 4.3% (95% CI 1.5%-7.2%), respectively, for every 10 ng·h/mL increase in tenofovir monoester. CONCLUSIONS: Tenofovir monoester Cmax and AUC0-4 were 59.2% and 20.6% of corresponding plasma tenofovir concentrations. Tenofovir monoester was significantly associated with intracellular tenofovir diphosphate concentrations in PBMC and DBS, whereas tenofovir concentrations were not. Tenofovir monoester likely facilitates cell loading, thereby increasing tenofovir diphosphate exposures in vivo.
Assuntos
Adenina/análogos & derivados , Fármacos Anti-HIV/administração & dosagem , Fármacos Anti-HIV/farmacocinética , Organofosfatos/análise , Ácidos Fosforosos/administração & dosagem , Ácidos Fosforosos/farmacocinética , Adenina/administração & dosagem , Adenina/análise , Adenina/farmacocinética , Adulto , Análise Química do Sangue , Estudos Cross-Over , Emtricitabina/administração & dosagem , Feminino , Infecções por HIV/tratamento farmacológico , Humanos , MasculinoRESUMO
A fluorescent quantitation method to determine PBMC-derived DNA amounts using purified human genomic DNA (gDNA) as the reference standard was developed and validated. gDNA was measured in a fluorescence-based assay using a DNA intercalant, SYBR green. The fluorescence signal was proportional to the amount (mass) of DNA in the sample. The results confirmed a linear fit from 0.0665 to 1.17⯵g/µL for gDNA, corresponding to 2.0â¯×â¯106 to 35.0â¯×â¯106â¯cells/PBMC sample. Intra-batch and inter-batch accuracy (%RE) was within ±15%, and precision (%CV) was <15%. Benchtop stability, freeze/thaw stability and long term storage stability of gDNA in QC sample matrix, PBMC pellets samples, and pellet debris samples, respectively, as well as dilution linearity had been established. Consistency between hemocytometry cell counting method and gDNA-based counting method was established. 6 out of 6 evaluated PBMC lots had hemocytometry cell counts that were within ±20% of the cell counts determined by the gDNA method. This method was used in conjunction with a validated LC-MS/MS method to determine the level of tenofovir diphosphate (TFV-DP), the active intracellular metabolite of the prodrugs tenofovir alafenamide (TAF) and tenofovir disoproxil fumarate (TDF), measured in PBMCs in clinical trials of TAF or TDF-containing fixed dose combinations.