A fluorometric study on the effect of DNA methylation on DNA interaction with graphene quantum dots

Role of charge in enhanced nuclear transport and retention of graphene quantum dots

The nuclear pore complexes on the nuclear membrane serve as the exclusive gateway for communication between the nucleus and the cytoplasm, regulating the transport of various molecules, including nucleic acids and proteins. The present work investigates the kinetics of the transport of negatively charged graphene quantum dots through nuclear membranes, focusing on quantifying their transport characteristics. Experiments are carried out in permeabilized HeLa cells using time-lapse confocal fluorescence microscopy. Our findings indicate that negatively charged graphene quantum dots exhibit rapid transport to the nuclei, involving two distinct transport pathways in the translocation process. Complementary experiments on the nuclear import and export of graphene quantum dots validate the bi-directionality of transport, as evidenced by comparable transport rates. The study also shows that the negatively charged graphene quantum dots possess favorable retention properties, underscoring their potential as drug carriers.

Fluorimetric detection of DNA methylation by cerium oxide nanoparticles for early cancer diagnosis

In this study, a very sensitive fluorescence nano-biosensor was developed using CeO2 nanoparticles for the rapid detection of DNA methylation. The characteristics of CeO2 nanoparticles were determined by transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), X-ray diffraction (XRD) spectroscopy, UV-visible spectroscopy, and fluorescence spectroscopy. The CeO2 nanoparticles were reacted with a single-stranded DNA (ssDNA) probe, and then methylated and unmethylated target DNAs hybridized with an ssDNA probe, and the fluorescence emission was measured. Upon adding the target unmethylated and methylated ssDNA, the fluorescence intensity increased in the linear range of concentration from 2 × 10-13 - 10-18 M. The limit of detection (LOD) was 1.597 × 10-6 M for methylated DNA and 1.043 × 10-6 M for unmethylated DNA. The fluorescence emission intensity of methylated sequences was higher than of that unmethylated sequences. The fabricated DNA nanobiosensor showed a fluorescence emission at 420 nm with an excitation wavelength of 280 nm. The impact of CeO2 binding on methylated and unmethylated DNA was further demonstrated by agarose gel electrophoresis. Finally, the actual sample analysis suggested that the nanobiosensor could have practical applications for detecting methylation in the human plasma samples.

Tannic acid-accelerated fenton chemical reaction amplification for fluorescent biosensing: The proof-of-concept towards ultrasensitive detection of DNA methylation

As a promising biomarker, the level of methylated DNA usually changes in the early stage of the cancer. Ultrasensitive detection of the changes of methylated DNA offers possibility for early diagnosis of cancer. In this work, a tannic acid-accelerated Fenton chemical reaction amplification was firstly proposed for the construction of ultrasensitive fluorescent assay. Tannic acid was used as reductant to accelerate Fenton reaction procedure through the conversion of Fe3+/Fe2+, generating hydroxyl radicals (·OH) continuously. The produced ·OH oxidized massive non-fluorescent terephthalic acid (TA) to fluorescent-emitting hydroxy terephthalic acid (TAOH). In this way, the fluorescent signal could be greatly enhanced and the sensitivity was improved almost 116 times. The proposed signal amplification strategy was further applied to detect of DNA methylation with the assistance of liposome encapsulated with tannic-Fe3+ complexes. The methylated DNA was firstly captured through the hybridization with its complementary DNA that were pre-modified in the 96-well plate via the combination between streptavidin (SA) and biotin. Then, 5 mC antibody on the surface of liposomes specially recognized and combined with methylation sites, which brought large amount of tannic-Fe3+ complexes to participate Fenton reaction. The fluorescence of generated TAOH was depended on the concentration of methylated DNA. The assay showed good analytical performance for methylated DNA with a limit of detection (LOD) of 1.4 fM. It's believed that tannic acid-accelerated Fenton chemical reaction amplification strategy provides a promising platform for ultrasensitive fluorescent detection of low abundant biomarkers.

Dual-Responsive Carbon Quantum Dots for the Simultaneous Detection of Cytosine and 5-Methylcytosine Interpreted by a Machine Learning-Assisted Smartphone

DNA methylation is an epigenetic alteration that results in 5-methylcytosine (5-mC) through the addition of a methyl group to the fifth carbon of a cytosine (C) residue. The methylation level, the ratio of 5-mC to C, in urine might be related to the whole-body epigenetic status and the occurrence of common cancers. To date, never before have any nanomaterials been developed to simultaneously determine C and 5-mC in urine samples. Herein, a dual-responsive fluorescent sensor for the urinary detection of C and 5-mC has been developed. This assay relied on changes in the optical properties of nitrogen-doped carbon quantum dots (CQDs) prepared by microwave-assisted pyrolysis. In the presence of C, the blue-shifted fluorescence intensity of the CQDs increased. However, fluorescence quenching was observed upon the addition of 5-mC. This was primarily due to photoinduced electron transfer as confirmed by the density functional theory calculation. In urine samples, our sensitive fluorescent sensor had detection limits for C and 5-mC of 43.4 and 74.4 μM, respectively, and achieved satisfactory recoveries ranging from 103.5 to 115.8%. The simultaneous detection of C and 5-mC leads to effective methylation level detection, achieving recoveries in the range of 104.6-109.5%. Besides, a machine learning-enabled smartphone was also developed, which can be effectively applied to the determination of methylation levels (0-100%). These results demonstrate a simple but very effective approach for detecting the methylation level in urine, which could have significant implications for predicting the clinical prognosis.

Theranostic Applications of 2D Graphene-Based Materials for Solid Tumors Treatment

Solid tumors are a leading cause of cancer-related deaths globally, being characterized by rapid tumor growth and local and distant metastases. The failures encountered in cancer treatment are mainly related to the complicated biology of the tumor microenvironment. Nanoparticles-based (NPs) approaches have shown the potential to overcome the limitations caused by the pathophysiological features of solid cancers, enabling the development of multifunctional systems for cancer diagnosis and therapy and allowing effective inhibition of tumor growth. Among the different classes of NPs, 2D graphene-based nanomaterials (GBNs), due to their outstanding chemical and physical properties, easy surface multi-functionalization, near-infrared (NIR) light absorption and tunable biocompatibility, represent ideal nanoplatforms for the development of theranostic tools for the treatment of solid tumors. Here, we reviewed the most recent advances related to the synthesis of nano-systems based on graphene, graphene oxide (GO), reduced graphene oxide (rGO), and graphene quantum dots (GQDs), for the development of theranostic NPs to be used for photoacoustic imaging-guided photothermal-chemotherapy, photothermal (PTT) and photodynamic therapy (PDT), applied to solid tumors destruction. The advantages in using these nano-systems are here discussed for each class of GBNs, taking into consideration the different chemical properties and possibility of multi-functionalization, as well as biodistribution and toxicity aspects that represent a key challenge for their translation into clinical use.

Emerging Biosensing Methods to Monitor Lung Cancer Biomarkers in Biological Samples: A Comprehensive Review

Lung cancer is the most commonly diagnosed of all cancers and one of the leading causes of cancer deaths among men and women worldwide, causing 1.5 million deaths every year. Despite developments in cancer treatment technologies and new pharmaceutical products, high mortality and morbidity remain major challenges for researchers. More than 75% of lung cancer patients are diagnosed in advanced stages, leading to poor prognosis. Lung cancer is a multistep process associated with genetic and epigenetic abnormalities. Rapid, accurate, precise, and reliable detection of lung cancer biomarkers in biological fluids is essential for risk assessment for a given individual and mortality reduction. Traditional diagnostic tools are not sensitive enough to detect and diagnose lung cancer in the early stages. Therefore, the development of novel bioanalytical methods for early-stage screening and diagnosis is extremely important. Recently, biosensors have gained tremendous attention as an alternative to conventional methods because of their robustness, high sensitivity, inexpensiveness, and easy handling and deployment in point-of-care testing. This review provides an overview of the conventional methods currently used for lung cancer screening, classification, diagnosis, and prognosis, providing updates on research and developments in biosensor technology for the detection of lung cancer biomarkers in biological samples. Finally, it comments on recent advances and potential future challenges in the field of biosensors in the context of lung cancer diagnosis and point-of-care applications.

Label-Free Physical-Analytical Techniques Reveal Epigenetic Modifications of Breast Cancer Chromosomes

Epigenetic dysregulation including DNA methylation and histone modifications is being increasingly recognized as a promising biomarker for the diagnosis and prognosis of cancer. Herein, we devised a label-free analytical toolbox comprising IR, UV-vis, CD spectroscopy, and cyclic voltammetry, which is capable to differentiate significantly hyper-methylated breast cancer chromosomes from the normal breast epithelial counterparts.

Bioanalytical Applications of Graphene Quantum Dots for Circulating Cell-Free Nucleic Acids: A Review

Graphene quantum dots (GQDs) are carbonaceous nanodots that are natural crystalline semiconductors and range from 1 to 20 nm. The broad range of applications for GQDs is based on their unique physical and chemical properties. Compared to inorganic quantum dots, GQDs possess numerous advantages, including formidable biocompatibility, low intrinsic toxicity, excellent dispensability, hydrophilicity, and surface grating, thus making them promising materials for nanophotonic applications. Owing to their unique photonic compliant properties, such as superb solubility, robust chemical inertness, large specific surface area, superabundant surface conjugation sites, superior photostability, resistance to photobleaching, and nonblinking, GQDs have emerged as a novel class of probes for the detection of biomolecules and study of their molecular interactions. Here, we present a brief overview of GQDs, their advantages over quantum dots (QDs), various synthesis procedures, and different surface conjugation chemistries for detecting cell-free circulating nucleic acids (CNAs). With the prominent rise of liquid biopsy-based approaches for real-time detection of CNAs, GQDs-based strategies might be a step toward early diagnosis, prognosis, treatment monitoring, and outcome prediction of various non-communicable diseases, including cancers.

An innovative fluorometric bioanalysis strategy towards recognition of DNA methylation using opto-active polymer: A new platform for DNA damage studies by genosensor technology

Efficient pharmacotherapy of cancer is related to accurate recognition of genetic mutations and epigenetic alterations in the early-stage diagnosis. In the present study, a novel optical genosensor based on toluidine blue as photonic probe was developed to detection of DNA methylation using hybridization of pDNA with cDNA. Biomedical analysis was performed using UV-vis and fluorometric methods. For the first time, this strategy was applied for the distinction of methylated DNA from unmethylated-DNA-based on the interaction of optical probe with methylated-DNA and unmethylated DNA. Fluorescence spectroscopic data showed that poly-toluidine blue could be bind to DNA sequences and lead to different fluorescence patterns and could be used as an efficient geno-platform for the sensitive bioassay of mutation. The excitation and emission wavelengths were 580 and 630 nm, respectively. Non-binding of mismatch sequences with the optical probe was used as negative control. Under optimal conditions, linear range was 1 zM to 0.2 pm and the lower limit of quantitation was obtained as target concentrations ranging 1 zM. The designed genosensor showed high capability to distinct methylation from un-methylated. Therefore, the designed DNA-based bioassay could detect DNA methylation significantly. Finally, bioanalysis of real samples showed that the designed genosensor could use to detect DNA methylation which is a new platform for point of care analysis.

Fabrication of Graphene-Based TiO2@CeO2 and CeO2@TiO2 Core-Shell Heterostructures for Enhanced Photocatalytic Activity and Cytotoxicity

Development of light-harvesting properties and inhibition of photogenerated charge carrier recombination are of paramount significance in the photocatalytic process. In the present work, we described the synthesis of core-shell heterostructures, which are composed of titanium oxide (TiO₂) and cerium oxide (CeO₂) deposited on a reduced graphene oxide (rGO) surface as a conductive substrate. Following the synthesis of ternary rGO-CeO₂@TiO₂ and rGO-TiO₂@CeO₂ nanostructures, their photocatalytic activity was investigated toward the degradation of rhodamine B dye as an organic pollutant under UV light irradiation. The obtained structures were characterized with high-resolution transmission electron microscopy, field-emission scanning electron microscopy, energy-dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, Brunauer-Emmett-Teller, X-ray photoelectron spectroscopy surface analysis, and UV-Vis spectroscopy. Various parameters including pH, catalyst dosage, temperature, and contact time were studied for photocatalysis optimization. Heterostructures showed considerable advantages because of their high surface area and superior photocatalytic performance. In contrast, rGO-CeO₂@TiO₂ showed the highest photocatalytic activity, which is attributed to the more effective electron-hole separation and quick suppression of charge recombination at core-shell phases. A biological assay of the prepared heterostructure was performed to determine the cytotoxicity against breast cancer cells (MCF-7) and demonstrated a very low survival rate at 7.65% of cells at the 17.5 mg mL^-1 concentration of applied photocatalyst.

Photocatalytic activity of green synthesized cadmium sulfide quantum dots on the removal of RhB dye and its cytotoxicity and antibacterial studies

Presence of inorganic pollutants in water reservoirs is the treating factor for human health and environment. Semiconductor quantum dots (QDs) has been regarded as one of the most efficient nanoparticles for their enhanced photocatalytic activity. Medicinal plants are the safe sources to provide green template for biosynthesis of inorganic nanoparticles such as quantum dots. In order to determine the photocatalytic and biological application of cadmium sulfide quantum dots (CdS QDs), a biosynthesis approach was employed using saffron (Crocus sativus L.) stigma extract as the green reaction substrate. The biosynthesis process was evaluated at different pH condition to obtain the most efficient CdS QDs. Characterization of prepared CdS QDs were determined through UV-vis and fluorescence spectroscopy, FTIR and TEM analysis. The obtained results showed well dsispersed and uniform QDs during green synthesis at the optimum condition. The absorption and electrical properties of green synthesized CdS QDs showed the lowest energy bandgap of 2.4 at pH 11. Photocatalytic activity of CdS QDs on Rhodamine B degradation showed 92% degradation after 80 min under UV light irradiation. The antibacterial and cell cytotoxicity of green synthesized CdS QDs were assayed by disk diffusion and MTT assays respectively. Obtained results showed significant antibacterial effect of CdS QDs against gram-positive and gram-negative bacteria includingB. subtilis(90%) andE. coli(96%) respectively. Moreover, cytotoxicity of prepared CdS Qds through MTT assay indicated 79% apoptosis induction on MCF-7 breast cancer cells.

Optical bio-sensing of DNA methylation analysis: an overview of recent progress and future prospects

DNA methylation as one of the most important epigenetic modifications has a critical role in regulating gene expression and drug resistance in treating diseases such as cancer. Therefore, the detection of DNA methylation in the early stages of cancer plays an essential role in disease diagnosis. The majority of routine methods to detect DNA methylation are very tedious and costly. Therefore, designing easy and sensitive methods to detect DNA methylation directly and without the need for molecular methods is a hot topic issue in bioscience. Here we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation. In addition, various types of labeled and label-free reactions along with the application of molecular methods and optical biosensors have been surveyed. Also, the effect of nanomaterials on the sensitivity of detection methods is discussed. Furthermore, a comprehensive overview of the advantages and disadvantages of each method are provided. Finally, the use of microfluidic devices in the evaluation of DNA methylation and DNA damage analysis based on smartphone detection has been discussed.

Here, we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation.

A novel colorimetric biosensor for sensitive detection of aflatoxin mediated by bacterial enzymatic reaction in saffron samples

Aflatoxin is regarded as the potent carcinogenic agent which is secreted from fungi and present in some food products. So far, many detection methods have been developed to determine the trace amounts of aflatoxin in foods. In the present study a colorimetric competitive assay for detection of aflatoxin B1 (AFB1) has been developed based on interaction of gelatin functionalized gold nanoparticles (AuNPs@gelatin) in specific enzymatic reaction. Bacterial supernatant containing gelatinase enzyme were used as the substrate that could digest the coated gelatin on the surface of AuNPs and following in the presence of NaCl medium ingredient resulted to color change of AuNPs colloidal solution from red to purple. It was observed that with addition of aflatoxin to the bacterial supernatant, aflatoxin could interfere in aggregation of AuNPs and inhibited the process which subsequently prevent the expected color change induced by AuNPs aggregation. The supernatant containing AuNPs were investigated to analyze their induced surface plasmon resonance spectra through UV-visible spectroscopy. The absorption values were directly proportional with the applied AFB1 concentration. The experiment conditions including incubation time, AuNPs concentration and pH were investigated. The obtained results showed that through this approach we could detect the AFB1 in a linear range from 10 to 140 pg ml^-1, with detection limit of 4 pg ml^-1. Real sample assay in saffron samples showed recoveries percentage of 92.4%-95.3%. The applied approach proposed simple, cost effective and specific method for detection of AFB1 toxin in food samples.

Biocompatible nucleus-targeted graphene quantum dots for selective killing of cancer cells via DNA damage

Graphene quantum dots (GQDs) are nano-sized graphene slices. With their small size, lamellar and aromatic-ring structure, GQDs tend to enter into the cell nucleus and interfere with DNA activity. Thus, GQD alone is expected to be an anticancer reagent. Herein, we developed GQDs that suppress the growth of tumor by selectively damaging the DNA of cancer cells. The amine-functionalized GQDs were modified with nucleus targeting TAT peptides (TAT-NGs) and further grafted with cancer-cell-targeting folic acid (FA) modified PEG via disulfide linkage (FAPEG-TNGs). The resulting FAPEG-TNGs exhibited good biocompatibility, nucleus uptake, and cancer cell targeting. They adsorb on DNA via the π-π and electrostatic interactions, which induce the DNA damage, the upregulation of the cell apoptosis related proteins, and the suppression of cancer cell growth, ultimately. This work presents a rational design of GQDs that induce the DNA damage to realize high therapeutic performance, leading to a distinct chemotherapy strategy for targeted tumor therapy.

Engineered nanoparticle-induced epigenetic changes: An important consideration in nanomedicine

Engineered nanoparticles (ENPs) are now being applied across a range of disciplines, and as a result numerous studies have now assessed ENP-related bioeffects. Among them, ENP-induced epigenetic changes including DNA methylation, histone modifications, and miRNA-mediated regulation of gene expression have recently attracted attention. In this review, we describe the diversity of ENP-induced epigenetic changes, focusing on their interplay with related functional biological events, especially oxidative stress, MAPK pathway activation, and inflammation. In doing so, we highlight the underlying mechanisms and biological effects of ENP-induced epigenetic changes. We also summarize how high-throughput technologies have helped to uncover ENP-induced epigenetic changes. Finally, we discuss future perspectives and the challenges related to ENP-induced epigenetic changes that still need to be addressed.

Molybdenum disulfide@5-carboxyfluorescein-probe biosensor for unamplified specific fragment detection in long nucleic acids based on magnetic composite probe-actuated deblocking of secondary structure

Secondary structures in long circulating tumor nucleic acids have potential obstacles for specific location point hybridized detection of gene fragments. The exploration of biosensing strategies requires selectively changing the nucleic acids conformation and inducing signal switching. Herein, a self-assembled magnetic composite probe (MCP) was fabricated by the hybridization reaction of Linker DNA and a "Y"-junction-DNA nanostructure on the surface of magnetic beads, contributing to the capture, secondary structure unlocking, and enrichment of the PML/RARα DNA "L" subtype. Then, by integrating the MCP-actuated reactor, a one-step "off-on" signal switching MoS2@FAM-probe biosensing method was developed for the efficient detection of the PML/RARα DNA "L" subtype. The proposed biosensor was capable of detecting 100 bases PML/RARα DNA "L" subtype with a wide linear range of 1 pM to 200 nM and a limit of detection down to 0.223 pM without signal amplification. In addition, the biosensing method was successfully applied for the detection of target in serum samples. It is worth pointing out that this simple biosensing strategy could enable long nucleic acids fragments with secondary structures from ctDNA and ctRNA to be quantitatively assayed based on direct hybridization.

A signal-on fluorescence based biosensing platform for highly sensitive detection of DNA methyltransferase enzyme activity and inhibition

DNA methylation mediated by DNA methyltransferase (MTase) enzyme is internal cell mechanism which regulate the expression or suppression of crucial genes involve in cancer early diagnosis. Herein, highly sensitive fluorescence biosensing platform was developed for monitoring of DNA Dam MTase enzyme activity and inhibition based on fluorescence signal on mechanism. The specific Au NP functionalized oligonucleotide probe with overhang end as a template for the synthesis of fluorescent silver nanoclusters (Ag NCs) was designed to provide the FRET occurrence. Following, methylation and cleavage processes by Dam MTAse and DpnI enzymes respectively at specific probe recognition site could resulted to release of AgNCs synthesizer DNA fragment and returned the platform to fluorescence signal-on state through interrupting in FRET. Subsequently, amplified fluorescence emission signals of Ag NCs showed increasing linear relationship with amount of Dam MTase enzyme at the range of 0.1-20 U/mL and the detection limit was estimated at 0.05 U/mL. Superior selectivity of experiment was illustrated among other tested MTase and restriction enzymes due to the specific recognition of MTase toward its substrate. Furthermore, the inhibition effect of applied Dam MTase drug inhibitors screened and evaluated with satisfactory results which would be helpful for discovery of antimicrobial drugs. The real sample assay also showed the applicability of proposed method in human serum condition. This novel strategy presented an efficient and cost effective platform for sensitive monitoring of DNA MTase activity and inhibition which illustrated its great potential for further application in medical diagnosis and drug discovery.

Epigenetic Aspects of Engineered Nanomaterials: Is the Collateral Damage Inevitable?

The extensive application of engineered nanomaterial (ENM) in various fields increases the possibilities of human exposure, thus imposing a huge risk of nanotoxicity. Hence, there is an urgent need for a detailed risk assessment of these ENMs in response to their toxicological profiling, predominantly in biomedical and biosensor settings. Numerous "toxico-omics" studies have been conducted on ENMs, however, a specific "risk assessment paradigm" dealing with the epigenetic modulations in humans owing to the exposure of these modern-day toxicants has not been defined yet. This review aims to address the critical aspects that are currently preventing the formation of a suitable risk assessment approach for/against ENM exposure and pointing out those researches, which may help to develop and implement effective guidance for nano-risk assessment. Literature relating to physicochemical characterization and toxicological behavior of ENMs were analyzed, and exposure assessment strategies were explored in order to extrapolate opportunities, challenges, and criticisms in the establishment of a baseline for the risk assessment paradigm of ENMs exposure. Various challenges, such as uncertainty in the relation of the physicochemical properties and ENM toxicity, the complexity of the dose-response relationships resulting in difficulty in its extrapolation and measurement of ENM exposure levels emerged as issues in the establishment of a traditional risk assessment. Such an appropriate risk assessment approach will provide adequate estimates of ENM exposure risks and will serve as a guideline for appropriate risk communication and management strategies aiming for the protection and the safety of humans.

Cooperative Effects of Cytosine Methylation on DNA Structure and Dynamics

The behavior of the structural parameters of DNA considering different levels of methylation in CpG islands is studied by means of full-atom molecular dynamics simulations and electronic circular dichroism, both in an artificial model system and in a gene promoter sequence. It is demonstrated that methylation although intrinsically brings quite local perturbations may, if its level is high enough, induce cooperative effects that strongly modify the DNA backbone torsional parameters altering the helicity as compared to the nonmethylated case. Because methylation of the CpG island is correlated with the regulation of gene expression, understanding the structural modifications induced in DNA is crucial to characterize all the fine equilibria into play in epigenetics phenomena.