Label free colorimetric and fluorimetric direct detection of methylated DNA based on silver nanoclusters for cancer early diagnosis

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.

An electrochemical biosensor for detecting DNA methylation based on AuNPs/rGO/g-C3N4 nanocomposite

DNA methylation as a ubiquitously regulation is closely associated with cell proliferation and differentiation. Growing data shows that aberrant methylation contributes to disease incidence, especially in tumorigenesis. The approach for identifying DNA methylation usually depends on treatment of sodium bisulfite, which is time-consuming and conversion-insufficient. Here, with a special biosensor, we establish an alternative approach for detecting DNA methylation. The biosensor is consisted of two parts, which are gold electrode and nanocomposite (AuNPs/rGO/g-C₃N₄). Nanocomposite was fabricated by three components, which are gold nanoparticles (AuNPs), reduced graphene oxide (rGO) and graphite carbon nitride (g-C₃N₄). For methylated DNA detection, the target DNA was captured by probe DNA immobilized on the gold electrode surface through thiolating process and subjected to hybrid with anti-methylated cytosine conjugated to nanocomposite. When the methylated cytosines in target DNA were recognized by anti-methylated cytosine, a change of electrochemical signals will be observed. With different size of target DNAs, the concentration and methylation level were tested. It is shown that in short size methylated DNA fragment, the linear range and LOD of concentration is 10^-7M-10^-15M and 0.74 fM respectively; in longer size methylated DNA, the linear range of methylation proportion and LOD of copy number is 3%-84% and 10³ respectively. Also, this approach has a high sensitivity and specificity as well as anti-disturbing ability.

Fluorometric detection of phytase enzyme activity and phosphate ion based on gelatin supported silver nanoclusters

Phytase is the commercial enzyme for bioconversion of phytate substrate to digestible phosphate ions. Recently silver nanoclusters (AgNCs) have received great attention as the optical transducer nanoparticles in biosensors structure. The novel detection platform was developed to detect the phytase enzyme activity and phosphate ions based on fluorescence quenching of AgNCs. The AgNCs were synthesized through gelatin supported reaction and characterized by TEM, FTIR and XRD analysis. The hydrolytic effect of phytase enzyme and subsequent phosphate release led to suppression of AgNCs fluorescence. The linear range was observed for enzyme in the range of 0.5-5 U/mL with the detection limit of 0.2 U/mL. Also, the same fluorescence quenching effect was observed in the presence of phosphate ion in the linear range of 1 to 16 µM with a detection limit of 0.5 µM. The proposed mechanism showed effectiveness of detection strategy for detection of phytase enzyme and phosphate ion.

Microwave-Assisted Rapid Synthesis of Luminescent Tryptophan-Stabilized Silver Nanoclusters for Ultra-Sensitive Detection of Fe(III), and Their Application in a Test Strip

A new preparation method for extreme fluorescent green emission tryptophan-stabilized silver nanoclusters (Tryp-AgNCs) is presented in this scientific research. The produced silver nanoclusters are dependent on tryptophan amino acid which contributes to normal growth in infants and the sublimation and recovery of human protein, muscles, and enzymes. Herein, we have introduced a green method by using microwave-assisted rapid synthesis. The subsequent silver nanoclusters (AgNCs) have excitation/emission peaks at 408/498 nm and display a considerable selectivity to Fe(III) ions. The tryptophan amino acid molecule was used in the synthesis process as a reducing and stabilizing agent. The Tryp-AgNCs' properties were investigated in terms of morphology, dispersity, and modification of the synthesized particles using different advanced instruments. The luminescent nanoclusters traced the Fe(III) ions by the luminescence-quenching mechanism of the Tryp-AgNCs luminescence. Therefore, the extreme selectivity of the prepared nanoclusters was exhibited to the Fe(III) ions, permitting the sensitive tracing of ferric ions in the lab and in the real environmental samples. The limit of detection for Fe(III) ions based on Tryp-AgNCs was calculated to be 16.99 nM. The Tryp-AgNCs can be efficiently applied to a paper test strip method. The synthesized nanoclusters were used efficiently to detect the Fe(III) ions in the environmental samples. Moreover, we examined the reactivity of Tryp-AgNCs on various human tumor cell lines. The results show that the Tryp-AgNCs exhibited their activity versus the cancer cells in a dose-dependent routine for the perceived performance versus the greatest-used cancer cell lines.

Synergistic enhanced rolling circle amplification based on mutS and radical polymerization for single-point mutation DNA detection

The detection of nucleic acids in biofluids is essential for changing the paradigm of disease diagnosis. As there are very few nucleic acids present in human biofluids, a high sensitivity method is required to detect nucleic acids for disease diagnosis. The Kirsten rat sarcoma viral oncogene homolog (KRAS) mutation is associated with non-small cell lung cancer. It is a point mutation and requires a highly selective detection technique. In this study, high sensitivity and selectivity were achieved for the detection of KRAS mutation using rolling circle amplification (RCA), atomic transfer radical polymerization (ATRP), mutS enzyme, and electrochemical sensors. Although RCA can isothermally amplify DNA, it has low selectivity for detecting single-base mismatch DNA, and its sensitivity is not suitable for circulating tumor DNA detection. The selectivity of RCA was improved by using mutS, which can bind specifically to point mutations. In addition, as a method of isothermal radical polymerization, ATRP was used to amplify the weak signal of RCA. Since RCA and ATRP reactions occur simultaneously, detection time was reduced, and the calculated detection limit was 3.09 aM. Computational and experimental analyses were conducted to verify each detection step and the combination of mutS, ATRP, and RCA. The experiment was performed using normal human serum samples for biological application, and the proposed detection method was confirmed to have excellent potential for diagnosing cancer patients.

Phenylalanine gold nanoclusters as sensing platform for π-π interfering molecules: a case study of iodide

The photo-physical properties of metal nano clusters are sensitive to their surrounding medium. Fluorescence enhancement, quenching, and changes in the emitted photon properties are usual events in the sensing applications using these nano materials. Combining this sensitivity with unique properties of self-assembled structures opens new opportunities for sensing applications. Here, we synthesized gold nanoclusters by utilizing phenylalanine amino acid as both capping and reducing molecule. Phenylalanine is able to self-assemble to rod-shaped nano structure in which the π-π interaction between the aromatic rings is a major stabilizing force. Any substance as iodide anion or molecule that is able to weaken this interaction influence the fluorescence of metal nano-clusters. Since the building blocks of the self-assembled structure are made through the reaction of gold ions and phenylalanine, the oxidized products and their effect of sensing features are explored.

SERS-based DNA methylation profiling allows the differential diagnosis of malignant lymphadenopathy

This study highlights the potential of surface-enhanced Raman scattering (SERS) to differentiate between B-cell lymphoma (BCL), T-cell lymphoma (TCL), lymph node metastasis of melanoma (Met) and control (Ctr) samples based on the specific SERS signal of DNA extracted from lymph node tissue biopsy. Differences in the methylation profiles as well as the specific interaction of malignant and non-malignant DNA with the metal nanostructure are captured in specific variations of the band at 1005 cm^-1, attributed to 5-methylcytosine and the band at 730 cm^-1, attributed to adenine. Thus, using the area ratio of these two SERS marker bands as input for univariate classification, an area under the curve (AUC) of 0.70 was achieved in differentiating between malignant and non-malignant DNA. In addition, DNA from the BCL and TCL groups exhibited differences in the area of the SERS band at 730 cm^-1, yielding an AUC of 0.84 in differentiating between these two lymphadenopathies. Lastly, using multivariate data analysis techniques, an overall accuracy of 94.7% was achieved in the differential diagnosis between the BCL, TCL, Met and Ctr groups. These results pave the way towards the implementation of SERS as a novel tool in the clinical setting for improving the diagnosis of malignant lymphadenopathy.

Diagnosis of cancer at early stages based on the multiplex detection of tumor markers using metal nanoclusters

Traditional cancer diagnosis strategies are not considered by most people until the last resort, which delays many cancer treatments leading to advanced stages. Tumor marker sensors show great potential for detecting cancer because of its cost-effective and harmless checking procedures. Normally, one tumor marker is detected each time by using one type of sensor, but the accuracy to declare cancer is not always satisfied. Metal nanoclusters are ultra-small nanomaterials with low toxicity, distinct optical properties, catalytic activities, and cost-effective performance. Some metal nanoclusters have been designed to detect more than one tumor marker in a single step. The consideration of combined parameters using such facile sensing strategies has the potential to simplify the test procedure, and increase the diagnostic accuracy of early cancer. Therefore, various sensing strategies for the multiplex detection of tumor markers using metal nanoclusters are summarized.

DNA Methylation in Solid Tumors: Functions and Methods of Detection

DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.

Recent advances in nanomaterials for colorimetric cancer detection

The early diagnosis of cancer can significantly improve patient survival rates. Colorimetric methods for real-time naked-eye detection have aroused growing interest owing to their low cost, simplicity, and practicability. With the rapid development of nanotechnology, compared with conventional diagnostic methods, nanomaterials with unique physical and chemical properties were applied to improve selectivity and sensitivity in colorimetric detection of cancer biomarkers, such as MUC1 aptamer conjugated PtAuNPs to specifically recognize MUC1 proteins on the cancer cell surfaces, etching of silver nanoprisms to detect prostate-specific antigen, and aggregation or dispersion of AuNPs to sense prostate cancer antigen gene 3 or glutathione, by which the limit of detection (LOD) could approach values down to a few cancer cells per mL, several fg per mL proteins, several ng of nucleic acids, or even tens of nM of organic molecules. Herein, we review the recent progress achieved in developing colorimetric nanosensors for cancer diagnosis, particularly providing an overview of the sensing principles, target biomarkers, advanced nanomaterials employed in the fabrication of sensing platforms, and strategies for improving signal sensitivity and specificity. Finally, we sum up the nanomaterial-based colorimetric cancer detection as well as existing challenges that should be resolved to extend their clinical application.

Recent Advances of Silver Nanoparticles in Cancer Diagnosis and Treatment

Background:

Silver nanoparticles (AgNPs) are well-known as a promising antimicrobial material; they have been widely used in many commercial products against pathogenic agents. Despite a growing concern regarding the cytotoxicity, AgNPs still have attracted considerable interest worldwide to develop a new generation of diagnostic tool and effective treatment solution for cancer cells.

Objective:

This paper aims to review the advances of AgNPs applied for cancer diagnosis and treatment.

Methods:

The database has been collected, screened and analysed through up-to-date scientific articles published from 2007 to May 2019 in peer-reviewed international journals.

Results:

The findings of the database have been analysed and divided into three parts of the text that deal with AgNPs in cancer diagnosis, their cytotoxicity, and the role as carrier systems for cancer treatment. Thanks to their optical properties, high conductivity and small size, AgNPs have been demonstrated to play an essential role in enhancing signals and sensitivity in various biosensing platforms. Furthermore, AgNPs also can be used directly or developed as a drug delivery system for cancer treatment.

Conclusion:

The review paper will help readers understand more clearly and systematically the role and advances of AgNPs in cancer diagnosis and treatment.

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.

Paper based colorimetric detection of miRNA-21 using Ag/Pt nanoclusters

Abnormal expression of MicroRNA-21 (miRNA-21) is considered to be a reliable biomarker for the early diagnosis of cancer. In this work, a novel paper based biosensor was fabricated to detect sub-micro molar concentrations of miRNA-21 based on peroxidase mimetic activity of DNA-templated Ag/Pt nanoclusters (DNA-Ag/Pt NCs), which could catalyze the reaction of hydrogen peroxide and 3,3',5,5' tetramethylbenzidine (TMB), to produce a blue color. The Mechanism of reaction was based on the inhibition effect of miRNA-21 on peroxidase-like activity of nanosensor which resulted to quantitative determination of miRNA-21 concentration. It was found that miRNA-21 could be linearly detected in the range from 1-700 pM (A₆₅₂ = 0.16x-0.96, R² = 0.99; x = -log [miRNA-21]) with a detection limit of 0.6 pM. Moreover, a paper assay was carried out on a Y-shaped paper-based microfluidic device in order to use the distinctive features of micro-channels such as short response time, very low reagent volume, low fabrication cost, etc. After performing paper based assay, a good linear range was observed between 10-1000 pM (y = 0.06x+147.48, R² = 0.99; x = [miRNA-21]) with detection limit of 4.1 pM. The practical application of proposed method for detection of miRNA-21 in real sample was assayed in the human urine sample and indicated the colorimetric method had acceptable accuracy.

Significance of MUC2 gene methylation detection in pancreatic cancer diagnosis

PURPOSE

This study was conducted to explore the diagnostic value of MUC2 gene methylation in pancreatic cancer.

METHODS

Methylation restriction enzyme digestion (Msp I/Hap II) and polymerase chain reaction (PCR) were performed to detect methylation of the MUC2 gene in fecal and blood specimens from seven study subjects with pancreatic cancer (PC), chronic pancreatitis (CP), or normal controls (CON). Simultaneously, blood CA 19-9 levels were detected as a positive indicator of PC.

RESULTS

MUC2 methylation was detected in 50% of PC cell lines. In fecal samples, the MUC2 methylation rate in PC (n = 30) was 43.3%, which was significantly higher than those in CP (n = 8, 0%, P < 0.05) and CON (n = 20, 5.0%, P < 0.05). In blood samples, the MUC2 methylation rate in PC (n = 40) was 52.5%, which was significantly higher than those in CP (n = 15, 0%, P < 0.01) and CON (n = 25, 4.0%, P < 0.01). For PC diagnosis, MUC2 gene methylation in blood samples showed higher specificity and positive predictive value than CA 19-9. The combined detection in the feces and blood showed a 60% MUC2 methylation rate in PC (n = 10), which was higher than those in the CP (n = 5, 0%, P < 0.01) and CON (n = 12, 0%, P < 0.01).

CONCLUSIONS

The study can clearly indicate that combined detection of MUC2 gene methylation in the peripheral blood and feces could be used as a new screening and early diagnosis method for pancreatic cancer.

Dual-Signal Readout of DNA Methylation Status Based on the Assembly of a Supersandwich Electrochemical Biosensor without Enzymatic Reaction

A highly sensitive and selective biosensing system was designed to analyze DNA methylation using a dual-signal readout technique in combination with the signal amplification of supersandwich DNA structure. Through the ingenious design of target-triggered cascade of hybridization chain reaction, one target DNA could initiate the formation of supersandwich structure with multiple signal probes. As a result, one-to-multiple amplification effect was achieved, which conferred high sensitivity to target molecular recognition. Based on probe 1 labeled with ferrocene and probe 2 modified with methylene blue, the target DNA was clearly recognized by two electrochemical signals at independent potentials, which was helpful for the acquisition of more accurate detection results. Taking advantage of bisulfite conversion, the methylation status of cytosine (C) was changed to nucleic acid sequence status, which facilitated the hybridization-based detection without enzymatic reaction. Consequently, the methylated DNA was detected at the femtomolar level with satisfactory analytical parameters. The proposed system was effectively used to assess methylated DNA in human blood serum samples, illuminating the possibility of the sensing platform for applications in disease diagnosis and biochemistry research.

Energy transfer in liquid and solid nanoobjects: application in luminescent analysis

Radiationless resonance electronic excitation energy transfer (ET) is a fundamental physical phenomenon in luminescence spectroscopy playing an important role in natural processes, especially in photosynthesis and biochemistry. Besides, it is widely used in photooptics, optoelectronics, and protein chemistry, coordination chemistry of transition metals and lanthanides as well as in luminescent analysis. ET involves the transfer of electronic energy from a donor (D) (molecules or particles) which is initially excited, to an acceptor (A) at the ground state to emit it later. Fluorescence or phosphorescence of the acceptor that occurs during ET is known as sensitized. There do many kinds of ET exist but in all cases along with other factors the rate and efficiency of ET in common solvents depends to a large extent on the distance between the donor and the acceptor. This dependency greatly limits the efficiency of ET and, correspondingly, does not allow the determination of analytes in highly diluted (10–9–10–15 M) solutions. To solve the problem of distance-effect, the effects of concentrating and bring close together the donor and acceptor in surfactant micelles (liquid nanosystems) or sorption on solid nanoparticles are used. Various approaches to promote the efficiency of ET for improvement determination selectivity and sensitivity using liquid and solid nanoobjects is reviewed and analyzed.

DNA-Templated Silver Nanoclusters for DNA Methylation Detection

DNA methylation entails the covalent addition of a methyl group to C-5 position of cytosine by a family of DNA methyltransferase enzymes and has a significant role in gene regulation. Epigenetic changes such as DNA methylation of CpG islands located in the promoter region of some tumor suppressor genes are very common in human diseases such as cancer. Detection of aberrant methylation pattern could serve as an excellent diagnostic approach. It is key to develop methods for the direct and simple detection of methylated DNA or of methyltransferase activity without using antibodies, chemical modification, labeling and enzymatic treatments. In this study, we employ DNA-templated silver nanoclusters for detection of DNA methylation. This method entails use of cytosine rich DNA sequence as an effective template. By monitoring changes in fluorescence intensity, DNA methylation and DNA methyltransferase activity is detected. Upon DNA methylation, the fluorescence intensity of DNA templated Ag/NCs is decreased in a linear range when the concentration of methylated DNA is increased.

Sensitive detection of methylated DNA and methyltransferase activity based on the lighting up of FAM-labeled DNA quenched fluorescence by gold nanoparticles

DNA methylation of cytosine bases, which is catalyzed by methyltransferase enzymes, involve biochemical processes that contribute to gene expression and gene regulation in cells. Detection of abnormal patterns of both methylated DNA and methyltransferase enzyme activity at early stages could be considered as promising targets for early cancer diagnosis. In the present study, a novel and facile method is introduced for the sensitive detection of the M.SssI methyltransferase (M.SssI MTase) enzyme and methylated DNA based on the fluorescence recovery of FAM-labeled DNA coupled with gold nanoparticles (AuNPs). Thiol-modified probes were functionalized with AuNPs, which brought the FAM fluorophore into the close proximity of the AuNPs. This led to the overlap between the FAM fluorescence emission and AuNPs absorption spectra, introducing a FRET occurrence and causing fluorescence quenching. The hybridization of the probe and its complementary target provided specific CpG sites for M.SssI MTase enzyme activity. The methylation process gradually converted the quenched FAM fluorophore into an emissive fluorophore upon the addition of the MTase enzyme, and the observed fluorescence recovery proved the efficiency of the assay for the detection of MTase enzyme. The fluorescence intensity showed an increasing trend with M.SssI MTase enzyme activity in the range of 1–8 U mL⁻¹ with a detection limit of 0.14 U mL⁻¹. The addition of methylated ssDNA targets to a ssDNA FAM-labeled probe resulted in a DNA duplex formation, leading to a strong fluorescence signal emission due to the recovery of the fluorophore signal. Conversely, the unmethylated ssDNA target caused no changes in the fluorescence signal. In the presence of methylated DNA targets, the biosensor could specifically recognize it and accordingly trigger the methylated targets through a fluorescence enhancement in the range of 5–100 pM by monitoring the increase in the fluorescence intensity with a detection limit of 2.2 pM. The obtained results showed that the assay could realize the detection of M.SssI MTase and methylated DNA effectively in diluted human serum samples. Human serum conditions showed no significant interference with the assay performance, indicating that the present method has great potential for further application in real samples.

A novel method for detection of DNA methylation based on fluorescence recovery of FAM labeled DNA/Au NPs was introduced.

DNA methylation detection: recent developments in bisulfite free electrochemical and optical approaches

DNA methylation is one of the significant epigenetic modifications involved in mammalian development as well as in the initiation and progression of various diseases like cancer. Over the past few decades, an enormous amount of research has been carried out for the quantification of DNA methylation in the mammalian genome. Earlier, most of these methodologies used bisulfite treatment. However, the low conversion, false reading, longer assay time and complex chemical reaction are the common limitations of this method that hinder their application in routine clinical screening. Thus, as an alternative to bisulfite conversion-based DNA methylation detection, numerous bisulfite-free methods have been proposed. In this regard, electrochemical biosensors have gained much attention in recent years for being highly sensitive yet cost-effective, portable, and simple to operate. On the other hand, biosensors with optical readouts enable direct real time detection of biological molecules and are easily adaptable to multiplexing. Incorporation of electrochemical and optical readouts into bisulfite free DNA methylation analysis is paving the way for the translation of this important biomarker into standard patient care. In this review, we provide a critical overview of recent advances in the development of electrochemical and optical readout based bisulfite free DNA methylation assays.

Towards DNA methylation detection using biosensors

DNA methylation, a stable and heritable covalent modification which mostly occurs in the context of a CpG dinucleotide, has great potential as a biomarker to detect disease, provide prognoses and predict therapeutic responses. It can be detected in a quantitative manner by many different approaches both genome-wide and at specific gene loci, in various biological fluids such as urine, plasma, and serum, which can be obtained without invasive procedures. The current, classical methods are effective in studying DNA methylation patterns, however, for the most part; they have major drawbacks such as expensive instruments, complicated and time consuming protocols as well as relatively low sensitivity, and high false positive rates. To overcome these obstacles, great efforts have been made toward the development of reliable sensor devices to solve these limitations, providing sensitive, fast and cost-effective measurements. The use of biosensors for DNA methylation biomarkers has increased in recent years, because they are portable, simple, rapid, and inexpensive which offers a straightforward way to detect methylated biomarkers. In this review, we give an overview of the conventional techniques for the detection of DNA methylation and then will focus on recent advances in biosensor based methylation detection that eliminate bisulfite conversion and PCR amplification.

Colorimetric aptasensor for Campylobacter jejuni cells by exploiting the peroxidase like activity of Au@Pd nanoparticles

The authors describe a method for colorimetric determination of Campylobacter jejuni (C. jejuni) in milk samples. It is based on the interaction of a specific DNA aptamer with surface protein in the cell membranes of C. jejuni. Specific binding of the aptamer with the cell membrane leads to an uptake of aptamer from solution. As a result, the concentration of aptamer floating in the solution is reduced. In the presence of large quantities of aptamer, the surface of added Au@Pd nanoparticles (NPs) is covered with aptamer via electrostatic interactions. Hence, they cannot act as a peroxidase mimic and oxidize the substrate 3,3^',5,5^'-tetramethylbenzidine (TMB) to give a blue product. However, when the aptamer is bound by the target cells, the surface of the NPs is not blocked by aptamer and the NPs exert a strong peroxidase -like activity. Under defined experimental conditions, the intensity of the blue color increases with the concentration of C. jejuni, and as little as 100 CFU·mL^-1 can bedetected in milk. Graphical abstract A colorimetric aptasensor for assay Campylobacter jejuni whole cell in food samples was investigated. This assay was designed based on interaction of specific DNA aptamer with surface protein in c. jejuni cell membrane without any modification of aptamer.

Double signal enhancement strategy based on rolling circle amplification and photoinduced electron transfer for ultrasensitive fluorometric detection of methylated DNA

The authors describe a novel assay for the detection of methylated DNA site. Rolling circle amplification and CdSe/ZnS quantum dots with high fluorescence efficiency are applied in this method. The CdSe/ZnS quantum dots act as electron donors, and hemin and oxygen (derived from hydrogen peroxide act as acceptors in photoinduced electron transfer. The assay, best performed at excitation/emission peaks of 450/620 nm, is sensitive and specific. Fluorometric response is linear in the 1 pM to 100 nM DNA concentration range, and the lowest detectable concentration of methylated DNA is 142 fM (S/N = 3). The method is capable of recognizing 0.01% methylated DNA in a mixture of methylated/unmethylated DNA. Graphical abstract A novel method for methylated sites detection in DNA is established. Rolling circle amplification and photoinduced electron transfer. CdSe/ZnS quantum dots with high fluorescence efficiency act as the electron donor, while G-quadruplex/hemin and hydrogen peroxide derived oxygen act as electron acceptor. It presents a linear response towards 1 pM to 100 nM methylated DNA with a correlation coefficient of 0.9968, and the lowest detectable concentration of methylated DNA was 142 fM, with selectivity significantly superior to other methods.

Naked-eye detection of potassium ions in a novel gold nanoparticle aggregation-based aptasensor

In this work, we studied the feasibility of interaction among gold nanoparticles (AuNPs) and a cationic dye in an aptasensor system for the detection of potassium ions. The presence and absence of potassium in the solution was distinguishable by different colors (between orange and green) appeared after reaction. Cationic dye (Y5GL) acts as a new aggregator for AuNP-based sensors which changes the aggregated AuNP solution color from blue-purple to green. In the presence of K⁺ ions, the aptamer dissociated from the surface of the AuNP so that free AuNPs and cationic dye make the solution green. The aptasensor showed that the analytical linear range was from 10 nM to 50 mM and the detection limit was 4.4 nM. Also, we examined the practicality of this method on a simple paper based platform. The linear range of the colorimetric paper sensor covered of K⁺ concentration from 10 μM to 40 mM and the detection limit of 6.2 μM was obtained. The selectivity of AuNP aggregation-based sensor improved by the use of cationic dye. Rapidity, simplicity, high sensitivity and excellent selectivity made this assay suitable for practical determination of K⁺ in real urine samples.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

An approach toward miRNA detection via different thermo-responsive aggregation/disaggregation of CdTe quantum dots

A novel and “light shift” spectral method for the detection of miRNA based on different thermal-responsive aggregation/disaggregation of CdTe quantum dots was investigated.

Metallic Nanoclusters for Cancer Imaging and Therapy

BACKGROUND

Nanoclusters are made of a few to tens of atoms with a size below 2 nm. Compared with nanoparticles, they exhibited excellent properties, such as tunable fluorescence, ease of conjugation, high quantum yield and biocompatibility, which are highly desired in the development of cancer nanotheranostics. Hence, the metallic nanoclusters have emerged as a newcomer in cancer nanomedicines. This review aims to summarize recently developed approaches to preparing metallic nanoclusters, highlight their applications in cancer theranostics, and provide a brief outlook for the future developments of nanoclusters in nanomedicine.

METHOD

We carried out a thorough literature search using online databases. The search was focused on a centered question. Irrelevant articles were excluded after further examination and directly relevant articles were included. The relevant articles were classified by the subjects and the information from these articles was synthesized.

RESULTS

One hundred and forty-three articles were included in this review. About eighty articles outlined the development in the synthetic methods of nanoclusters. The synthesis approaches include chemical reduction, photoreduction and so on. The progress in the application of gold and silver nanoclusters to cancer theranostics was described in fifteen and eight articles, respectively. The rest articles were about the advancements in the use of other metal nanoclusters and nanocluster nanocomposites as cancer theranostic agents.

CONCLUSION

This review summarizes the synthesis and use of metallic nanoclusters or their nanocomposites as cancer theranostic agents. It confirms their importance, advantages and potentials in serving as a new generation of cancer theranostics in clinics.

Detection of large deletion in human BRCA1 gene in human breast carcinoma MCF-7 cells by using DNA-Silver Nanoclusters

Here we describe a label-free detection strategy for large deletion mutation in breast cancer (BC) related gene BRCA1 based on a DNA-silver nanocluster (NC) fluorescence upon recognition-induced hybridization. The specific hybridization of DNA templated silver NCs fluorescent probe to target DNAs can act as effective templates for enhancement of AgNCs fluorescence, which can be used to distinguish the deletion of BRCA1 due to different fluorescence intensities. Under the optimal conditions, the fluorescence intensity of the DNA-AgNCs at emission peaks around 440 nm (upon excitation at 350 nm) increased with the increasing deletion type within a dynamic range from 1.0 × 10^-10 to 2.4 × 10^-6 M with a detection limit (LOD) of 6.4 × 10^-11 M. In this sensing system, the normal type shows no significant fluorescence; on the other hand, the deletion type emits higher fluorescence than normal type. Using this nanobiosensor, we successfully determined mutation using the non-amplified genomic DNAs that were isolated from the BC cell line.

Silver Nanocluster-Embedded Zein Films as Antimicrobial Coating Materials for Food Packaging

Highly efficient antimicrobial agents with low toxicity and resistance have been enthusiastically pursued to address public concerns on microbial contamination in food. Silver nanoclusters (AgNCs) are known for their ultrasmall sizes and unique optical and chemical properties. Despite extensive studies of AgNCs for biomedical applications, previous research on their application as antimicrobials for food applications is very limited. Here, for the first time, by incorporating AgNCs (∼2 nm in diameter) into zein films that are widely used as food packaging materials, we developed a novel coating material with potent antimicrobial activity, low toxicity to human cells, and low potential to harm the environment. In addition, we systematically evaluated the antimicrobial activities and cytotoxicity of AgNCs-embedded zein films and compared them to zein films embedded with AgNO₃ or Ag nanoparticles with diameters of 10 and 60 nm (AgNP10 and AgNP60, respectively). At equivalent silver concentrations, AgNCs and AgNO₃ solutions exhibited considerably higher antimicrobial activities than those of AgNP10 and AgNP60 solutions. Moreover, AgNCs exhibited less cytotoxicity to human cells than AgNO₃, with a half maximal inhibitory concentration (IC₅₀) of 34.68 μg/mL for AgNCs, compared to 9.14 μg/mL for AgNO₃. Overall, the novel AgNCs coating developed in this research has great potential for antimicrobial applications in food packaging materials due to its high antimicrobial efficacy, ultrasmall size, and low cytotoxicity.

Current trends in electrochemical sensing and biosensing of DNA methylation

DNA methylation plays an important role in physiological and pathological processes. Several genetic diseases and most malignancies tend to be associated with aberrant DNA methylation. Among other analytical methods, electrochemical approaches have been successfully employed for characterisation of DNA methylation patterns that are essential for the diagnosis and treatment of particular diseases. This article discusses current trends in the electrochemical sensing and biosensing of DNA methylation. Particularly, it provides an overview of applied electrode materials, electrode modifications and biorecognition elements applications with an emphasis on strategies that form the core DNA methylation detection approaches. The three main strategies as (i) bisulfite treatment, (ii) cleavage by restriction endonucleases, and (iii) immuno/affinity reaction were described in greater detail. Additionally, the availability of the reviewed platforms for early cancer diagnosis and the approval of methylation inhibitors for anticancer therapy were discussed.