A carbon nanoparticle-based low-background biosensing platform for sensitive and label-free fluorescent assay of DNA methylation

Vertical Flow Immunoassay Based on Carbon Black Nanoparticles for the Detection of IgG against SARS-CoV-2 Spike Protein in Human Serum: Proof-of-Concept

Point-of-care tests play an important role in serological diagnostics of infectious diseases and post-vaccination immunity monitoring, including in COVID-19. Currently, lateral flow tests dominate in this area and show good analytical performance. However, studies to improve the effectiveness of such tests remain important. In comparison with lateral flow tests, vertical flow immunoassays allow for a reduction in assay duration and the influence of the hook effect. Additionally, the use of carbon black nanoparticles (CNPs) as a color label can provide a lower detection limit (LOD) compared to conventional colloidal gold. Therefore, we have developed a vertical flow immunoassay for the detection of IgG against SARS-CoV-2 spike protein in human serum samples by applying a conjugate of CNPs with anti-human IgG mouse monoclonal antibodies (CNP@MAb). The vertical flow assay device consists of a plastic cassette with a hole on its top containing a nitrocellulose membrane coated with spike protein and an absorbent pad. The serum sample, washing buffer, and CNP@MAb flow vertically through the nitrocellulose membrane and absorbent pads, reducing assay time and simplifying the procedure. In positive samples, the interaction of CNP@MAb with anti-spike antibodies leads to the appearance of black spots, which can be visually detected. The developed method allows for rapid visual detection (5-7 min) of IgG vs. spike protein, with a LOD of 7.81 BAU/mL. It has been shown that an untrained operator can perform the assay and visually evaluate its results. Thus, the presented assay can be used in the further development of test systems for the serological diagnostics of COVID-19 or post-vaccination immunity monitoring.

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.

Ultrasensitive Label-Free DNA Detection Based on Solution-Gated Graphene Transistors Functionalized with Carbon Quantum Dots

Developing highly sensitive, reliable, cost-effective label-free DNA biosensors is challenging with traditional fluorescence, electrochemical, and other techniques. Most conventional methods require labeling fluorescence, enzymes, or other complex modification. Herein, we fabricate carbon quantum dot (CQD)-functionalized solution-gated graphene transistors for highly sensitive label-free DNA detection. The CQDs are immobilized on the surface of the gate electrode through mercaptoacetic acid with the thiol group. A single-stranded DNA (ssDNA) probe is immobilized on CQDs by strong π-π interactions. The ssDNA probe can hybridize with the ssDNA target and form double-stranded DNA, which led to a shift of Dirac voltage and the channel current response. The limit of detection can reach 1 aM which is 2-5 orders of magnitude lower than those of other methods reported previously. The sensor also exhibits a good linear range from 1 aM to 0.1 nM and has good specificity. It can effectively distinguish one-base mismatched target DNA. The response time is about 326 s for the 1 aM target DNA molecules. This work provides good perspectives on the applications in biosensors.

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.

In Situ Electrical Monitoring of Methylated DNA Based on Its Conformational Change to G-Quadruplex Using a Solution-Gated Field-Effect Transistor

Methylated DNA is not only a diagnostic but also a prognostic biomarker for early-stage cancer. However, sodium bisulfite sequencing as a "gold standard" method for detection of methylation markers has some drawbacks such as its time-consuming and labor-intensive procedures. Therefore, simple and reliable methods are required to analyze DNA sequences with or without methylated residues. Herein, we propose a simple and direct method for detecting DNA methylation through its conformation transition to G-quadruplex using a solution-gated field-effect transistor (SG-FET) without using labeled materials. The BCL-2 gene, which is involved in the development of various human tumors, contains G-rich segments and undergoes a conformational change to G-quadruplex depending on the K⁺ concentration. Stacked G-quadruplex strands move close to the SG-FET sensor surface, resulting in large electrical signals based on intrinsic molecular charges. In addition, a dense hydrophilic polymer brush is grafted using surface-initiated atom transfer radical polymerization onto the SG-FET sensor surface to reduce electrical noise based on nonspecific adsorption of interfering species. In particular, control of the polymer brush thickness induces electrical signals based on DNA molecular charges in the diffusion layer, according to the Debye length limit. A platform based on the SG-FET sensor with a well-defined polymer brush is suitable for in situ monitoring of methylated DNA and realizes a point-of-care device with a high signal-to-noise ratio and without the requirement for additional processes such as bisulfite conversion and polymerase chain reaction.

Förster Resonance Energy Transfer from Carbon Nanoparticles to a DNA-Bound Compound: A Method to Detect the Nature of Binding

A drug molecule can bind in various orientations to a DNA strand. Nature of the binding decides the functionality and efficacy of the drug. To innovate a new method to detect the nature of binding of a drug to DNA strands, herein we have used the dipole-dipole interaction driven Förster resonance energy transfer (FRET) between carbon nanoparticles (CNPs) and a DNA-bound small molecule, (E)-3-ethyl-2-(4-(pyrrolidin-1-yl)styryl)benzo[d]thiazol-3-ium (EPSBT), which belongs to the hemicyanine family and binds typically to the minor groove of a DNA duplex. EPSBT was designed to obtain appreciable fluorescence quantum yield, which constructed an efficient FRET pair with the synthesized CNPs. The tested compound prefers the thymine nucleobase to bind to the DNA strand. Orientation of its dipole on attachment to the DNA strand and the donor-acceptor distance dictate the FRET efficiency with the CNPs. The results provided a precise estimation of the nature of binding of EPSBT to the DNA backbone and, hence, supposedly will help in deciding the functional efficacy.

Fullerenol as a photoelectrochemical nanoprobe for discrimination and ultrasensitive detection of amplification-free single-stranded DNA

Traditional approaches for nucleic acids detection require prior amplification of target genes, while nanomaterials-aided DNA biosensors are very magnificent but still suffer from the nanomaterial acquirement and limited sensitivity (above picomolar level). Herein, fullerenol C60(OH)25, a representative fullerene derivative, was employed as a photoelectrochemical (PEC) nanoprobe to achieve discrimination and ultrasensitive detection of amplification-free single-stranded DNA (ssDNA) down to sub-femtomolar level. The bonded hydroxyl groups with intense density endowed fullerenol to directly recognize and capture ssDNA-AuNPs via the hydrogen bonding interactions (H-bonds), leading to a sharply decreased photocurrent with quenching efficiency up to 85%, which could be attributed to the photo-generated electrons on the conduction band of fullerenol (-4.66 eV) preferentially migrating to the Fermi level of AuNPs (-5.1 eV) rather than the electrode. In the presence of target gene (mutant human p53 gene fragment), the H-bonds between fullerenol and ssDNA were competitively depleted during the base pairing process of complete hybridization between ssDNA and target, making double-stranded DNA-AuNPs (dsDNA-AuNPs) depart so that the photocurrent powerfully recovered. On basis of the photocurrent variation before and after target introduction, this proposed simple, rapid and ultrasensitive PEC biosensor for amplification-free target gene detection illustrated a wide liner ranged from 1 fM to 100 pM and a detection limit of 0.338 fM. This work presented an ingenious strategy for the discrimination and ultrasensitive detection of nucleic acids, and the well-designed PEC biosensor was further conducive to the impetus of clinic diagnostics.

Immuno-HCR based on contact quenching and fluorescence resonance energy transfer for sensitive and low background detection of Escherichia coli O157:H7

Escherichia coli O157:H7 makes a major threat to human health. Aiming to detect Escherichia coli O157:H7 sensitively, hybridization chain reaction signal amplified immunoassay (immuno-HCR) based on contact quenching (CQ) and fluorescence resonance energy transfer (FRET) was developed. The background of the new designed HCR hairpins (CQ-FRET hairpins) was reduced by contact-quenching fluorescein (FAM) and breaking FRET from donor (FAM) to acceptor (Cy5). The F/F₀ ratio of CQ-FRET hairpins (37.02) was obviously higher than that of two other common HCR fluorescent hairpins (CQ hairpins, 21.45; FRET hairpins, 4.61). The limit of detection of the assay was 3.5 × 10¹ CFU/mL and obviously lower than that of CQ hairpins based immuno-HCR (3.28 × 10³ CFU/mL) and FRET hairpins based immuno-HCR (6.49 × 10⁴ CFU/mL). The proposed low fluorescent background immuno-HCR with high sensitivity which was verified in contaminated milk samples could be potentially used in the detection of various pathogens.

Meso-tetra(4-carboxyphenyl)porphine-Enhanced DNA Methylation Sensing Interface on a Light-Addressable Potentiometric Sensor

DNA methylation (DNAm) sensors are an emerging branch in the discipline of sensors. It is believed to be able to promote the next generation of epigenetics-based diagnostic technology. Differing from the traditional biochemical sensors that aimed at individual molecules, the challenge in DNAm sensors is how to determine the amount of 5-methylcytosine (5mC) in a continuous nucleotide sequence. Here, we report a comparative study about meso-tetra(4-carboxyphenyl)porphine (TCPP)-based DNAm sensing interfaces on a light-addressable potentiometric sensor (LAPS), depending on TCPP's postures that are flat in the π-conjugated TCPP layer on reduced-graphene-oxide-decorated LAPS (#1) and stand-up in the covalently anchored TCPP on glutaraldehyde (GA)-treated LAPS (#2), along with the blank one (only GA-treated LAPS, #3). These DNAm sensing interfaces are also distinct from the traditional biosensing interface on LAPS, that is: it is not functionalized by the sensing indicator (5mC antibody, in this case) but by the target nucleotide sequence. The surface characterization techniques such as Raman spectra, scanning electron microscopy, and X-ray photoelectron spectroscopy are conducted to prove the decorations, as well as the anchored nucleotides. It is found that, though all of them can detect as low as one 5mC in the target sequence, the enhanced DNAm sensitivity is obtained by #2, which is evidenced by the higher output-voltage changing ratio for the 5mC site of #2 than those of #1 and #3. Furthermore, the underlying causes for the improved sensitivity in #2 are proposed, according to the conformational and electronic properties of TCPP molecules. Conclusively, TCPP's synergetic function, including the molecular configuration and the activate (carboxyl) groups on its peripheral substituents, to improve the DNAm sensing interface on LAPS is investigated and demonstrated. This can shed light on a new approach for DNA methylation detection, with the merits of low cost, independence on bisulfite conversion, and polymerase chain reaction.

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.

Transition Metal Dichalcogenide Nanosheets for Visual Monitoring PCR Rivaling a Real-Time PCR Instrument

Monitoring the progress of polymerase chain reactions (PCRs) is of critical importance in bioanalytical chemistry and molecular biology. Although real-time PCR thermocyclers are ideal for this purpose, their high cost has limited their applications in resource-poor areas. Direct visual detection would be a more attractive alternative. To monitor the PCR amplification, DNA-staining dyes, such as SYBR Green I (SG), are often used. Although these dyes give higher fluorescence when binding to double-stranded DNA products, they also yield strong background fluorescence in the presence of a high concentration of single-stranded (ss) DNA primers. In this work, we screened various nanomaterials and found that graphene oxide (GO), reduced GO, molybdenum disulfide (MoS₂), and tungsten disulfide (WS₂) can quench the fluorescence of nonamplified negative samples while still retaining strong fluorescence of positive ones. The signal ratio of positive-over-negative samples was enhanced by around 50-fold in the presence of these materials. In particular, MoS₂ and WS₂ nearly fully retained the fluorescence of the positive samples. The mechanism for MoS₂ and WS₂ to enhance PCR signaling is attributed to the adsorption of both the ssDNA PCR primers and SG with an appropriate strength. MoS₂ can also suppress nonspecific amplification caused by excess polymerase. Finally, this method was used to detect extracted transgenic soya GTS 40-3-2 DNA after PCR amplification. Compared with the samples without nanomaterials, the addition of MoS₂ could better distinguish the concentration difference of the template DNA, and the sensitivity of visual detection rivaled that from a real-time PCR instrument.

Highly efficient electrochemical sensing platform for sensitive detection DNA methylation, and methyltransferase activity based on Ag NPs decorated carbon nanocubes

In this paper, we reported a sensitive and selective electrochemical method for quantify DNA methylation, analyzing DNA MTase activity and screening of MTase inhibitor based on silver nanoparticles (Ag NPs) decorated carbon nanocubes (CNCs) as signal tag. The Ag NPs/CNCs was prepared by in situ growth of nanosilver on carboxylated CNCs and used as a tracing tag to label antibody. The sensor was prepared by immobilizing the double DNA helix structure on the surface of gold electrode. When DNA MTase was introduced, the probe was methylated. Successively, anti-5-methylcytosine antibody labeled Ag NPs/CNCs was specifically conjugated on the CpG methylation site. The electrochemical stripping signal of the Ag NPs was used to monitor the activity of MTase. The electrochemical signal has a linear relationship with M.SssI activities ranging from 0.05 to 120U/mL with a detection limit of 0.03U/mL. In addition, we also demonstrated the method could be used for rapid evaluation and screening of the inhibitors of MTase. The newly designed strategy avoid the requirement of deoxygenation for electrochemical assay, and thus provide a promising potential in clinical application.

Utilizing Gold Nanoparticle Probes to Visually Detect DNA Methylation

The surface plasmon resonance (SPR) effect endows gold nanoparticles (GNPs) with the ability to visualize biomolecules. In the present study, we designed and constructed a GNP probe to allow the semi-quantitative analysis of methylated tumor suppressor genes in cultured cells. To construct the probe, the GNP surfaces were coated with single-stranded DNA (ssDNA) by forming Au-S bonds. The ssDNA contains a thiolated 5'-end, a regulatory domain of 12 adenine nucleotides, and a functional domain with absolute pairing with methylated p16 sequence (Met-p16). The probe, paired with Met-p16, clearly changed the color of aggregating GNPs probe in 5 mol/L NaCl solution. Utilizing the probe, p16 gene methylation in HCT116 cells was semi-quantified. Further, the methylation of E-cadherin, p15, and p16 gene in Caco2, HepG2, and HCT116 cell lines were detected by the corresponding probes, constructed with three domains. This simple and cost-effective method was useful for the diagnosis of DNA methylation-related diseases.

Carbon Nanomaterials and DNA: from Molecular Recognition to Applications

DNA is polymorphic. Increasing evidence has indicated that many biologically important processes are related to DNA's conformational transition and assembly states. In particular, noncanonical DNA structures, such as the right-handed A-form, the left-handed Z-form, the triplex, the G-quadruplex, the i-motif, and so forth, have been specific targets for the diagnosis and therapy of human diseases. Meanwhile, they have been widely used in the construction of smart DNA nanomaterials and nanoarchitectures. As rising stars in materials science, the family of carbon nanomaterials (CNMs), including two-dimensional graphene, one-dimensional carbon nanotubes (CNTs), and zero-dimensional graphene or carbon quantum dots (GQDs or CQDs), interact with DNA and are able to regulate the conformational transitions of DNA. The interaction of DNA with CNMs not only opens new opportunities for specific molecular recognition, but it also expands the promising applications of CNMs from materials science to biotechnology and biomedicine. In this Account, we focus on our contributions to the field of interactions between CNMs and DNA in which we have explored their promising applications in nanodevices, sensing, materials synthesis, and biomedicine. For one-dimensional CNTs, two-dimensional graphene, and zero-dimensional GQDs and CQDs, the basic principles, binding modes, and applications of the interactions between CNMs and DNA are reviewed. We aim to give prominence to the important status of CNMs in the field of molecular recognition for DNA. First, we summarized our discovery of the interactions between single-walled carbon nanotubes (SWNTs) with duplex, triplex, and human telomeric i-motif DNA and their interesting applications. For example, SWNTs are the first chemical agents that can selectively stabilize human telomeric i-motif DNA and induce its formation under physiological conditions. On the basis of this principle, two types of nanodevices were designed. One was used for highly sensitive detection of ppm levels of SWNTs in cells, and the other monitored i-motif DNA formation. Further studies indicated that SWNTs could inhibit telomerase activity in living cells and cause telomere dysfunction, providing new insight into the biological effects of SWNTs. Then, some applications that are based on the interactions between graphene and DNA are also summarized. Combined with other nanomaterials, such as metal and upconversion nanoparticles, several hybrid nanomaterials were successfully constructed, and a series of DNA logic gates were successfully developed. Afterwards, the newcomer of the carbon nanomaterials family, carbon quantum dots (CQDs), were found to be capable of modulating right-handed B-form DNA to left-handed Z-form DNA. These were further used to design FRET logic gates that were based on the CQD-derived DNA conformational transition. Taking into account the remaining challenges and promising aspects, CNM-based DNA nanotechnology and its biomedical applications will attract more attention and produce new breakthroughs in the near future.

Green synthesis of fluorescence carbon nanoparticles from yum and application in sensitive and selective detection of ATP

Fluorescent carbon nanoparticles (CPs), a fascinating class of recently discovered nanocarbons, have been widely known as some of the most promising sensing probes in biological or chemical analysis. In this study, we demonstrate a green synthetic methodology for generating water-soluble CPs with a quantum yield of approximately 24% via a simple heating process using yum mucilage as a carbon source. The prepared carbon nanoparticles with an ~10 nm size possessed excellent fluorescence properties, and the fluorescence of the CPs was strongly quenched by Fe(3+), and recovered by adenosine triphosphate (ATP), thus, an 'off' and 'on' system can be easily established. This 'CPs-Fe(3+)-ATP' strategy was sensitive and selective at detecting ATP with the linear range of 0.5 µmol L(-1) to 50 µmol L(-1) and with a detection limit of 0.48 µmol L(-1).

Carbon nanoparticle-protected aptamers for highly sensitive and selective detection of biomolecules based on nuclease-assisted target recycling signal amplification

Based on the protective properties of carbon nanoparticles for aptamers against the digestion of nuclease, we have developed a nuclease-assisted target recycling signal amplification method for highly sensitive detection of biomolecules, such as ATP and kanamycin. The high binding specificity between aptamers and targets leads to excellent selectivity of the assay.

A label free fluorescent assay for uracil-DNA glycosylase activity based on the signal amplification of exonuclease I

A label free fluorescent assay for uracil-DNA glycosylase activity was developed based on the signal amplification of exonuclease I.

Polydopamine-embedded Cu2−xSe nanoparticles as a sensitive biosensing platform through the coupling of nanometal surface energy transfer and photo-induced electron transfer

This study innovatively highlights the mechanistic details of NSET and PET (NSET©PET) coupling processes, and the disclosed mechanism provides new opportunities for sensitive biosensing applications.

MoS2nanosheets as an effective fluorescence quencher for DNA methyltransferase activity detection

A fluorometric DNA methyltransferase activity assay is described. MoS₂nanosheets are employed as the fluorescence quencherviavan der Waals interactions with fluorophore labeled substrate DNA.

A sensitive strategy for the fluorescence detection of DNA methyltransferase activity based on the graphene oxide platform and T7 exonuclease-assisted cyclic signal amplification

A sensitive fluorescence detection method for DNA methyltransferase is developed based on graphene oxide and T7 exonuclease-assisted signal amplification.

Magnetic nanoparticles-cooperated fluorescence sensor for sensitive and accurate detection of DNA methyltransferase activity coupled with exonuclease III-assisted target recycling

A magnetic nanoparticles-cooperated fluorescence sensor for DNA methyltransferase activity was developed by coupling with exonuclease III-assisted target recycling.

The determination of DNA methyltransferase activity by quenching of tris(2,2′-bipyridine)ruthenium electrogenerated chemiluminescence with ferrocene

An electrogenerated chemiluminescence biosensing method for the determination of DNA methyltransferase activity is developed by the quenching of tris(2,2′-bipyridine)ruthenium ECL by ferrocene.

Label-free molecular beacon-based quadratic isothermal exponential amplification: a simple and sensitive one-pot method to detect DNA methyltransferase activity

An illustration of the label-free molecular beacon-mediated quadratic isothermal exponential amplification strategy (LFMB-QIEA) for target Dam MTase detection.

A recyclable carbon nanoparticle-based fluorescent probe for highly selective and sensitive detection of mercapto biomolecules

Hg²⁺quenched CNPs (CNP-Hg²⁺) as a highly sensitive and selective reversible probe for the detection of mercapto biomolecules in aqueous solutions and in living cells.

DNA methylation detection with end-to-end nanorod assembly-enhanced surface plasmon resonance

The Au nanorod (AuNR) assembly-enhanced SPR system coupling with polymerization and nicking reactions was developed for amplified detection of DNA methylation and Dam MTase activity assay.

Carbon nanoparticle-based ratiometric fluorescent sensor for detecting mercury ions in aqueous media and living cells

A novel nanohybrid ratiometric fluorescence sensor is developed for selective detection of mercuric ions (Hg(2+)), and the application has been successfully demonstrated in HEPES buffer solution, lake water, and living cells. The sensor comprises water-soluble fluorescent carbon nanoparticles (CNPs) and Rhodamine B (RhB) and exhibits their corresponding dual emissions peaked at 437 and 575 nm, respectively, under a single excitation wavelength (350 nm). The photoluminescence of the CNPs in the nanohybrid system can be completely quenched by Hg(2+) through effective electron or energy transfer process due to synergetic strong electrostatic interaction and metal-ligand coordination between the surface functional group of CNPs and Hg(2+), while that of the RhB remains constant. This results in an obviously distinguishable fluorescence color variation (from violet to orange) of the nanohybrid solution. This novel sensor can effectively identify Hg(2+) from other metal ions with relatively low background interference even in a complex system such as lake water. The detection limit of this method is as low as 42 nM. Furthermore, the sensing technique is applicable to detect Hg(2+) in living cells.

Highly sensitive fluorescence assay of DNA methyltransferase activity by methylation-sensitive cleavage-based primer generation exponential isothermal amplification-induced G-quadruplex formation

Site-specific identification of DNA methylation and assay of MTase activity are imperative for determining specific cancer types, provide insights into the mechanism of gene repression, and develop novel drugs to treat methylation-related diseases. Herein, we developed a highly sensitive fluorescence assay of DNA methyltransferase by methylation-sensitive cleavage-based primer generation exponential isothermal amplification (PG-EXPA) coupled with supramolecular fluorescent Zinc(II)-protoporphyrin IX (ZnPPIX)/G-quadruplex. In the presence of DNA adenine methylation (Dam) MTase, the methylation-responsive sequence of hairpin probe is methylated and cleaved by the methylation-sensitive restriction endonuclease Dpn I. The cleaved hairpin probe then functions as a signal primer to initiate the exponential isothermal amplification reaction (EXPAR) by hybridizing with a unimolecular DNA containing three functional domains as the amplification template, producing a large number of G-quadruplex nanostructures by utilizing polymerases and nicking enzymes as mechanical activators. The G-quadruplex nanostructures act as host for ZnPPIX that lead to supramolecular complexes ZnPPIX/G-quadruplex, which provides optical labels for amplified fluorescence detection of Dam MTase. While in the absence of Dam MTase, neither methylation/cleavage nor PG-EXPA reaction can be initiated and no fluorescence signal is observed. The proposed method exhibits a wide dynamic range from 0.0002 to 20U/mL and an extremely low detection limit of 8.6×10(-5)U/mL, which is superior to most conventional approaches for the MTase assay. Owing to the specific site recognition of MTase toward its substrate, the proposed sensing system was able to readily discriminate Dam MTase from other MTase such as M.SssI and even detect the target in a complex biological matrix. Furthermore, the application of the proposed sensing strategy for screening Dam MTase inhibitors was also demonstrated with satisfactory results. This novel method not only provides a promising platform for monitoring activity and inhibition of DNA MTases, but also shows great potentials in biological process researches, drugs discovery and clinical diagnostics.