Highly Sensitive and Quality Self-Testable Electrochemiluminescence Assay of DNA Methyltransferase Activity Using Multifunctional Sandwich-Assembled Carbon Nitride Nanosheets

Importance of DNA nanotechnology for DNA methyltransferases in biosensing assays

DNA methylation is the process by which specific bases on a DNA sequence acquire methyl groups under the catalytic action of DNA methyltransferases (DNMT). Abnormal changes in the function of DNMT are important markers for cancers and other diseases; therefore, the detection of DNMT and the selection of its inhibitors are critical to biomedical research and clinical practice. DNA molecules can undergo intermolecular assembly to produce functional aggregates because of their inherently stable physical and chemical properties and unique structures. Conventional DNMT detection methods are cumbersome and complicated processes; therefore, it is necessary to develop biosensing technology based on the assembly of DNA nanostructures to achieve rapid analysis, simple operation, and high sensitivity. The design of the relevant program has been employed in life science, anticancer drug screening, and clinical diagnostics. In this review, we explore how DNA assembly, including 2D techniques like hybridization chain reaction (HCR), rolling circle amplification (RCA), catalytic hairpin assembly (CHA), and exponential isothermal amplified strand displacement reaction (EXPAR), as well as 3D structures such as DNA tetrahedra, G-quadruplexes, DNA hydrogels, and DNA origami, enhances DNMT detection. We highlight the benefits of these DNA nanostructure-based biosensing technologies for clinical use and critically examine the challenges of standardizing these methods. We aim to provide reference values for the application of these techniques in DNMT analysis and early cancer diagnosis and treatment, and to alert researchers to challenges in clinical application.

Ultrasensitive fluorescence detection of multiple DNA methyltransferases based on DNA walkers and hyperbranched rolling circle amplification

The accurate and ultrasensitive detection of multiple methyltransferases was in great request for clinical diagnosis and epigenetic therapy. Here, a novel fluorescence assay was proposed for ultrasensitive CpG methyltransferase (M.SssI) and DNA adenine methyltransferase (Dam) activity detection based on hyperbranched rolling circle amplification (HRCA) and DNA walkers. The biosensor showed an extremely high sensitivity due to the dual-amplification strategy of HRCA and DNA walker. The LOD of the biosensor for M.SssI and Dam methyltransferase was estimated at 0.0004 U/mL and 0.001 U/mL, respectively. Without the presence of M.SssI methyltransferase, the corresponding recognition site of hairpin H_M was cleaved by HpaII endonuclease, generating a DNA fragment (T-DNA) and inducing the DNA walker-HRCA reaction. Since the HRCA products contained numerous double-strand DNA (dsDNA), SYBR Green I could be embedded in the dsDNA, leading to a high fluorescent signal. In the presence of M.SssI methyltransferase, the corresponding recognition site of hairpin H_M was methylated and the HpaII endonuclease-catalyzed stem of hairpin H_M dissociation was hindered, leading to no DNA fragment (T-DNA) present. Hence, the DNA walker-HRCA reaction was not initiated and the fluorescent signal of SYBR Green I remained at a low level. Similarly, DNA adenine methyltransferase (Dam) and its inhibitors could also be detected by redesigning hairpin H_D with the Dam recognition sequences. Furthermore, the sensing system was applied to analyze the endogenic Dam methyltransferase in the real samples such as E. coli cell lysate.

Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria

Epigenetics modulates expression levels of various important genes in both prokaryotes and eukaryotes. These epigenetic traits are heritable without any change in genetic DNA sequences. DNA methylation is a universal mechanism of epigenetic regulation in all kingdoms of life. In bacteria, DNA methylation is the main form of epigenetic regulation and plays important roles in affecting clinically relevant phenotypes, such as virulence, host colonization, sporulation, biofilm formation et al. In this review, we survey bacterial epigenomic studies and focus on the recent developments in the structure, function, and mechanism of several highly conserved bacterial DNA methylases. These methyltransferases are relatively common in bacteria and participate in the regulation of gene expression and chromosomal DNA replication and repair control. Recent advances in sequencing techniques capable of detecting methylation signals have enabled the characterization of genome-wide epigenetic regulation. With their involvement in critical cellular processes, these highly conserved DNA methyltransferases may emerge as promising targets for developing novel epigenetic inhibitors for biomedical applications.

Construction of an ECL Detection Platform for Sensitive Detection of Carbaryl Based on an Eu3+-Functionalized Metal–Organic Framework Encapsulated with Nanogold

In this work, an Eu3+-MOF-253@Au electrochemiluminescence sensor was successfully constructed for the first time by encapsulating nanogold in the metal–organic frameworks (MOFs) backbone and pore channels, and assembling Eu3+ on the MOF backbone. Firstly, the introduction of nanogold overcomes the weakness of MOFs, which was difficult to achieve, and enhances its catalytic performance, followed by the modification of Eu3+ to confer the electrochemiluminescence performance and the function of target detection on the sensor. Moreover, carbaryl was placed in an alkaline working solution to enhance the intensity of electrochemiluminescence signal, as well as to promote the hydrolysis of carbaryl into 1-naphthol, which caused the burst of Eu3+-MOF-253@Au electrochemiluminescence sensor, thereby achieving the sensitive detection of carbaryl. On this basis, the electrochemiluminescence detection conditions were optimized, the performance was analyzed, and finally it was successfully used for the detection of carbaryl with good linearity in the range of 0.2–200 μg L−1 and a low detection limit (0.14 μg L−1).

A dual-mechanism-driven electrochemiluminescence aptasensor for sensitive detection of β-amyloid peptides

β-Amyloid (Aβ) peptides can bind both Cu²⁺ and heme cofactors simultaneously to form heme-Cu²⁺-Aβ complexes, which are proposed to generate toxic partially reduced oxygen species (PROS, e.g., H₂O₂) and play a vital role in Alzheimer's disease (AD). In this paper, a competitive dual-mechanism-driven electrochemiluminescence (ECL) aptasensor integrating the synergistic enhancement and steric hindrance effect was described for Aβ detection. Specifically, graphite carbon nitride (g-C₃N₄) as an effective ECL luminescent substrate and Au nanoparticles were sequentially assembled on the Au electrode surface, and then a thiol-modified aptamer for capturing Aβ peptide was attached to the surface of the electrode through the Au-S bond. Aβ peptides were simultaneously incubated with heme and Cu²⁺, and the forming heme-Cu²⁺-Aβ complexes were subsequently anchored on the electrode through the specific recognition between the target Aβ and the aptamer. When the concentration of the target Aβ is low, the synergistic enhancement effect arising from K₂S₂O₈ with in situ generated H₂O₂ is predominant, resulting in an increase in the ECL signal of g-C₃N₄. In contrast, when the concentration of Aβ is high, the steric hindrance effect generated from heme-Cu²⁺-Aβ complexes is dominant, leading to a decrease in the ECL signal. The present sensor exhibits a favorable linear response for the detection of Aβ with a relatively low detection limit of 0.24 pM, and provides a more sensitive and selective platform for bioanalysis.

An Isothermal Autocatalytic Hybridization Reaction Circuit for Sensitive Detection of DNA Methyltransferase and Inhibitors Assay

Abnormal DNA methylation contributes to the annoying tumorigenesis and the elevated expression of methylation-related methyltransferase (MTase) is associated with many diseases. Hence DNA MTase could serve as a promising biomarker for cancer-specific diagnosis as well as a potential therapeutic target. Herein, we developed an isothermal autocatalytic hybridization reaction (AHR) circuit for the sensitive detection of MTase and its inhibitors by integrating the catalytic hairpin assembly (CHA) converter with the hybridization chain reaction (HCR) amplifier. The initiator-mediated HCR amplifier could generate amplified fluorescent readout, as well as numerous newly activated triggers for motivating the CHA converter. The CHA converter is designed to expose the identical sequence of HCR initiators that reversely powered the HCR amplifier. Thus, the trace amount of target could produce exponentially amplified fluorescent readout by the autocatalytic feedback cycle between HCR and CHA systems. Then an auxiliary hairpin was introduced to mediate the assay of Dam MTase via the well-established AHR circuit. The Dam MTase-catalyzed methylation of auxiliary hairpin leads to its subsequent efficient cleavage by DpnI endonuclease, thus resulting in the release of HCR initiators to initiate the AHR circuit. The programmable nature of the auxiliary hairpin allows its easy adaption into other MTase assay by simply changing the recognition site. This proposed AHR circuit permits a sensitive, robust, and versatile analysis of MTase with the limit of detection (LOD) of 0.011 U/mL. Lastly, the AHR circuit could be utilized for MTase analysis in real complex samples and for evaluating the cell-cycle-dependent expression of MTase. This developed MTase-sensing strategy holds promising potential for biomedical analysis and clinical diagnosis.

Self-enhanced luminol-based electrochemiluminescent hydrogels: An ultrasensitive biosensing platform for fusion gene analysis coupled with target-initiated DNAzyme motor

BCR/ABL fusion gene has been discovered as an important and reliable biomarker for early diagnosis of chronic myeloid leukemia (CML). Herein, a novel and switching electrochemiluminescence (ECL) biosensor was developed for ultrasensitive determination of the fusion gene based on the self-enhanced polyethyleneimine-luminol (PEI-Lum) hydrogels coupled with target-initiated DNAzyme motor. The facilely prepared PEI-Lum hydrogels could not only immobilize enormous luminol but shorten the distance of binary system, thus facilitating the mass and electron transfer efficiency of the sensing interface, so that the enhanced ECL signal was achieved. Moreover, the engineering DNA motor was powered by Mg²⁺-dependent DNAzyme for isothermal DNA signal amplification. As a result, the fabricated ECL biosensor enabled highly sensitive detection of BCR/ABL fusion gene with a broad linear range from 10.0 fM to 10.0 nM and a low detection limit of 3.75 fM (S/N = 3). Significantly, the developed biosensing method provides a potential tool for nucleic acid analysis in clinical diagnosis and a new avenue to design high-efficient ECL nanomaterials.

Ultrasensitive detection of DNA methyltransferase activity: a novel dual-amplification fluorescence technique

A dual amplification fluorescence strategy was developed for the ultrasensitive detection of Dam MTase activity based on strand displacement amplification coupled with rolling circle amplification.

Superior sponge-like carbon self-doping graphitic carbon nitride nanosheets derived from supramolecular pre-assembly of a melamine-cyanuric acid complex for photocatalytic H2 evolution

The photocatalytic evolution of hydrogen (H₂) from water splitting is considered a promising route to overcome the energy crisis, and the key lies in the preparation of efficient photocatalysts. Herein, superior ordered sponge-like carbon self-doped graphitic carbon nitride (g-C₃N₄) nanosheets (SCCNS) were prepared via a combined strategy of melamine-cyanuric acid complex supramolecular pre-assembly and solvothermal pre-treatment using ethylene glycol (EG) aqueous solutions (EG:water = 50:50 vol.%) as a solvent and carbon doping source. The following pyrolysis converts the naturally arranged melamine-EG-cyanuric acid supramolecular intermediates to highly crystalline SCCNS with large specific surface areas. The optimal SCCNS-180 exhibits superior photocatalytic H₂ evolution activities (∼4393 and 11 320 μmol h^-1 g^-1) when irradiated with visible light and simulated sunlight; these values are up to ∼17- and ∼18-fold higher than that of bulk g-C₃N₄. The quantum efficiency of SCCNS-180 at λ = 420 nm can reach 6.0%. The excellent photocatalytic performance of SCCNS-180 derives from its distinct ordered sponge-like nanosheet structure with highly crystallinity and the carbon doping, leading to its improved optical absorption, accelerated photoinduced electron-hole pair transfer and separation rate and enlarged specific surface area (134.4 m² g^-1).

Nitrogen Vacancy Engineering in Graphitic Carbon Nitride for Strong, Stable, and Wavelength Tunable Electrochemiluminescence Emissions

As an attractive electrochemiluminescence (ECL) emitter, graphitic carbon nitride (CN) still suffers from weak and unstable ECL signals for its poor conductivity and the occurrence of electrode passivation. In this study, a simple nitrogen vacancy (NV) engineering strategy has been developed for the improvement of ECL performances (intensity and stability) for the first time. In comparison to pristine CN (RSD = 51.98% for 10 continuous scan), ca. 60 times amplification in ECL intensity and 70 times enhancement in ECL efficiency for CN modified with NVs (CN-NVs) were obtained. In addition, more stable ECL emissions (RSD = 0.53%) were achieved for CN-NV-550 by thermal treatment of pristine CN in a N₂ atmosphere for another 2 h at 550 °C. The mechanism study for the vital role of NVs on the ECL of CN-NVs revealed that NVs can not only facilitate electron transfer to amplify the ECL intensity but also serve as the electron trap to inhibit electrode passivation. More interestingly, a series of CN-NVs exhibited a tunable ECL wavelength range from 470 to 516 nm with different NV contents. Moreover, their ECL spectra showed an obvious red-shift of the wavelength with their corresponding fluorescence spectra. These findings confirmed that the ECL emissions of CN-NVs were susceptible to the relevant surface states of NVs. Our work may open up a promising pathway for improving ECL performances of CN and create new possibilities for multitarget simultaneous detection based on ECL and construction of color tunable light-emitting devices.

Cas12a-based electrochemiluminescence biosensor for target amplification-free DNA detection

CRISPR/Cas system have drawn increasing attention in accurate and sensitive nucleic acids detection. Herein, we reported a novel Cas12a-based electrochemiluminescence biosensor for target amplification-free human papilloma virus subtype (HPV-16) DNA detection. During this detection process, Cas12a employed its two-part recognition mechanism to improve the specificity and trans-cleavage capability to achieve signal amplification, while L-Methionine stabilized gold nanoclusters (Met-AuNCs) were served as high-efficiency ECL emitters to achieve ECL signal transition. Given the unique combination of Cas12a with ECL technique, the detection limit was determined as 0.48 pM and the whole detection could be completed within 70 min. We also validated the practical application of the proposed biosensor by using undiluted human blood samples, which gives impetus to the design of new generations of CRISPR/Cas detection system beyond the traditional ones with ultimate applications in sensing analysis and diagnostic technologies.

Nanomaterial-based biosensors for DNA methyltransferase assay

We review the recent advances in the development of nanomaterial-based biosensors for DNA methyltransferase assay.

Immuno-DNA binding directed template-free DNA extension and enzyme catalysis for sensitive electrochemical DNA methyltransferase activity assay and inhibitor screening

A new electrochemical immuno-DNA sensing platform for DNA methyltransferase activity assay and inhibitor screening.

An integrated-molecular-beacon based multiple exponential strand displacement amplification strategy for ultrasensitive detection of DNA methyltransferase activity

DNA methylation is a significant epigenetic mechanism involving processes of transferring a methyl group onto cytosine or adenine. Such DNA modification catalyzed by methyltransferase (MTase) plays important roles in the modulation of gene expression and other cellular activities. Herein, we develop a simple and sensitive biosensing platform for the detection of DNA MTase activity by using only two oligonucleotides. The fluorophore labeled molecular beacon (MB) can be methylated by MTase and subsequently cleaved by endonuclease DpnI at the stem, giving a shortened MB. The shortened MB can then hybridize with a primer DNA, initiating a cycle of strand displacement amplification (SDA) reactions. The obtained SDA products can unfold new MB and initiate another cycle of SDA reaction. Therefore, continuous enlargement of SDA and exponential amplification of the fluorescence signal are achieved. Because the triple functions of substrate, template and probe are elegantly integrated in one oligonucleotide, only two oligonucleotides are necessary for multiple amplification cycles, which not only reduces the complexity of the system, but also overcomes the laborious and cumbersome operation that is always a challenge in conventional methods. This platform exhibits an extremely low limit of detection of 3.3 × 10-6 U mL-1, which is the lowest to our knowledge. The proposed MTase-sensing platform was also demonstrated to perform well in a real-time monitoring mode, which can achieve a further simplified and high-throughput detection. The sensing strategy might be extended to the activity detection of other enzymes, thus showing great application potential in bioanalysis and clinical diagnosis.

Dual-Amplification Strategy-Based SERS Chip for Sensitive and Reproducible Detection of DNA Methyltransferase Activity in Human Serum

Herein, we present a dual-amplification sensing strategy-based surface-enhanced Raman scattering (SERS) chip, which combines rolling circle amplification (RCA) and polyadenine (PolyA) assembly for sensitive and reproducible determination of the activity of M.SssI, a cytosine-guanine dinucleotide (CpG) methyltransferase (MTase). Typically, in the presence of M.SssI, RCA process is triggered, resulting in long, single-stranded DNA (ssDNA) fragments that are hybridized with thousands of Raman reporters of Cy3. Afterward, the resultant ssDNA fragments are conjugated to SERS-active substrates made of silver core-gold satellite nanocomposites-modified silicon wafer (Ag-Au NPs@Si), with the SERS enhancement factor of ∼5 × 10⁶. The core-satellite nanostructures are assembled relied on the strong affinity of PolyA toward gold/silver surface. Of particular significance, the developed SERS chip displays an ultrahigh sensitivity with a low limit of detection (LOD) of 2.8 × 10^-3 U/mL, which is around 2 orders of magnitude higher than most reported methods. In addition, the constructed chip features a broad detection range covering from 0.05 to 50 U/mL. Besides for the ultrahigh sensitivity and broad dynamic range, the chip also features good reproducibility (e.g., the relative standard deviation (RSD) is less than ∼12%). Taking advantages of these merits, the developed chip is feasible for accurate discrimination of M.SssI with various concentrations spiked in human serum samples with good recoveries ranging from 99.6% to 107%.

Antimony selenide/graphene oxide composite for sensitive photoelectrochemical detection of DNA methyltransferase activity

An Sb₂Se₃/graphene oxide composite was applied as both the photoelectrochemical probe and substrate for biomolecule conjugation for the construction of a “signal-off” sandwich-type biosensor for DNA methyltransferase activity detection.

A sensitive cyclic signal amplification fluorescence strategy for determination of methyltransferase activity based on graphene oxide and RNase H

A sensitive fluorometric method for DNA methyltransferase activity detection based on graphene oxide and RNase H-assisted signal amplification.

Highly Sensitive Assay of Methyltransferase Activity Based on an Autonomous Concatenated DNA Circuit

Methyltransferase-involved DNA methylation is one of the most important epigenetic processes, making the ultrasensitive MTase assay highly desirable in clinical diagnosis as well as biomedical research. Traditional single-stage amplification means often achieve linear amplification that might not fulfill the increasing demands for detecting trace amount of target. It is desirable to construct multistage cascaded amplifiers that allow for enhanced signal amplifications. Herein, a powerful nonenzymatic MTase-sensing platform is successfully engineered based on a two-layered DNA circuit, in which the upstream catalytic hairpin assembly (CHA) circuit successively generates DNA product that could be used to activate the downstream hybridization chain reaction (HCR) circuit, resulting in the generation of a dramatically amplified fluorescence signal. In the absence of M.SssI MTase, HpaII endonuclease could specifically recognize the auxiliary hairpin substrate and then catalytically cleave the corresponding recognition site, releasing a DNA fragment that triggers the CHA-HCR-mediated FRET transduction. Yet the M.SssI-methylated hairpin substrate could not be cleaved by HpaII enzyme, and thus prohibits the CHA-HCR-mediated FRET generation, providing a substantial signal difference with that of MTase-absent system. Taking advantage of the high specificity of multiple-guaranteed recognitions of MTase/endonuclease and the synergistic amplification features of concatenated CHA-HCR circuit, this method enables an ultrasensitive detection of MTase and its inhibitors in serum and E. coli cells. Furthermore, the rationally assembled CHA-HCR also allows for probing other different biotransformations through a facile design of the corresponding substrates. It is anticipated that the infinite layer of multilayered DNA circuit could further improve the signal gain of the system for accurately detecting other important biomarkers, and thus holds great promise for cancerous treatment and biomedical research.

A label-free aptasensor for ultrasensitive Pb2+ detection based on electrochemiluminescence resonance energy transfer between carbon nitride nanofibers and Ru(phen)32

A label-free aptasensor was developed for ultrasensitive detection of Pb²⁺ based on electrochemiluminescence resonance energy transfer (ECL-RET) from graphitic carbon nitride nanofibers (CNNFs) to Ru(phen)₃²⁺. The CNNFs synthesized via a facile two-step hydrolysis-electrolysis strategy showed intense and stable ECL signal by taking advantages of amplifying and stabilizing effect of carbon nanotubes and Au nanoparticles. After the specific hybridation between capture DNA and Pb²⁺ specific aptamer, Ru(phen)₃²⁺ could be captured onto CNNFs modified electrode by effectively intercalating into the grooves of double-strand DNA, thus triggering the ECL-RET and leading to highly enhanced ECL intensity. The presence of Pb²⁺ would result in the detachment of Ru(phen)₃²⁺ and then the inhibition of ECL-RET. Then Pb²⁺ concentration could be quantified based on ECL change before and after introduction of Pb²⁺. The target recycling based on exonuclease I (Exo I) mediated digestion of Pb²⁺-aptamer complex was implemented to further improve the sensitivity. These synergistic amplification strategies enabled the aptasensor to be ultrasensitive for Pb²⁺ determination with a detection limit of 0.04 pM. The proposed probe was utilized to analyze environmental samples with satisfactory results.

Development of hierarchical Fe3O4 magnetic microspheres as solid substrates for high sensitive immunoassays

Improving the detection sensitivity of enzyme linked immunosorbent assay (ELISA) is of the utmost importance for meeting the demand of early disease diagnosis. In this work, a sensitive solid substrate for ELISA, i.e., hierarchical iron oxide magnetic microspheres, Fe₃O₄@mSiO₂@poly[poly(ethylene glycol) methacrylate-co-glycidyl methacrylate], was developed via a novel surface-initiated photoiniferter-mediated polymerization (SI-PIMP) strategy. The magnetic microspheres consist of a magnetic Fe₃O₄ core that gives a high magnetic response, a 3D backbone, a mesoporous SiO₂ middle layer, that facilitates microsphere stability and provides anchoring sites, and polymer brushes, that serve as an antifouling and oriented antibody immobilization layer. As a result, the as-prepared microspheres possess a high antibody loading capacity, an enhanced detection signal and a dramatically improved sensitivity, resulting in a 25-fold improvement over conventional ELISA solid substrates.