Electrochemical Biosensor for DNA Methylation Detection through Hybridization Chain-Amplified Reaction Coupled with a Tetrahedral DNA Nanostructure

Dual-mode aptasensor based on P-CeO2NR@Mxene and exonuclease I-assisted target recycling for malachite green detection

Malachite green (MG) has been illicitly employed in aquaculture as a parasiticide, however, its teratogenic and carcinogenic effects pose a significant human health threat. Herein, a dual-mode colorimetric and electrochemical aptasensor was fabricated for MG detection, capitalizing on the robust catalytic and peroxidase-like activity of P-CeO2NR@Mxene and good capture efficiency of a tetrahedral DNA nanostructure (TDN) designed with multiple aptamers (m-TDN). P-CeO2NR@Mxene-modified complementary DNA (cDNA) served as both colorimetric and electrochemical probe. m-TDN was attached to AuE to capture MG and P-CeO2NR@Mxene/cDNA. The superior aptamer and MG binding to cDNA regulated signals and enabled precise MG quantification. The further introduced Exo I enabled aptamer hydrolysis, releasing MG for further binding rounds, allowing target recycling amplification. Under the optimal conditions, the aptasensor reached an impressively low detection limit 95.4 pM in colorimetric mode and 83.6 fM in electrochemical mode. We believe this dual-mode approach holds promise for veterinary drug residue detection.

Strategies for the detection of site-specific DNA methylation and its application, opportunities and challenges in the field of electrochemical biosensors

DNA methylation is an epigenetic modification that plays a crucial role in various biological processes. Aberrant DNA methylation is closely associated with the onset of diseases, and the specific localization of methylation sites in the genome offers further insight into the connection between methylation and diseases. Currently, there are numerous methods available for site-specific methylation detection. Electrochemical biosensors have garnered significant attention due to their distinct advantages, such as rapidity, simplicity, high sensitivity, low cost, and the potential for miniaturization. In this paper, we present a systematic review of the primary sensing strategies utilized in the past decade for analyzing site-specific methylation and their applications in electrochemical sensors, from a novel perspective focusing on the localization analysis of site-specific methylation. These strategies include bisulfite treatment, restriction endonuclease treatment, other sensing strategies, and deamination without direct bisulfite treatment. We hope that this paper can offer ideas and references for establishing site-specific methylation electrochemical analysis in clinical practice.

Immunochromatographic Strip Based on Tetrahedral DNA Immunoprobe for the Detection of Aflatoxin B1 in Rice Bran Oil

Aflatoxin B1 (AFB1), a widespread contaminant in food and feeds, poses a threat to the health of animals and humans. Consequently, it is significant to develop a rapid, precise and highly sensitive analytical method for the detection of AFB1. Herein, we developed an immunochromatographic strip (ICS) based on a tetrahedral DNA (TDN) immunoprobe for AFB1 determination in rice bran oil. Three sizes of TDN immunoprobes (AuNP-TDN13bp-mAb, AuNP-TDN17bp-mAb, AuNP-TDN26bp-mAb) were constructed, and the performance of these three immunoprobes, including the effective antibody labeling density and immunoaffinity, was measured and compared with that of the immunoprobe (AuNP-mAb) developed using the physical adsorption method. Subsequently, the optimal TDN immunoprobe, namely AuNP-TDN13bp-mAb, was selected to prepare the immunochromatographic strip (ICS) for the qualitative and quantitative detection of AFB1 in rice bran oil. The visual limits of detection (vLODs) of the ICS based on AuNP-TDN13bp-mAb and AuNP-mAb were 0.2 ng/mL and 2 ng/mL, with scanning quantitative limits (sLOQs) of 0.13 ng/mL and 1.4 ng/mL, respectively. The ICS demonstrated a wide linear range from 0.02 ng/mL to 0.5 ng/mL, with good specificity, accuracy, precision, repeatability, and stability. Moreover, a high consistency was observed between the constructed ICS and ultra-high-performance liquid chromatography (UPLC) in the quantification of AFB1. The results indicated that the introduction of TDN was beneficial for promoting efficient antibody labeling, protecting the bioactivity of immunoprobes, and increasing the sensitivity of detection, which would provide new perspectives for the achievement of the highly sensitive detection of mycotoxins.

Recent Advances in Biosensor Technology for Early-Stage Detection of Hepatocellular Carcinoma-Specific Biomarkers: An Overview

Hepatocellular carcinoma is currently the most common malignancy of the liver. It typically occurs due to a series of oncogenic mutations that lead to aberrant cell replication. Most commonly, hepatocellular carcinoma (HCC) occurs as a result of pre-occurring liver diseases, such as hepatitis and cirrhosis. Given its aggressive nature and poor prognosis, the early screening and diagnosis of HCC are crucial. However, due to its plethora of underlying risk factors and pathophysiologies, patient presentation often varies in the early stages, with many patients presenting with few, if any, specific symptoms in the early stages. Conventionally, screening and diagnosis are performed through radiological examination, with diagnosis confirmed by biopsy. Imaging modalities tend to be limited by their requirement of large, expensive equipment; time-consuming operation; and a lack of accurate diagnosis, whereas a biopsy's invasive nature makes it unappealing for repetitive use. Recently, biosensors have gained attention for their potential to detect numerous conditions rapidly, cheaply, accurately, and without complex equipment and training. Through their sensing platforms, they aim to detect various biomarkers, such as nucleic acids, proteins, and even whole cells extracted by a liquid biopsy. Numerous biosensors have been developed that may detect HCC in its early stages. We discuss the recent updates in biosensing technology, highlighting its competitive potential compared to conventional methodology and its prospects as a tool for screening and diagnosis.

Periodic magnetic modulation enhanced electrochemical analysis for highly sensitive determination of genomic DNA methylation

DNA methylation aberrations have a strong correlation with cancer in early detection, diagnosis, and prognosis, which make them possible candidate biomarkers. Electrochemical biosensors offer rapid protocols for detecting DNA methylation status with minimal pretreatment of samples. However, the inevitable presence of background current in the time domain, including electrochemical noise and variations, limits the detection performance of these biosensors, especially for low concentration analytes. Here, we propose an ultrasensitive frequency-domain electrochemical analysis strategy to effectively separate the weak signals from background current. To achieve this, we employed periodic magnetic field modulation of magnetic beads (MBs) on and off the electrode surface to generate a periodic electrochemical signal for subsequent frequency-domain analysis. By capturing labeled MBs with as low as 0.5 pg of DNA, we successfully demonstrated a highly sensitive electrochemical method for determination of genome-wide DNA methylation levels. We also validated the effectiveness of this methodology using DNA samples extracted from three types of hepatocellular carcinoma (HCC) cell lines. The results revealed varying genomic methylation levels among different HCC cell lines, indicating the potential application of this approach for early-stage cancer detection in terms of DNA methylation status.

Recent advances in the applications of DNA frameworks in liquid biopsy: A review

Cancer is one of the serious threats to public life and health. Early diagnosis, real-time monitoring, and individualized treatment are the keys to improve the survival rate and prolong the survival time of cancer patients. Liquid biopsy is a potential technique for cancer early diagnosis due to its non-invasive and continuous monitoring properties. However, most current liquid biopsy techniques lack the ability to detect cancers at the early stage. Therefore, effective detection of a variety of cancers is expected through the combination of various techniques. Recently, DNA frameworks with tailorable functionality and precise addressability have attracted wide spread attention in biomedical applications, especially in detecting cancer biomarkers such as circulating tumor cells (CTCs), exosomes and circulating tumor nucleic acid (ctNA). Encouragingly, DNA frameworks perform outstanding in detecting these cancer markers, but also face some challenges and opportunities. In this review, we first briefly introduced the development of DNA frameworks and its typical structural characteristics and advantages. Then, we mainly focus on the recent progress of DNA frameworks in detecting commonly used cancer markers in liquid-biopsy. We summarize the advantages and applications of DNA frameworks for detecting CTCs, exosomes and ctNA. Furthermore, we provide an outlook on the possible opportunities and challenges for exploiting the structural advantages of DNA frameworks in the field of cancer diagnosis. Finally, we envision the marriage of DNA frameworks with other emerging materials and technologies to develop the next generation of disease diagnostic biosensors.

New advances in signal amplification strategies for DNA methylation detection in vitro

5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.

Ultrasensitive Detection of Tumor Suppressor Gene Methylation by Piezoelectric Sensing Based on Enrichment of Transcription Activator-Like Effectors

The detection of DNA methylation at cytosine/guanine dinucleotide (CpG) islands in promoter regions of tumor suppressor genes has great potential for early cancer screening, diagnosis, and prognosis monitoring. Nevertheless, achieving accurate, sensitive, cost-effective, and quantitative detection of target methylated DNA remains challenging. Herein, we propose a novel piezoelectric sensor (series piezoelectric quartz crystal (SPQC)) based on transcription activator-like effectors (TALEs) for detecting DNA methylation of Ras association domain family 1 isoform A (RASSF1A) tumor suppressor genes (R-5mC). The sensor employs TALEs-Ni magnetic beads to specifically recognize and separate the R-5mC, thereby improving the detection selectivity. The TALEs-Ni magnetic beads-R-5mC complex is sheared by a nucleic acid enzyme (DNAzyme) to release the single-stranded DNA (ST). ST initiates a catalyzed hairpin assembly (CHA) reaction on the surface of the electrode, which in turn triggers the hybridization chain reaction (HCR) and silver staining for enhanced detection sensitivity. The strategy exhibits a linear response in the detection of R-5mC in the range of 1 fM to 1 nM with a detection limit of 0.79 fM. R-5mC as low as 0.01% can be detected, even in the presence of large numbers of unmethylated DNA. The detection of R-5mC in circulating cell-free DNA (cfDNA) derived from clinical plasma specimens of lung cancer patients yielded satisfactory results.

Electrically Oriented Antibodies on Transistor for Monitoring Several Copies of Methylated DNA

An antibody transistor is a promising biosensing platform for the diagnosis and monitoring of various diseases. Nevertheless, the low concentration and short half-life of biomarkers require biodetection at the trace-molecule level, which remains a challenge for existing antibody transistors. Herein, we demonstrate a graphene field-effect transistor (gFET) with electrically oriented antibody probes (EOA-gFET) for monitoring several copies of methylated DNA. The electric field confines the orientation of antibody probes on graphene and diminishes the distance between graphene and methylated DNAs captured by antibodies, generating more induced charges on graphene and amplifying the electric signal. EOA-gFET realizes a limit of detection (LoD) of ∼0.12 copy μL-1, reaching the lowest LoD reported before. EOA-gFET shows a distinguishable signal for liver cancer clinical serum samples within ∼6 min, which proves its potential as a powerful tool for disease screening and diagnosis.

Triple multivalent aptamers within DNA tetrahedron on reduced graphene oxide electrode: Unlocking enhanced sensitivity and accelerated reactions in electrochemical sensing

DNA nanostructures are emerging as promising biosensing platforms due to their programmability, predictable assembly, and compatibility with aptamers for enhanced selectivity. This study focuses on a triple-multivalent aptamer (tApt) complex immobilized on a tetrahedral DNA nanostructure (TDN) and integrated with an electrochemically reduced graphene oxide (ERGO) electrode for highly sensitive mercury ion (Hg2+) detection. Compared to a linear multivalent aptamer-modified electrode (S2/ERGO-GCE), the 3D tApt/ERGO-GCE aptasensor exhibits superior sensitivity, signal amplification, and reaction kinetics. The tApt/ERGO-GCE sensor achieves an exceptional limit of detection (LOD) of 4.1 zM, surpassing the LOD of 0.71 fM for S2/ERGO-GCE. Additionally, the tApt/ERGO-GCE sensor demonstrates faster response times, with a half-saturation time (T1/2) of 6 minutes compared to 17 minutes for S2/ERGO/GCE. The 3D tApt aptamer's superior performance is attributed to its tetrahedral DNA structure integrated on ERGO, providing multiple aptamer binding sites, facilitating oriented immobilization on the electrode surface, and enhancing analyte capture and concentration. In contrast, the linear S2 aptamers lack rigidity, resulting in a disordered orientation on the electrode surface, hindering efficient Hg2+ binding and reducing target molecule binding efficiency. This study underscores the potential of triple-multivalent aptamer-based nanostructures for ultrasensitive and rapid biosensing applications. The tApt/ERGO-GCE aptasensor's exceptional sensitivity, signal amplification, and reaction kinetics make it a promising tool for Hg2+ detection and other biosensing applications.

Force-Encoding DNA Nanomachines for Simultaneous and Direct Detection of Multiple Pathogenic Bacteria in Blood

Pathogen detection is growing in importance in the early stages of bacterial infection and treatment due to the significant morbidity and mortality associated with bloodstream infections. Although various diagnostic approaches for pathogen detection have been proposed, most of them are time-consuming, with insufficient sensitivity and limited specificity and multiplexing capability for clinical use. Here, we report a force-encoding DNA nanomachine for simultaneous and high-throughput detection of multiple pathogens in blood through force-induced remnant magnetization spectroscopy (FIRMS). The force-encoding DNA nanomachines coupled with DNA walkers enable analytical sensitivity down to a single bacterium via a cascade signal amplification strategy. More importantly, it allows for rapid and specific profiling of various pathogens directly in blood samples, without being affected by factors such as light color and solution properties. We expect that this magnetic sensing platform holds great promise for various applications in biomedical research and clinical diagnostics.

All-in-one fabrication of a ratiometric electrochemical aptasensor with tetrahedral DNA nanostructure for fumonisin B1 detection

Here, we develop an all-in-one strategy for efficient assembly of an electrochemical aptasensor. A multifunctional structure based on a tetrahedral DNA nanostructure (TDN) was synthesized via a one-step annealing process, providing DNA fixation, target recognition, signal amplification and space regulation. Based on the integration of this multifunctional structure, the sensing interface was assembled in one step. A ratiometric aptasensor was constructed by anchoring methylene blue (MB) to the TDN and ferrocene (Fc) on the cDNA. Using the ratio of the currents obtained from Fc and MB as a measure, the developed aptasensor shows excellent analytical performance for fumonisin B1 detection. This strategy is universal and could simplify the fabrication of aptasensors.

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

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

Laser induced graphene electrochemical aptasensor based on tetrahedral DNA for ultrasensitive on-site detection of microcystin-LR

The development of accurate and reliable sensor for on-site detection of microcystin-LR (MC-LR), one of hazardous environmental pollutants, is highly required. Herein, a laser induced graphene (LIG)-based electrochemical aptasensor for sensitive on-site detection of MC-LR was reported. LIG electrode, the substrate of aptasensor, was prepared via thermal transfer with ethylene-vinyl acetate copolymer, and LIG acted as quasi-reference electrode to replace conventional Ag/AgCl electrode for better operability and robustness. LIG electrode provided large surface area to assemble tetrahedral DNA to absorb methylene blue (MB) for the signal amplification. For detection, the specific recognition of MC-LR with aptamer led to the stripping of tetrahedral DNA complex and further the decreased redox current of MB (IMB). Consequently, the fabricated aptasensor offered high analytical performance for MC-LR detection with a linear range of 1 × 10-2-1 × 105 pM and a detection limit of 3 × 10-3 pM, which was successfully used for water sample analysis with comparable reliability and accuracy of standard method. Furthermore, a portable detection platform by coupling of LIG-based electrochemical aptasensor with electrochemical workstation was constructed for on-site detection of MC-LR. This work offers a novel method for the on-site monitoring of MC-LR, which promotes the investigation of LIG-based electrochemical biosensing in the field of environmental analysis.

Flexible genosensors based on polypyrrole and graphene quantum dots for PML/RARα fusion gene detection: A study of acute promyelocytic leukemia in children

Acute promyelocytic leukemia (APL) in children is associated with a favorable initial prognosis. However, minimal residual disease (MRD) follow-up remains poorly defined, and relapse cases are concerning due to their recurrent nature. Thus, we report two electrochemical flexible genosensors based on polypyrrole (PPy) and graphene quantum dots (GQDs) for label-free PML-RARα oncogene detection. Atomic force microscopy (AFM), scanning electron microscope (SEM), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) were used to characterize the technological biosensor development. M7 and APLB oligonucleotide sequences were used as bioreceptors to detect oncogenic segments on chromosomes 15 and 17, respectively. AFM characterization revealed heterogeneous topographical surfaces with maximum height peaks for sensor layers when tested with positive patient samples. APLB/Genosensor exhibited a percentage change in anode peak current (ΔI) of 423 %. M7/Genosensor exhibited a ΔI of 61.44 % for more concentrated cDNA samples. The described behavior is associated with the biospecific recognition of the proposed biosensors. Limits of detection (LOD) of 0.214 pM and 0.677 pM were obtained for APLB/Genosensor and M7/Genosensor, respectively. The limits of quantification (LOQ) of 0.648 pM and 2.05 pM were estimated for APLB/Genosensor and M7/Genosensor, respectively. The genosensors showed reproducibility with a relative standard deviation of 7.12 % for APLB and 1.18 % for M7 and high repeatability (9.89 % for APLB and 1.51 % for M7). In addition, genetic tools could identify the PML-RARα oncogene in purified samples, plasmids, and clinical specimens from pediatric patients diagnosed with APL with high bioanalytical performance. Therefore, biosensors represent a valuable alternative for the clinical diagnosis of APL and monitoring of MRD with an impact on public health.

Methylation specific enzyme-linked oligonucleotide assays (MS-ELONA) for ultrasensitive DNA methylation analysis

Methylation of the promoter region of cancer related genes plays a crucial role in the occurrence and development of cancer, and the degree of methylation has great potential for the early cancer diagnosis. At present, the technology used to quantify DNA methylation is mainly based on the DNA sequencing which are time-consuming and high-cost in the relating application. We have developed an ultrasensitive method of methylation specific enzyme-linked oligonucleotide assays (MS-ELONA) to detect and quantify the level of DNA methylation. We could detect as little as 2 pg of methylated DNA in the 100000-fold excess of unmethylated genes, and discriminate prostate cancer from benign prostatic hyperplasia (BPH) and control with serum samples. We also demonstrate the reversibility of DNA methylation modification by treatment with demethylation drugs. With 16-channel electrochemical work station, our research reveals a simple and inexpensive method to quantify the methylation level of specially appointed genes, and have the potential to be applied in the clinical research.

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.

Electrochemical biosensors in healthcare services: bibliometric analysis and recent developments

Biosensors are nowadays being used in various fields including disease diagnosis and clinical analysis. The ability to detect biomolecules associated with disease is vital not only for accurate diagnosis of disease but also for drug discovery and development. Among the different types of biosensors, electrochemical biosensor is most widely used in clinical and health care services especially in multiplex assays due to its high susceptibility, low cost and small in size. This article includes comprehensive review of biosensors in medical field with special emphasis on electrochemical biosensors for multiplex assays and in healthcare services. Also, the publications on electrochemical biosensors are increasing rapidly; therefore, it is crucial to be aware of any latest developments or trends in this field of research. We used bibliometric analyses to summarize the progress of this research area. The study includes global publication counts on electrochemical biosensors for healthcare along with various bibliometric data analyses by VOSviewer software. The study also recognizes the top authors and journals in the related area, and determines proposal for monitoring research.

Isotope-encoded tetrahedral DNA for multiple SARS-CoV-2 variant diagnosis

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed an unprecedented demand for accurate and cost-effective diagnostic assays to discriminate between different variants. Whilst many bioassays have been successfully demonstrated for SARS-CoV-2 detection, diagnosis of its variants remains challenging and mainly relies on time-consuming and costly sequencing techniques. Herein, we proposed a triplevalent tetrahedral DNA nanostructure (tTDN) with three overhang isotope probes capable of multiplex simultaneous analysis. HV69/70 del (alpha-specific), K417N (beta-specific) and T478K (delta-specific) and omicron with common mutations above of the SARS-CoV-2 S gene were detected selectively with the aid of the TDN scaffold and MNAzyme system, and a sensitive strategy enabling the screening of four kinds of variants of concern (VOC) was achieved.

Signal Amplification in Electrochemical DNA Biosensors Using Target-Capturing DNA Origami Tiles

Electrochemical DNA (e-DNA) biosensors are feasible tools for disease monitoring, with their ability to translate hybridization events between a desired nucleic acid target and a functionalized transducer, into recordable electrical signals. Such an approach provides a powerful method of sample analysis, with a strong potential to generate a rapid time to result in response to low analyte concentrations. Here, we report a strategy for the amplification of electrochemical signals associated with DNA hybridization, by harnessing the programmability of the DNA origami method to construct a sandwich assay to boost charge transfer resistance (R_CT) associated with target detection. This allowed for an improvement in the sensor limit of detection by two orders of magnitude compared to a conventional label-free e-DNA biosensor design and linearity for target concentrations between 10 pM and 1 nM without the requirement for probe labeling or enzymatic support. Additionally, this sensor design proved capable of achieving a high degree of strand selectivity in a challenging DNA-rich environment. This approach serves as a practical method for addressing strict sensitivity requirements necessary for a low-cost point-of-care device.

Ultrasensitive photoelectrochemical biosensor for DNA 5-methylcytosine analysis based on co-sensitization strategy combined with bridged DNA nanoprobe

Altered DNA methylation in the form of 5-methylcytosine (5-mC) patterns is correlated with disease diagnosis, prognosis, and treatment response. Therefore, accurate analysis of 5-mC is of great significance for the diagnosis of diseases. Here, an efficient enhanced photoelectrochemical (PEC) biosensor was designed for the quantitative analysis of DNA 5-mC based on a cascaded energy level aligned co-sensitization strategy coupling with the bridged DNA nanoprobe (BDN). Firstly, Au nanoparticle/graphite phase carbon nitride/titanium dioxide (AuNPs/g-C₃N₄@TiO₂) nanocomposite was synthesized through in situ growth of AuNPs on g-C₃N₄@TiO₂ surface as a matrix to provide a stable background signal. Next, BDN with a high mass transfer rate synthesized from a pair of DNA tetrahedral as nanomechanical handles was used as a capture probe to bind to the target sequence. The polydopamine nanosphere was applied to load with CdTe QDs (PDANS-CdTe QDs) as a photocurrent label of 5-mC antibodies. When the 5-mC existed, a large number of PDANS-Ab-CdTe QDs were introduced to the electrode surface, the formed CdTe QDs/AuNPs/g-C₃N₄@TiO₂ co-sensitive structure could effectively enhance the electron transfer capability and photocurrent response rate due to the effective cascade energy level arrangement, leading to a significantly enhanced photocurrent signal. The proposed PEC biosensor manifested a wide range from 10^-17 M to 10^-7 M and a detection limit of 2.2 aM. Meanwhile, the excellent performance indicated the practicability of the designed strategy, thus being capable of the clinical diagnosis of 5-mC.

Locus-Specific Detection of DNA Methylation: The Advance, Challenge, and Perspective of CRISPR-Cas Assisted Biosensors

Deoxyribonucleic acid (DNA) methylation is one of the epigenetic characteristics that result in heritable and revisable phenotype changes but without sequence changes in DNA. Aberrant methylation occurring at a specific locus was reported to be associated with cancers, insulin resistance, obesity, Alzheimer's disease, Parkinson's disease, etc. Therefore, locus-specific DNA methylation can serve as a valuable biomarker for disease diagnosis and therapy. Recently, Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are applied to develop biosensors for DNA, ribonucleic acid, proteins, and small molecules detection. Because of their highly specific binding ability and signal amplification capacity, CRISPR-Cas assisted biosensor also serve as a potential tool for locus-specific detection of DNA methylation. In this perspective, based on the detection principle, a detailed classification and comprehensive discussion of recent works about the latest advances in locus-specific detection of DNA methylation using CRISPR-Cas systems are provided. Furthermore, current challenges and future perspectives of CRISPR-based locus-specific detection of DNA methylation are outlined.

Rapid detection of cancer DNA in human blood using cysteamine-capped AuNPs and a machine learning-enabled smartphone

DNA methylation occurs when a methyl group is added to a cytosine (C) residue's fifth carbon atom, forming 5-methylcytosine (5-mC). Cancer genomes have a distinct methylation landscape (Methylscape), which could be used as a universal cancer biomarker. This study developed a simple, low-cost, and straightforward Methylscape sensing platform using cysteamine-decorated gold nanoparticles (Cyst/AuNPs), in which the sensing principle is based on methylation-dependent DNA solvation. Normal and cancer DNAs have distinct methylation profiles; thus, they can be distinguished by observing the dispersion of Cyst/AuNPs adsorbed on these DNA aggregates in MgCl₂ solution. After optimising the MgCl₂, Cyst/AuNPs, DNA concentration, and incubation time, the optimised conditions were used for leukemia screening, by comparing the relative absorbance (ΔA _650/525). Following the DNA extraction from actual blood samples, this sensor demonstrated effective leukemia screening in 15 minutes with high sensitivity, achieving 95.3% accuracy based on the measurement by an optical spectrophotometer. To further develop for practical realisation, a smartphone assisted by machine learning was used to screen cancer patients, achieving 90.0% accuracy in leukemia screening. This sensing platform can be applied not only for leukemia screening but also for other cancers associated with epigenetic modification.

Screen-printed electrode-based biosensors modified with functional nucleic acid probes and their applications in this pandemic age: a review

Electrochemical methodology has probably been the most used sensing platform in the past few years as they provide superior advantages. In particular, screen-printed electrode (SPE)-based sensing applications stand out as they provide extraordinary miniaturized but robust and user-friendly detection system. In this context, we are focusing on the modification of SPE with functional nucleic acid probes and nanostructures to improve the electrochemical detection performance in versatile sensing applications, particularly in the fight against the COVID-19 pandemic. Aptamers are immobilized on the electrode surface to detect non-nucleic acid targets and complementary probes to recognize and capture nucleic acid targets. In a step further, SPE-based biosensors with the modification of self-assembled DNA nanostructures are emphasized as they offer great potential for the interface engineering of the electrode surface and promote the excellent performance of various interface reactions. By equipping with a portable potentiostat and a smartphone monitoring device, the realization of this SPE-based miniaturized diagnostic system for the further requirement of fast and POC detection is revealed. Finally, more novel and excellent works are previewed and future perspectives in this field are mentioned.

Ratiometric immunosensor with DNA tetrahedron nanostructure as high-performance carrier of reference signal and its applications in selective phoxim determination for vegetables

A ratiometric electrochemical immunosensor, based on DNA tetrahedron nanostructure (DTNS), is introduced for vegetable phoxim determination. DTNS spontaneously adheres onto gold-nanoparticle-modified electrode and forms stable three-dimensional structure, providing plenty of binding sites to the built-in reference, methylene blue (MB). Monoclonal antibody (m-Ab) is vertically linked onto DTNS vertex, selectively responses antigenic phoxim, and promotes the target signal of I_PHO. Thus, a ratiometric indicator, I_PHO/I_MB, is sensibly established with the target signal (I_PHO) and the reference signal (I_MB). Modifications, mechanisms and advances of the proposed method are subsequently examined with morphological methods and electrochemical experiments. This method brings considerable advances in analytical behaviors. The ratiometric signal presents better performance than solo system in repeatability and long-time stability. As-fabricated sensor presents wide dynamic range as 0.1∼30 μg/L, and limit of detection is well defined as 0.003 μg/L (S/N = 3). Finally, this method is verified with real-vegetable-sample analysis, certified HPLC and recovery test.

Rapid and ultrasensitive electrochemical detection of DNA methylation for ovarian cancer diagnosis

Alterations in DNA methylation, a stable epigenetic marker, are important components in the development of cancer. It is vital to develop diagnostic systems with the ability to rapidly quantify DNA methylation with high sensitivity and selectivity. However, the analysis of DNA methylation must address two main challenges: (i) ultralow abundance and (ii) differentiating methylated cytosine from normal cytosine on target DNA sequence in the presence of an overwhelming background of circulating cell-free DNA. Here we report the development of an ultrasensitive and highly-selective electrochemical biosensor for the rapid detection of DNA methylation in blood. The sensing of DNA methylation involves the hybridization on a network of probe DNA modified gold-coated magnetic nanoparticles (DNA-Au@MNPs) complementary to target DNA, and subsequently enzymatic cleavage to differentiate methylated DNA strands from corresponding unmethylated DNA strands. The biosensor presents a dynamic range from 2 aM to 20 nM for 110 nucleotide DNA sequences containing a single-site methylation with the lowest detected concentration of 2 aM. This DNA-Au@MNPs based sensor provides a promising method to achieve 35 min response time and minimally invasive diagnosis of ovarian cancer.

Smartphone-Based Electrochemiluminescence for Visual Simultaneous Detection of RASSF1A and SLC5A8 Tumor Suppressor Gene Methylation in Thyroid Cancer Patient Plasma

Visual one-step simultaneous detection of low-abundance methylation is a crucial challenge in early cancer diagnosis in a simple manner. Through the design of a closed split bipolar electrochemistry system (BE), detection of promoter methylation of tumor suppressor genes in papillary thyroid cancer, RASSF1A and SLC5A8, was achieved using electrochemiluminescence. For this purpose, electrochemiluminescence of luminol loaded into the Fe₃O₄@UiO-66 and gold nanorod-functionalized graphite-like carbon nitride nanosheet (AuNRs@C₃N₄ NS), separately, on the anodic and cathodic pole bipolar electrodes (BPEs) in two different chambers of a bipolar cell were recorded on a smartphone camera. To provide the same electric potential (ΔE_elec) through the BPEs to conduct simultaneous light emission, as well as to achieve higher sensitivity, anodic and cathodic poles BPEs were separately connected to ruthenium nanoparticles electrodeposited on nitrogen-doped graphene-coated Cu foam (fCu/N-GN/RuNPs) to provide a hydrogen evolution reaction (HER) and polycatechol-modified reduced graphene oxide/pencil graphite electrode (PC-rGO/PGE) to provide electrooxidation of hydrazine. Moreover, taking advantages of the strong cathodic ECL activity due to the roles of AuNRs, as well as the high density of capture probes on the UiO-66 and Fe₃O₄ roles in improving the signal-to-background ratio (S/B) in complicated plasma media, a sensitive visual ECL immunosensor was developed to detect two different genes as model target analytes in patient plasma samples. The ability of discrimination of methylation levels as low as 0.01% and above 90% clinical sensitivity in thyroid cancer patient plasma implies that the present strategy is able to diagnose cancer early, as well as monitor responses of patients to therapeutic agents.

Detection of a Double-Stranded MGMT Gene Using Electrochemically Reduced Graphene Oxide (ErGO) Electrodes Decorated with AuNPs and Peptide Nucleic Acids (PNA)

The ability to detect double-stranded DNA (dsDNA) as a biomarker without denaturing it to single-stranded DNA (ss-DNA) continues to be a major challenge. In this work, we report a sandwich biosensor for the detection of the ds-methylated MGMT gene, a potential biomarker for brain tumors and breast cancer. The purpose of this biosensor is to achieve simultaneous recognition of the gene sequence, as well as the presence of methylation. The biosensor is based on reduced graphene oxide (rGO) electrodes decorated with gold nanoparticles (AuNPs) and uses Peptide Nucleic Acid (PNA) that binds to the ds-MGMT gene. The reduction of GO was performed in two ways: electrochemically (ErGO) and thermally (TrGO). XPS and Raman spectroscopy, as well as voltammetry techniques, showed that the ErGO was more efficiently reduced, had a higher C/O ratio, showed a smaller crystallite size of the sp2 lattice, and was more stable during measurement. It was also revealed that the electro-deposition of the AuNPs was more successful on the ErGO surface due to the higher At% of Au on the ErGO electrode. Therefore, the ErGO/AuNPs electrode was used to develop biosensors to detect the ds-MGMT gene. PNA, which acts as a bio-recognition element, was used to form a self-assembled monolayer (SAM) on the ErGO/AuNPs surface via the amine-AuNPs interaction, recognizing the ds-MGMT gene sequence by its invasion of the double-stranded DNA and the formation of a triple helix. The methylation was then detected using biotinylated-anti-5mC, which was then measured using the amperometric technique. The selectivity study showed that the proposed biosensor was able to distinguish between blank, non-methylated, non-complementary, and target dsDNA spiked in mouse plasma. The LOD was calculated to be 0.86 pM with a wide linear range of 1 pM to 50 µM. To the best of our knowledge, this is the first report on using PNA to detect ds-methylated DNA. This sandwich design can be modified to detect other methylated genes, making it a promising platform to detect ds-methylated biomarkers.

A dual-modal aptasensor based on a multifunctional acridone derivate for exosomes detection

Exosomes are promising biomarkers for cancer screening, but the development of a robust approach that can sensitively and accurately detect exosomes remains challenging. In the present study, an aptasensor based on the multifunctional signal probe 10-benzyl-2-amino-acridone (BAA) was developed for the colorimetric and photoelectrochemical detection and quantitation of exosomes. Exosomes are captured by cholesterol DNA anchor-modified magnetic beads (MBs) through hydrophobic interactions. This capture process can be monitored under a confocal fluorescence microscope using BAA as the fluorescent signal probe. The aptamer modified copper oxide nanoparticles (CuO NPs) then bind to mucin 1 (MUC1) on the surface of the exosomes to form a sandwich structure (MBs-Exo-CuO NPs). Finally, the MBs-Exo-CuO NPs are dissolved in nitric acid to generate Cu²⁺, which inhibits the visible-light-induced oxidase mimic activity and photoelectrochemical activity of BAA simultaneously. The changes in absorbance and photocurrent intensities are directly proportional to the concentration of exosomes. In this dual-modal aptasensor, the colorimetric assay can achieve rapid screening and identification, which is especially useful for point-of-care testing. The UV-vis absorbance and photocurrent assays then provide quantitative information, with a limit of detection of 1.09 × 10³ particles μL^-1 and 1.38 × 10³ particles μL^-1, respectively. The proposed aptasensor thus performs dual-modal detection and quantitation of exosomes. This aptasensor provides a much-needed toolset for exploring the biological roles of exosomes in specific diseases, particularly in the clinical setting.

The TDs/aptamer cTnI biosensors based on HCR and Au/Ti3C2-MXene amplification for screening serious patient in COVID-19 pandemic

The accurate assay of cardiac troponin I (cTnI) is very important for acute myocardial infarction (AMI), it also can be employed as an effective index for screening serious patients in COVID-19 pandemic before fatal heart injury to reduce the mortality. A ratiometric sensing strategy was proposed based on electrochemiluminescent (ECL) signal of doxorubicin (Dox)-luminol or the electrochemical (EC) signal of methylene blue (MB) vs. referable EC signal of Dox. The bio-recognitive Tro4-aptamer ensures the high specificity of the sensor by affinity binding to catch cTnI, and the tetrahedral DNA (TDs) on Au/Ti₃C₂-MXene built an excellent sensing matrix. An in situ hybrid chain reaction (HCR) amplification greatly improved the sensitivity. The ratiometric sensing responses ECL_Dox-luminol/Current_Dox or Current_MB/Current_Dox linearly regressed to cTnI concentration in the range of 0.1 fM-1 pM or 0.1 fM-500 fM with the limit of detection (LOD) as 0.04 fM or 0.1 fM, respectively. Served as the reference signal, Current_Dox reflected the variation of sensor, it is very effective to ensure the accuracy of detection to obviate the false results. The proposed biosensors show good specificity, sensitivity, reproducibility and stability, have been applied to determine cTnI in real samples with satisfactory results. They are worth looking forward to be used for screening serious patient of COVID-19 to reduce the mortality, especially in mobile cabin hospital.

Ultra-sensitive detection of DNA N6-adenine methyltransferase based on a 3D tetrahedral fluorescence scaffold assisted by symmetrical double-ring dumbbells

DNA methylation is an epigenetic modification that plays a vital role in X chromosome inactivation, genome imprinting, and gene expression. DNA methyltransferase establishes and maintains a stable methylation state in genomic DNA. Efficient and specific DNA methyltransferase testing is essential for the early diagnosis and treatment of cancer. In this study, we designed an ultra-sensitive fluorescent biosensor, based on a 3D tetrahedral fluorescent scaffold assisted by symmetrical double-ring dumbbells, for the detection of DNA-[N 6-adenine]-methyltransferase (Dam MTase). Double-stranded DNA was methylated by Dam MTase and then digested by DpnI to form two identical dumbbell rings. The 3D tetrahedral fluorescent scaffold was synthesized from four oligonucleotide chains containing hairpins. When the sheared dumbbells reacted with the 3D tetrahedral fluorescent scaffold, the hairpins opened and a fluorescence signal could be detected. The strategy was successful over a wide detection range, from 0.002 to 100 U mL^-1 Dam MTase, and the lowest detection limit was 0.00036 U mL^-1. Control experiments with M.SssI methyltransferase and HpaII methylation restriction endonuclease confirmed the specificity of the method. Experiments with spiked human serum and the 5-fluorouracil inhibitor proved the suitability of the method for early cancer diagnosis.

A double-tetrahedral DNA framework based electrochemical biosensor for ultrasensitive detection and release of circulating tumor cells

Detecting circulating tumor cells (CTCs) in patients' blood is essential for early diagnosis, precise treatment and prognosis of cancer. Yet due to CTCs being extremely rare in the peripheral blood of patients, it is still a challenge to detect CTCs with high sensitivity and high selectivity. Here, we developed a double-tetrahedral DNA framework (DTDF) based electrochemical biosensor system (E-CTC sensor system) for ultrasensitive detection and release of CTCs. In this work, an upright tetrahedral DNA framework (UTDF) was used as a rigid scaffold to modify a screen-printed gold electrode (SPGE), and an inverted tetrahedral DNA framework (ITDF) provided three vertex chains to multivalently bind with aptamers. Meanwhile, a streptavidin tagged horseradish peroxidase homopolymer (SA-polyHRP) was linked to biotin-modified aptamers to significantly amplify the signal. Moreover, the captured CTCs could be effectively released via benzonase nuclease with little cell damage. Our E-CTC sensor system achieved a linear range from 1 to 10⁵ MCF-7 cells with an ultralow detection limit of 1 cell. The release efficiency reached 88.1%-97.6% and the viability of the released cells reached up to 98%. We also detected the MCF-7 cells in mimic whole blood samples, suggesting that the E-CTC sensor system shows promise for use in clinical research.

A functional peptide-mediated colorimetric assay for mercury ion based on dual-modified gold nanoparticles

In the work, a rapid and accurate biosensor for mercury ions (Hg²⁺) was constructed, with which aggregation of dual-modified (DGPFHR- and CALNN-) gold nanoparticles (D/C-AuNPs) could be triggered by the high specificity of peptides to Hg²⁺. The given peptide DGPFHR possesses great capability of capturing Hg²⁺, accompanied by the conformational folding. Under the circumstances, D/C-AuNPs were employed as the detection probes to accomplish the quantitative analysis of Hg²⁺. This is primarily because the specific Hg²⁺-induced folding of peptides reduces the electrostatic repulsion and steric hindrance, thus accelerating the AuNPs aggregation. The principle and application potential of this proposal was proved by evidence. And the results demonstrated that Hg²⁺ ions could be selectively detected as low as 28 nM with a linear range of 100-800 nM. In consideration of superior simplicity, selectivity, accuracy and stability, the protocol was advantageous over other projects in practical measurement of various water samples.

DNA Nanodevice as a Co-delivery Vehicle of Antisense Oligonucleotide and Silver Ions for Selective Inhibition of Bacteria Growth

DNA nanostructures possess unique programmability and addressability and exhibit a wide variety of potential applications. Recently, they demonstrated their ability to be ideal carriers of antibacterial drugs. In this study, the first use of a DNA six-helix bundle (6HB) nanostructure to co-deliver antisense oligonucleotide (ASO) and silver ions is reported. Although 6HB with Ag⁺ shows excellent antibacterial effect against both Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus, 6HB with ASO selectively inhibits S. aureus. Furthermore, 6HB with both Ag⁺ and ASO exhibits enhanced antibacterial efficacy on S. aureus, probably through two sequential activities. Specifically, Ag⁺-modified 6HB greatly delays bacterial growth by destroying its cell walls, whereas 6HB conjugated with ASO targeting the ftsZ gene of S. aureus effectively inhibits its growth in the logarithmic growth phase by inhibiting the expression of the ftsZ gene. Moreover, this synergistic antibacterial treatment shows excellent biosafety with human normal liver cell L02. This co-delivery system by DNA nanostructures provides a promising platform for antibacterial therapeutics.

An electrochemical genosensor for differentiation of fully methylated from fully unmethylated states of BMP3 gene

The methylation state of a part of the BMP3 gene was detected by our genosensor. This epigenetic biomarker is involved in the biomarker panel of the sDNA test, which is an FDA approved test for colorectal cancer screening. In the present genosensor, polyethyleneimine-stabilized silver nanoparticles (PEI-AgNPs) were used as a non-specific nanolabel for signal generation/amplification and lowering the limit of detection. After immobilization of capture probes and mercaptoethanol molecules on the gold electrode, a thermally treated mixture of the BMP3 targets and reporter probes was introduced to the electrode. Because of the specificity of the reporter probes for fully methylated targets, complete sandwich-like complexes are formed only with them. Therefore, such full-length double-stranded hybrids compared to fully unmethylated targets have more negative charges and can more attract positively charged PEI-AgNPs. For discrimination between methylated and unmethylated targets, electroimpedance spectroscopy and cyclic voltammetry were used for electrode modification monitoring and signal measurement. The sharp and narrow anodic peaks of cyclic voltammograms, which resulted from silver oxidation, were utilized for calibration plot analysis. The genosensor showed a linear response for the target concentration range from 1fM to 100 nM, while the detection limit for methylated and unmethylated target discrimination was 1 fM.

Dual-modality loop-mediated isothermal amplification for pretreatment-free detection of Septin9 methylated DNA in colorectal cancer

Currently, the determination of DNA methylation is still a challenge due to the limited efficiency of enrichment, bisulfite modification, and detection. In this study, a dual-modality loop-mediated isothermal amplification integrated with magnetic bead isolation is  proposed for the determination of methylated Septin9 gene in colorectal cancer. Magnetic beads modified with anti-methyl cytosine antibody were prepared for fast enrichment of methylated DNA through specific immunoaffinity (30 min). One-pot real-time fluorescence and colorimetric loop-mediated isothermal amplification were simultaneously developed for detecting methylated Septin9 gene (60 min). The real-time fluorescence generating by SYTO-9 dye (excitation: 470 nm and emission: 525 nm) and pH indicator (neutral red) was used for quantitative and visualized detection of methylated DNA. This method was demonstrated to detect methylated DNA from HCT 116 cells ranging from 2 to 0.02 ng/μL with a limit of detection of 0.02 ± 0.002 ng/μL (RSD: 9.75%). This method also could discriminate methylated Septin9 in 0.1% HCT 116 cells (RSD: 6.60%), suggesting its high specificity and sensitivity. The feasibility of this assay was further evaluated by clinical plasma samples from 20 colorectal cancer patients and 20 healthy controls, which shows the potential application in simple, low cost, quantitative, and visualized detection of methylated nucleic acids.

Recent Progress in DNA Hybridization Chain Reaction Strategies for Amplified Biosensing

With the continuous development of DNA nanotechnology, various spatial DNA structures and assembly techniques emerge. Hybridization chain reaction (HCR) is a typical example with exciting features and bright prospects in biosensing, which has been intensively investigated in the past decade. In this Spotlight on Applications, we summarize the assembly principles of conventional HCR and some novel forms of linear/nonlinear HCR. With advantages like great assembly kinetics, facile operation, and an enzyme-free and isothermal reaction, these strategies can be integrated with most mainstream reporters (e.g., fluorescence, electrochemistry, and colorimetry) for the ultrasensitive detection of abundant targets. Particularly, we select several representative studies to better illustrate the novel ideas and performances of HCR strategies. Theoretical and practical utilities are confirmed for a range of biosensing applications. In the end, a deep discussion is provided about the challenges and future tasks of this field.

Quantification and mapping of DNA modifications

Apart from the four canonical nucleobases, DNA molecules carry a number of natural modifications. Substantial evidence shows that DNA modifications can regulate diverse biological processes. Dynamic and reversible modifications of DNA are critical for cell differentiation and development. Dysregulation of DNA modifications is closely related to many human diseases. The research of DNA modifications is a rapidly expanding area and has been significantly stimulated by the innovations of analytical methods. With the recent advances in methods and techniques, a series of new DNA modifications have been discovered in the genomes of prokaryotes and eukaryotes. Deciphering the biological roles of DNA modifications depends on the sensitive detection, accurate quantification, and genome-wide mapping of modifications in genomic DNA. This review provides an overview of the recent advances in analytical methods and techniques for both the quantification and genome-wide mapping of natural DNA modifications. We discuss the principles, advantages, and limitations of these developed methods. It is anticipated that new methods and techniques will resolve the current challenges in this burgeoning research field and expedite the elucidation of the functions of DNA modifications.

Multifunctional electrochemical biosensor with "tetrahedral tripods" assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA

Nucleic acids are genetic materials in the human body that play important roles in storing, copying, and transmitting genetic information. Abnormal nucleic acid sequences, base mutations, and genetic changes often lead to cancer and other diseases. Meanwhile, methylated DNA is one of the main epigenetic modifications, which is considered to be an excellent biomarker in the early detection, prognosis, and treatment of cancers. Therefore, a multifunctional electrochemical biosensor was constructed with sturdy tetrahedral tripods, which assisted multiple tandem hairpins through base complementary pairing and effective ultra-sensitive detection of targets (DNA, microRNA, and methylated DNA). In the experiments, experimental conditions were optimized, and different DNA concentrations in serum were detected to verify the sensitivity of the biosensor and the feasibility of this protocol. In addition, microRNA and DNA methylation were detected through different designs of tetrahedral tripods (TTs) that capture probes to prove the superiority of this scheme. A sturdy pyramid structure of TTs extremely enhanced the capture efficiency of targets. The targets triggered the one-step isothermal multi-tandem amplification reaction by incubating multiple hairpin assemblies. To our knowledge, a combination of two parts, which greatly reduced background interference and decreased non-specific substance interference, has appeared for the first time in this paper. Moreover, the load area of electrochemical substances was significantly increased than that in previous studies. This greatly increased the detection range and detection limit of targets. The electrochemical signal responses were generated in freely diffusing hexaammineruthenium(iii) chloride (RuHex). RuHex could adhere to the DNA phosphate backbone by a powerful electrostatic attraction, causing increased current responses.

Schematic illustration of the fabricated electrochemical biosensor. TTs assisted multiple tandem hairpins assembly for ultra-sensitive detection of target DNA.

DNA nanostructure-based nucleic acid probes: construction and biological applications

In recent years, DNA has been widely noted as a kind of material that can be used to construct building blocks for biosensing, in vivo imaging, drug development, and disease therapy because of its advantages of good biocompatibility and programmable properties. However, traditional DNA-based sensing processes are mostly achieved by random diffusion of free DNA probes, which were restricted by limited dynamics and relatively low efficiency. Moreover, in the application of biosystems, single-stranded DNA probes face challenges such as being difficult to internalize into cells and being easily decomposed in the cellular microenvironment. To overcome the above limitations, DNA nanostructure-based probes have attracted intense attention. This kind of probe showed a series of advantages compared to the conventional ones, including increased biostability, enhanced cell internalization efficiency, accelerated reaction rate, and amplified signal output, and thus improved in vitro and in vivo applications. Therefore, reviewing and summarizing the important roles of DNA nanostructures in improving biosensor design is very necessary for the development of DNA nanotechnology and its applications in biology and pharmacology. In this perspective, DNA nanostructure-based probes are reviewed and summarized from several aspects: probe classification according to the dimensions of DNA nanostructures (one, two, and three-dimensional nanostructures), the common connection modes between nucleic acid probes and DNA nanostructures, and the most important advantages of DNA self-assembled nanostructures in the applications of biosensing, imaging analysis, cell assembly, cell capture, and theranostics. Finally, the challenges and prospects for the future development of DNA nanostructure-based nucleic acid probes are also discussed.

e-MagnetoMethyl IP: a magnetic nanoparticle-mediated immunoprecipitation and electrochemical detection method for global DNA methylation

The quantification of global 5-methylcytosine (5mC) content has emerged as a promising approach for the diagnosis and prognosis of cancers. However, conventional methods for the global 5mC analysis require large quantities of DNA and may not be useful for liquid biopsy applications, where the amount of DNA available is limited. Herein, we report magnetic nanoparticles-assisted methylated DNA immunoprecipitation (e-MagnetoMethyl IP) coupled with electrochemical quantification of global DNA methylation. Carboxyl (-COOH) group-functionalized iron oxide nanoparticles (C-IONPs) synthesized by a novel starch-assisted gel formation method were conjugated with anti-5mC antibodies through EDC/NHS coupling (anti-5mC/C-IONPs). Anti-5mC/C-IONPs were subsequently mixed with DNA samples, in which they acted as dispersible capture agents to selectively bind 5mC residues and capture the methylated fraction of genomic DNA. The target-bound Anti-5mC/C-IONPs were magnetically separated and directly adsorbed onto the gold electrode surface using gold-DNA affinity interaction. The amount of DNA adsorbed on the electrode surface, which corresponds to the DNA methylation level in the sample, was electrochemically estimated by differential pulse voltammetric (DPV) study of an electroactive indicator [Ru(NH₃)₆]³⁺ bound to the surface-adsorbed DNA. Using a 200 ng DNA sample, the assay could successfully detect differences as low as 5% in global DNA methylation levels with high reproducibility (relative standard deviation (% RSD) = <5% for n = 3). The method could also reproducibly analyze various levels of global DNA methylation in synthetic samples as well as in cell lines. The method avoids bisulfite treatment, does not rely on enzymes for signal generation, and can detect global DNA methylation using clinically relevant quantities of sample DNA without PCR amplification. We believe that this proof-of-concept method could potentially find applications for liquid biopsy-based global DNA methylation analysis in point-of-care settings.

Entropy-driven amplified electrochemiluminescence biosensor for RdRp gene of SARS-CoV-2 detection with self-assembled DNA tetrahedron scaffolds

Dependable, specific and rapid diagnostic methods for severe acute respiratory syndrome β-coronavirus (SARS-CoV-2) detection are needed to promote public health interventions for coronavirus disease 2019 (COVID-19). Herein, we have established an entropy-driven amplified electrochemiluminescence (ECL) strategy to detect the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 known as RdRp-COVID which as the target for SARS-CoV-2 plays an essential role in the diagnosis of COVID-19. For the construction of the sensors, DNA tetrahedron (DT) is modified on the surface of the electrode to furnish robust and programmable scaffolds materials, upon which target DNA-participated entropy-driven amplified reaction is efficiently conducted to link the Ru (bpy)32+ modified S3 to the linear ssDNA at the vertex of the tetrahedron and eventually present an "ECL on" state. The rigid tetrahedral structure of the DT probe enhances the ECL intensity and avoids the cross-reactivity between single-stranded DNA, thus increasing the sensitivity of the assays. The enzyme-free entropy-driven reaction prevents the use of expensive enzyme reagents and facilitates the realization of large-scale screening of SARS-CoV-2 patients. Our DT-based ECL sensor has demonstrated significant specificity and high sensitivity for SARS-CoV-2 with a limit of detection (LOD) down to 2.67 fM. Additionally, our operational method has achieved the detection of RdRp-COVID in human serum samples, which supplies a reliable and feasible sensing platform for the clinical bioanalysis.

A Label-Free DNA-Immunosensor Based on Aminated rGO Electrode for the Quantification of DNA Methylation

In this work, we developed a sandwich DNA-immunosensor for quantification of the methylated tumour suppressor gene O-6-methylguanine-DNA methyltransferase (MGMT), which is a potential biomarker for brain tumours and breast cancer. The biosensor is based on aminated reduced graphene oxide electrode, which is achieved by ammonium hydroxide chemisorption and anti-5-methylcytosine (anti-5mC) as a methylation bioreceptor. The target single-strand (ss) MGMT oligonucleotide is first recognised by its hybridisation with complementary DNA to form double-stranded (ds) MGMT, which is then captured by anti-5mC on the electrode surface due to the presence of methylation. Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and Scanning electron microscopy (SEM) techniques were used to characterise the electrode surface. Cyclic voltammetry (CV) and differential pulse voltammetry (DPV) techniques were used for electrochemical measurements. Under optimised conditions, the proposed biosensor is able to quantify a linear range of concentrations of the MGMT gene from 50 fM to 100 pM with a limit of detection (LOD) of 12 fM. The sandwich design facilitates the simultaneous recognition and quantification of DNA methylation, and the amination significantly improves the sensitivity of the biosensor. This biosensor is label-, bisulfite- and PCR-free and has a simple design for cost-efficient production. It can also be tailor-made to detect other methylated genes, which makes it a promising detection platform for DNA methylation-related disease diagnosis and prognosis.

Self-Assembled DNA Nanoflowers Triggered by a DNA Walker for Highly Sensitive Electrochemical Detection of Staphylococcus aureus

With the development of DNA nanotechnology, DNA has been widely used to construct a variety of nanomachines. Among them, a DNA walker is a unique nanomachine that can move continuously along a specific orbit to fulfill diverse functions. In this paper, a dual signal amplification electrochemical biosensor based on a DNA walker and DNA nanoflowers is constructed for high sensitivity detection of Staphylococcus aureus (S. aureus). Two groups of double-stranded DNA are modified on the surface of a gold electrode. The binding of S. aureus with its aptamer induces the disintegration of the long double strands and releases the DNA walker. With the help of exonuclease III (Exo III), the DNA walker moves along the electrode surface and continuously hydrolyzes the anchored short double strands. The introduction of a specially customized circular DNA and phi29 DNA polymerase initiates the rolling circle amplification (RCA) reaction. DNA nanoflowers are formed at high local concentration of DNA in the solution, which provide binding sites for electroactive methylene blue (MB) and thus produce intense signal. Under the best conditions, the current response is linearly related to the logarithm of the concentration of S. aureus ranging from 60 to 6 × 10⁷ CFU/mL, and the detection limit is 9 CFU/mL. In addition, the proposed biosensor has achieved satisfactory results in the detection of actual water samples and diluted honey samples, which confirm the practicability of the biosensor and its application potential in environmental monitoring and food safety.

Hybridizing clinical translatability with enzyme-free DNA signal amplifiers: recent advances in nucleic acid detection and imaging

Nucleic acids have become viable prognostic and diagnostic biomarkers for a diverse class of diseases, particularly cancer. However, the low femtomolar to attomolar concentration of nucleic acids in human samples require sensors with excellent detection capabilities; many past and current platforms fall short or are economically difficult. Strand-mediated signal amplifiers such as hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are superior methods for detecting trace amounts of biomolecules because one target molecule triggers the continuous production of synthetic double-helical DNA. This cascade event is highly discriminatory to the target via sequence specificity, and it can be coupled with fluorescence, electrochemistry, magnetic moment, and electrochemiluminescence for signal reporting. Here, we review recent advances in enhancing the sensing abilities in HCR and CHA for improved live-cell imaging efficiency, lowered limit of detection, and optimized multiplexity. We further outline the potential for clinical translatability of HCR and CHA by summarizing progress in employing these two tools for in vivo imaging, human sample testing, and sensing-treating dualities. We finally discuss their future prospects and suggest clinically-relevant experiments to supplement further related research.