Search Results (789)

This study presents a high-performance silicon nanowire (SiNW) array biosensor for the combined detection of two key colorectal cancer (CRC) biomarkers: circulating tumor DNA (ctDNA) and carcinoembryonic antigen (CEA). The device was fabricated using conventional micromachining techniques, enabling the integration of dual SiNW arrays on a single chip with precise control over structure and surface functionalization. Specific probe DNA and anti-CEA antibodies were immobilized on distinct array regions to facilitate targeted binding. The biosensor demonstrated exceptional performance, achieving an ultralow detection limit of 10 aM for ctDNA with a linear range from 0.1 fM to 10 pM, and a sensitivity of 1 fg/mL for CEA. It exhibited high selectivity against interfering substances, including single-base mismatched DNA and non-specific proteins, and maintained robust performance in human serum samples. The platform offers a scalable, label-free, and real-time detection solution with significant potential for application in early CRC screening and personalized medicine. Full article

Epigenetic biomarkers, such as DNA methylation, histone alterations, and non-coding RNAs, are increasingly recognized as essential instruments in disease diagnoses, prognostics, and customized therapy. As their clinical significance increases, so does the necessity for robust, interpretable, and scalable techniques that can accurately detect these molecular alterations. This review provides a critical and organized overview of contemporary technologies employed to characterize the principal categories of epigenetic modifications, encompassing PCR- and sequencing-based methods, high-resolution immunoprecipitation techniques, and CRISPR-enhanced detection systems. Although numerous procedures are technically well-established, their implementation outside research laboratories frequently faces substantial challenges: elevated prices, data intricacy, absence of standardization, and restricted translational frameworks. Furthermore, the interpretation of epigenetic data continues to pose a significant difficulty, especially for heterogeneous clinical samples and the swiftly advancing computational techniques. We examine the advantages and drawbacks of existing approaches, focusing on their incorporation into biomedical engineering platforms, including biosensors, lab-on-a-chip devices, and AI-assisted diagnostics. This review seeks to assist researchers, physicians, and engineers in choosing suitable technologies, comprehending their limitations, and pinpointing areas requiring urgent innovation by merging analytical rigor with a pragmatic viewpoint. Full article

The interaction between DNA and two-dimensional materials, such as graphene oxide (GO), has aroused significant research interest due to its potential applications, including biosensors, drug delivery, and gene therapy. However, the difference in interaction between DNA and oxygen functional groups on GO remains unclear, and direct observation at the experimental level is still challenging. In this work, we investigated the adsorption process of a single-stranded DNA (ssDNA) onto GO exhibiting a series of oxidation degrees by molecular dynamics simulations. We found that the ssDNA preferentially binds to hydroxyl groups (-OH) over epoxy groups (-O-) on the GO surface. This preferential adsorption feature may be attributed to the stronger tendency of ssDNA to form hydrogen bonds (HBs) with hydroxyl groups compared to epoxy groups in aqueous solutions. Further analysis indicates that the affinity interaction between ssDNA and hydroxyl groups presumably increases the oxidation degree of GO, thus suggesting a better binding between ssDNA and GO. This work is not only expected to provide the underlying mechanism of ssDNA onto graphene-based interfaces but also offers a deeper understanding of the structures of DNA-two-dimensional complexes, which may potentially contribute to designing new molecular structures for bio-sensing-related nano-devices and nanostructures. Full article

Salmonella poses a severe global threat to food safety and public health, necessitating rapid, sensitive, and reliable detection methods. Conventional techniques often suffer from complexity, time consumption, cost, or limited sensitivity. To address this, we developed a novel enzyme-free fluorescence detection platform, termed the MTAI-CHA system, integrating magnetic nanoparticle-based triangle multivalent aptamer-initiators (MTAI) with catalytic hairpin assembly (CHA) signal amplification. The triangular DNA nanostructure contained significantly enhanced binding affinity of multivalent aptamers, increasing the sensitivity compared to monovalent aptamers. The optimized MTAI-CHA system demonstrated exceptional performance: a low detection limit of 10 CFU/mL and excellent specificity against non-target pathogens. This sensitive, specific, and robust strategy, leveraging multivalent aptamer recognition and enzyme-free signal amplification, holds significant potential for rapid pathogen screening in food safety, clinical diagnostics, and environmental monitoring, with adaptability to other targets via aptamer substitution. Full article

Apurinic/apyrimidinic endonuclease 1 (APE1) selectively cleaves the apurinic/apyrimidinic site (AP site) in DNA, playing a critical role in base excision repair and genomic stability maintenance. Aberrant APE1 expression has been linked to numerous diseases, including cardiovascular disorders, neurological conditions, and various cancers. However, existing methods for detecting trace levels of APE1 remain suboptimal for certain applications. To address this limitation, we developed an innovative biosensing platform for ultrasensitive APE1 detection by integrating APE1-specific site recognition with hybridization chain reaction (HCR)-based signal amplification, enabling enzyme- and label-free bioassays. In this system, APE1 recognizes and cleaves the AP site-containing hairpin (HP) probe, releasing a single-stranded HCR initiator that triggers cascaded HCR amplification. Owing to the high efficiency of HCR, this method achieves ultrahigh sensitivity, with a calculated detection limit of 1.0 × 10⁻⁸ U/mL. Furthermore, the biosensor demonstrates robust performance in cell lysates and is applicable for screening and evaluating APE1 inhibitors. Full article

Lignin, the second most abundant biopolymer in nature after cellulose, has attracted attention for its compatibility with carbon-based materials. In this study, lignin-modified single-use pencil graphite electrodes (PGE/LG) were developed for the electrochemical detection of fish sperm DNA (fsDNA), the anticancer drug Mitomycin C (MC), and their interaction. The modified electrodes were characterized using field emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDX), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) techniques. Differential pulse voltammetry (DPV) in ferri/ferrocyanide redox probe solution was employed for signal monitoring. The detection limits were calculated as 2.95 ng/mL for fsDNA between 10¹ and 10⁵ ng/mL and 0.22 pg/mL for MC between 1 and 10⁶ pg/mL. Furthermore, the interaction of DNA with MC was evaluated by DPV and EIS techniques. The cross-linking between MC and the guanine bases of DNA inhibited electron transfer, resulting in a decrease in current response and an increase in charge transfer resistance. These results demonstrate the potential of the PGE/LG platform as a cost-effective, sensitive, and rapid biosensor for DNA detection, anticancer drug analysis, and drug–DNA interaction studies. Full article

Nanopore-based DNA sequencing has emerged as a transformative biosensing technology, enabling real-time molecular diagnostics in compact and mobile form factors. However, the computational complexity of the basecalling process—the step that translates raw nanopore signals into nucleotide sequences—poses a critical energy challenge for mobile deployment. While deep learning (DL) models currently dominate this task due to their high accuracy, they demand substantial power budgets and computing resources, making them unsuitable for portable or field-scale biosensor platforms. In this work, we propose an embedded hardware–software framework for DNA sequence detection that leverages a Viterbi-based Hidden Markov Model (HMM) implemented on a custom 64-bit RISC-V core. The proposed HMM detector is realized on an off-the-shelf Virtex-7 FPGA and evaluated against state-of-the-art DL-based basecallers in terms of energy efficiency and inference accuracy. From one side, the experimental results show that our system achieves an energy efficiency improvement of 6.5×, 5.5×, and 4.6×, respectively, compared to similar HMM-based detectors implemented on a commodity x86 processor, Cortex-A9 ARM embedded system, and a previously published Rocket-based system. From another side, the proposed detector demonstrates 15× and 2.4× energy efficiency superiority over state-of-the-art DL-based detectors, with competitive accuracy and sufficient throughput for field-based genomic surveillance applications and point-of-care diagnostics. This study highlights the practical advantages of classical probabilistic algorithms when tightly integrated with lightweight embedded processors for biosensing applications constrained by energy, size, and latency. Full article

Antimicrobial resistance (AMR) is a significant global threat and is driven by the overuse of antibiotics in both clinical and agricultural settings. This issue is further complicated by the lack of rapid surveillance tools to detect resistant bacteria in clinical, environmental, and food systems. Of particular concern is the rise in resistance to carbapenems, a critical class of beta-lactam antibiotics. Rapid detection methods are necessary for prevention and surveillance effort. This study utilized a gold nanoparticle-based plasmonic biosensor to detect three CR genes: bla_KPC-3, bla_NDM-1, and bla_OXA-1. Optical signals were analyzed using both a spectrophotometer and a smartphone app that quantified visual color changes using RGB values. This app, combined with a simple boiling method for DNA extraction and a portable thermal cycler, was used to evaluate the biosensor’s potential for POC use. Advantages of the portable bacterial detection device include real time monitoring for immediate decision-making in critical situations, field and on-site testing in resource-limited settings without needing to transport samples to a centralized lab, minimal training required, automatic data analysis, storage and sharing, and reduced operational cost. Bacteria were inoculated into sterile water, river water, and turkey rinse water samples to determine the biosensor’s success in detecting target genes from sample matrices. Magnetic nanoparticles were used to capture and concentrate bacteria to avoid time-consuming cultivation and separation steps. The biosensor successfully detected the target CR genes in all tested samples using three gene-specific DNA probes. Target genes were detected with a limit of detection of 2.5 ng/L or less, corresponding to ~10³ CFU/mL of bacteria. Full article

Electrochemical biosensors have emerged as a promising tool for the early detection of diseases in oilseed crops such as rapeseed, soybean, and peanut. These biosensors offer high sensitivity, portability, and cost-effectiveness. Timely diagnosis is critical, as many pathogens exhibit latent infection phases or produce invisible metabolic toxins, leading to substantial yield losses before visible symptoms occur. This review summarises recent advances in the field of nanomaterial-assisted electrochemical sensing for oilseed crop diseases, with a particular focus on sensor mechanisms, interface engineering, and biomolecular recognition strategies. The following innovations are highlighted: nanostructured electrodes, aptamer- and antibody-based probes, and signal amplification techniques. These innovations have enabled the detection of pathogen DNA, enzymes, and toxins at ultra-low concentrations. Notwithstanding these achievements, challenges persist, including signal interference from plant matrices, limitations in device miniaturization, and the absence of standardized detection protocols. Future research should explore the potential of AI-assisted data interpretation, the use of biodegradable sensor materials, and the integration of these technologies with agricultural IoT networks. The aim of this integration is to enable real-time, field-deployable disease surveillance. The integration of laboratory innovations with field applications has been demonstrated to have significant potential in supporting sustainable agriculture and strengthening food security through intelligent crop health monitoring. Full article

Staphylococcus aureus is the primary pathogen responsible for mastitis in dairy cows and foodborne illnesses, posing a significant threat to public health and food safety. Here, we developed an enhanced sensor based on solid-phase separation using gold-magnetic nanoparticles (Au@Fe₃O₄) and signal amplification via dendritic DNA nanostructures. The substrate chain was specifically immobilized using thiol–gold coordination, and a three-dimensional dendritic structure was constructed through sequential hybridization of DNAzymes, L chains, and Y chains, resulting in a 2.8-fold increase in initial fluorescence intensity. Upon specific cleavage of the substrate chain at the rA site by S. aureus DNA, the complex dissociates, resulting in fluorescence intensity decay. The fluorescence intensity is negatively correlated with the concentration of Staphylococcus aureus. After optimization, the biosensor maintains a detection limit of 1 CFU/mL within 3 min, with a linear range extended to 1–10⁷ CFU/mL (R² = 0.998) and recovery rates of 85.6–102.1%, significantly enhancing resistance to matrix interference. This provides an innovative solution for rapid on-site detection of foodborne pathogens. Full article

Early and accurate detection of plant diseases is critical for ensuring global food security and agricultural resilience. Ratoon stunting disease (RSD), caused by the bacterium Leifsonia xyli subsp. xyli (Lxx), is among the most economically significant diseases of sugarcane worldwide. Its cryptic nature—characterized by an absence of visible symptoms—renders timely diagnosis particularly difficult, contributing to substantial undetected yield losses across major sugar-producing regions. Here, we report the development of a potential-induced electrochemical (EC) nanobiosensor platform for the rapid, low-cost, and field-deployable detection of Lxx DNA directly from crude sugarcane sap. This method eliminates the need for conventional nucleic acid extraction and thermal cycling by integrating the following: (i) a boiling lysis-based DNA release from xylem sap; (ii) sequence-specific magnetic bead-based purification of Lxx DNA using immobilized capture probes; and (iii) label-free electrochemical detection using a potential-driven DNA adsorption sensing platform. The biosensor shows exceptional analytical performance, achieving a detection limit of 10 cells/µL with a broad dynamic range spanning from 10⁵ to 1 copy/µL (r = 0.99) and high reproducibility (SD < 5%, n = 3). Field validation using genetically diverse sugarcane cultivars from an inoculated trial demonstrated a strong correlation between biosensor signals and known disease resistance ratings. Quantitative results from the EC biosensor also showed a robust correlation with qPCR data (r = 0.84, n = 10, p < 0.001), confirming diagnostic accuracy. This first-in-class EC nanobiosensor for RSD represents a major technological advance over existing methods by offering a cost-effective, equipment-free, and scalable solution suitable for on-site deployment by non-specialist users. Beyond sugarcane, the modular nature of this detection platform opens up opportunities for multiplexed detection of plant pathogens, making it a transformative tool for early disease surveillance, precision agriculture, and biosecurity monitoring. This work lays the foundation for the development of a universal point-of-care platform for managing plant and crop diseases, supporting sustainable agriculture and global food resilience in the face of climate and pathogen threats. Full article

Microalgae, with their unparalleled capabilities for sunlight-driven growth, CO₂ fixation, and synthesis of diverse high-value compounds, represent sustainable cell factories for a circular bioeconomy. However, industrial deployment has been hindered by biological constraints and the inadequacy of conventional genetic tools. The advent of CRISPR-Cas systems initially provided precise gene editing via targeted DNA cleavage. This review argues that the true transformative potential lies in moving decisively beyond cutting to harness CRISPR as a versatile synthetic biology “Swiss Army Knife”. We synthesize the rapid evolution of CRISPR-derived tools—including transcriptional modulators (CRISPRa/i), epigenome editors, base/prime editors, multiplexed systems, and biosensor-integrated logic gates—and their revolutionary applications in microalgal engineering. These tools enable tunable gene expression, stable epigenetic reprogramming, DSB-free nucleotide-level precision editing, coordinated rewiring of complex metabolic networks, and dynamic, autonomous control in response to environmental cues. We critically evaluate their deployment to enhance photosynthesis, boost lipid/biofuel production, engineer high-value compound pathways (carotenoids, PUFAs, proteins), improve stress resilience, and optimize carbon utilization. Persistent challenges—species-specific tool optimization, delivery efficiency, genetic stability, scalability, and biosafety—are analyzed, alongside emerging solutions and future directions integrating AI, automation, and multi-omics. The strategic integration of this CRISPR toolkit unlocks the potential to engineer robust, high-productivity microalgal cell factories, finally realizing their promise as sustainable platforms for next-generation biomanufacturing. Full article

Infectious diseases poses a growing public health challenge. The COVID-19 pandemic has further emphasized the urgent need for rapid, accessible diagnostics. This study presents the development of an integrated, flexible point-of-care (POC) diagnostic system for the rapid detection of Corynebacterium diphtheriae, the pathogen responsible for diphtheria. The system comprises a microfluidic polymerase chain reaction (micro-PCR) device and an electrochemical DNA biosensor, both fabricated on flexible substrates. The micro-PCR platform offers rapid DNA amplification overcoming the time limitations of conventional thermocyclers. The biosensor utilizes specific molecular recognition and an electrochemical transducer to detect the amplified DNA fragment, providing a clear and direct indication of the pathogen’s presence. The combined system demonstrates the effective amplification and detection of a gene fragment from a toxic strain of C. diphtheriae, chosen due to its increasing incidence. The design leverages lab-on-a-chip (LOC) and microfluidic technologies to minimize reagent use, reduce cost, and support portability. Key challenges in microsystem design—such as flow control, material selection, and reagent compatibility—were addressed through optimized fabrication techniques and system integration. This work highlights the feasibility of using flexible, integrated microfluidic and biosensor platforms for the rapid, on-site detection of infectious agents. The modular and scalable nature of the system suggests potential for adaptation to a wide range of pathogens, supporting broader applications in global health diagnostics. The approach provides a promising foundation for next-generation POC diagnostic tools. Full article

Deoxyribonucleic acid (DNA) is not only a fundamental biological molecule but also a versatile material for constructing sensitive and specific biosensing platforms. Its ability to undergo sequence-specific hybridization via Watson–Crick base pairing enables both precise target recognition and the programmable construction of nanoscale structures. The demand for ultrasensitive detection increases in fields such as disease diagnostics, therapeutics, and other areas, and the inherent characteristics of DNA have driven the development of a wide range of signal amplification strategies. Among these, polymerase chain reaction (PCR), rolling circle amplification (RCA), and loop-mediated isothermal amplification (LAMP) represent powerful target-based methods that enzymatically increase the concentration of nucleic acid targets, thereby boosting detection sensitivity. In parallel, structure-based strategies leverage the nanoscale spatial programmability of DNA to construct functional architectures with high precision. DNA can be used as a scaffold, such as DNA nanostructures, to organize sensing elements and facilitate signal transduction. It can also function as a probe, like aptamers, to recognize targets with high affinity. These versatilities enable the creation of highly sophisticated sensing platforms that integrate molecular recognition and signal amplification. Driven by DNA nano-assembly capability, both target-based and structure-based approaches are driving the advancement of highly sensitive, selective, and adaptable diagnostic technologies. This review highlights recent developments in DNA nano-assembly-driven amplification strategies. Full article

Shaking off the forgetfulness towards the methodological power of inosine-mediated error-prone PCR (epPCR), this study reintroduces an often-underappreciated method as a considerably powerful approach for generating aptamer libraries from a single decameric ATCG-repeat-oligonucleotide. The aim was to demonstrate that this simple way of creating sequence diversity was suitable for delivering functional starting libraries for a set of ten whole-cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) processes. This epPCR method uses inosine to introduce targeted mutations, avoiding the need for commercial oligo pools or large-scale synthesis. We applied this method to a “universal aptamer” and subjected the three resulting libraries to two rounds of selection against ten diverse targets including probiotic and pathogenic bacteria (Gram-negative and -positive) as well as human cell lines. The enriched aptamers exhibited new binding specificities, demonstrating that the approach supports functional selection. Much like dusting off an old tool and finding it perfectly suited for a modern task, this work shows that revisiting established techniques can address current challenges in aptamer development. Our main finding is that epPCR provides a robust, cost-effective strategy for generating starting libraries and lowers the barrier for initiating successful SELEX campaigns. Full article