DNA nanotechnology: A recent advancement in the monitoring of microcystin-LR

A bulit-in self-calibration ratiometric self-powered photoelectrochemical sensor for high-precision and sensitive detection of microcystin-RR

A novel high-precision aptasensor of microcystin-RR (MC-RR) is developed based on a ratiometric self-powered photoelectrochemical platform. In detail, the defective MoS2/Ti3C2 nanocomposite with good photoelectric activity was designed to serve as the photoanode of the sensor for enhancing the signal and improving the detection sensitivity. In order to effectively eliminate external interferences, the key point of this ratiometric device is the introduction of the spatial-resolved technique, which includes the detection section and the reference section, generating reference signals and response signals, respectively. Moreover, output power was used as the detection signal, instead of the traditional photocurrent or photovoltage. Further, potassium persulfate was introduced as electron acceptor, which was beneficial for improving the electron transport efficiency, hindering electron-hole recombination, and significantly promoting the performance of the sensor. Finally, aptamer was adopted as recognition element to capture MC-RR molecules. The prepared sensor had a linear range from 10-12 to 10-6 M, and the detection limit was 5.6 × 10-13 M (S/N = 3). It has good precision, selectivity, and sensitivity, which shows great prospects in the on-site accurate analysis of samples with high energy output in the self-powered sensing field.

Light-Initiated Imprinted Membrane-Based Biomimetic SERS Sensor toward Selective Detection of Trace MC-LR

Microcystin-LR (MC-LR) is a severe threat to human and animal health; thus, monitoring it in the environment is essential, especially in water quality protections. Herein, in this work, we synthesize PVDF/CNT/Ag molecular imprinted membranes (PCA-MIMs) via an innovative combination of surface-enhanced Raman spectroscopy (SERS) detection, membrane separation, and molecular-imprinted technique toward the analysis of MC-LR in water. In particular, a light-initiated imprint is employed to protect the chemical structure of the MC-LR molecules. Furthermore, in order to ensure the detection sensitivity, the SERS substrates are combined with the membrane via the assistance of magnetism. The effect of synthesis conditions on the SERS sensitivity was investigated in detail. It is demonstrated from the characteristic results that the PCA-MIMs present high sensitivity to the MC-LR molecules with excellent selectivity against the interfere molecules. Results clearly show that the as-prepared PCA-MIMs hold great potential applications to detect trace MC-LR for the protection of water quality.

A Single Set of Well-Designed Aptamer Probes for Reliable On-site Qualitative and Ultra-Sensitive Quantitative Detection

Aptamer-based probes are pivotal components in various sensing strategies, owing to their exceptional specificity and versatile programmable structure. Nevertheless, numerous aptamer-based probes usually offer only a single function, limiting their capacity to meet the diverse requirements of multi-faceted sensing systems. Here, we introduced supersandwich DNA probes (SSW-DNA), designed and modified on the outer surface of nanochannels with hydrophobic inner walls, enabling dual functionality: qualitative detection for on-site analysis and quantitative detection for precise analysis. The fragmented DNAs resulting from the target recognition, are subsequently identified through lateral flow assays, enabling robust on-site qualitative detection of microcystin-LR with an impressively low limit of detection (LOD) at 0.01 μg/L. Meanwhile, the nanochannels enable highly sensitive quantification of microcystin-LR through the current analysis, achieving an exceptionally low LOD at 2.5×10-7  μg/L, with a broad dynamic range spanning from 1×10-6 to 1×102  μg/L. Furthermore, the process of target recognition introduces just a single potential error propagation, which reduces the overall risk of errors during the entire qualitative and quantitative detection process. This sensing strategy broadens the scope of applications for aptamer-based composite probes, holding promising implications across diverse fields, such as medical diagnosis, food safety, and environmental protection.

Nanotechnology-based analytical techniques for the detection of contaminants in aquatic products

Food safety of aquatic products has attracted considerable attention worldwide. Although a series of conventional bioassays and instrumental methods have been developed for the detection of pathogenic bacteria, heavy metal residues, marine toxins, and biogenic amines during the production and storage of fish, shrimp, crabs et al., the nanotechnology-based analyses still have their advantages and are promising since they are cost-efficient, highly sensitive and selective, easy to conduct, facial design, often require no sophisticated instruments but with excellent detection performance. This review aims to summarize the advances of various biosensing strategies for bacteria, metal ions, and small molecule contaminants in aquatic products during the last five years, The review highlights the development in nanotechnologies applied for biorecognition process, signal transduction and amplification methods in each novel approach, the nuclease-mediated DNA amplification, nanomaterials (noble metal nanoparticle, metal-organic frameworks, carbon dots), lateral flow-based biosensor, surface-enhanced Raman scattering, microfluidic chip, and molecular imprinting technologies were especially emphasized. Moreover, this study provides a view of current accomplishments, challenges, and future development directions of nanotechnology in aquatic product safety evaluation.

Application of aptamer-conjugated graphene oxide for specific enrichment of microcystin-LR in Achatina fulica prior to matrix-assisted laser desorption ionization mass spectrometry

Microcystin-LR (MC-LR), as a hepatotoxin, can cause liver swelling, hepatitis, and even liver cancer. In this study, MC-LR aptamer (Apt-3) modified graphene oxide (GO) was designed to enrich MC-LR in white jade snail (Achatina fulica) and pond water, followed by matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) analysis. Results indicated that the Apt-3/PEG/GO nanocomposites were highly specific to MC-LR, and the detection limit of MALDI-MS was 0.50 ng/mL. Moreover, the MC-LR can be released from nanocomposites at 75°C, thus, the reuse of Apt-3/PEG/GO is realized. Real sample analysis indicated that the Apt-3/PEG/GO nanocomposites coupled with MALDI-MS were efficient in detecting trace amounts of MC-LR in real samples. With the merits of being low cost, reusable, and easy to besynthesized, this Apt-3/PEG/GO MALDI-MS is expected to be comprehensively applied by anchoring suitable aptamers for different targets.

Cost-effective screen-printed carbon electrode biosensors for rapid detection of microcystin-LR in surface waters for early warning of harmful algal blooms

Microcystins (MCs) are toxins produced by cyanobacteria commonly found in harmful algal blooms (HABs). Due to their toxicity to humans and other organisms, the World Health Organization (WHO) sets a guideline of 1 μg L-1 for microcystin-leucine-arginine (MC-LR) in drinking water. However, current analytical techniques for the detection of MC-LR such as liquid chromatography-mass spectrometry (LC-MS) and ELISA are costly, bulky, time-consuming, and mostly conducted in a laboratory, requiring highly trained personnel. An analytical method that can be used in the field for rapid determination is essential. In this study, an anti-MC-LR/MC-LR/cysteamine-coated screen-printed carbon electrode (SPCE) biosensor was newly developed to detect MC-LR, bioelectrochemically, in water. The functionalization of the electrode surface was confirmed with surface characterization methods. The sensor performance was evaluated by electrochemical impedance spectroscopy (EIS), obtaining a linear working range of MC-LR concentrations between 0.1 and 100 μg L-1 with a limit of detection (LOD) of 0.69 ng L-1. Natural water samples experiencing HABs were collected and analyzed using the developed biosensor, demonstrating the excellent performance of the biosensor with a relative standard deviation (RSD) of 0.65%. The interference tests showed minimal error and RSD values against other common MCs and possible coexisting ions found in water. The biosensor showed acceptable functionality with a shelf life of up to 12 weeks. Overall, the anti-MC-LR/MC-LR/cysteamine/SPCE biosensors can be an innovative solution with characteristics that allow for in situ, low-cost, and easy-to-use capabilities which are essential for developing an overarching and integrated "smart" environmental management system.

CRISPR/Cas14 provides a promising platform in facile and versatile aptasensing with improved sensitivity

CRISPR is reshaping biosensing technology due to its programmability, sensitivity, and specificity. Most current CRISPR-based biosensors are developed based on Cas12 and Cas13, while the biosensing potentials of the newly discovered Cas14 have not been fully elucidated yet. Herein, a fluorometric biosensor named HARRY (highly sensitive aptamer-regulated Cas14 R-loop for bioanalysis) was developed. The diblock ssDNA is designed to contain the activator sequence of Cas14 and the aptamer sequence of specific targets. In the absence of targets, the ssDNA activates Cas14a, then the Cas14a trans-cleavages the fluorescent reporter, causing fluorescence enhancement. In the presence of the targets, ssDNA-target assembly is formed via aptamer interaction, resulting in the inhibition of Cas14a activation. HARRY can detect ATP, Cd²⁺, histamine, aflatoxin B1, and thrombin with detection limits at the low-nanomolar level, which shows improvement compared with Cas12a-based aptasensors in sensitivity and versatility. We reasoned that the improvement is derived from the ssDNA specificity of Cas14a and found that the detection limit of HARRY is correlated to the binding affinities of aptamers. This study unlocks the potential of Cas14a in versatile aptasensing, which may inspire the development of CRISPR-based biosensors from the Cas14a branch.

CRISPR-Cas12a-Based Aptasensor for On-Site and Highly Sensitive Detection of Microcystin-LR in Freshwater

On-site monitoring of trace organic pollutants with facile methods is critical to environmental pollutant prevention and control. Herein, we proposed a CRISPR-Cas12a-based aptasensor platform (named as MC-LR-Casor) for on-site and sensitive detection of microcystin-LR (MC-LR). After hybridization with blocker DNA, the MC-LR aptamers were conjugated to magnetic beads (MBs) to get the MB aptasensor. In the presence of MC-LR, their interactions with aptamers were triggered and the specific binding caused the release of blocker DNA. Using the programmability of the CRISPR-Cas system, the released blocker DNA was designed to activate a Cas12a-crRNA complex. Single strand DNA reporters were rapidly cleaved by the complex. Signal readout could be achieved by fluorometer or lateral flow strips, which were positively correlated to MC-LR concentration. Benefiting from the CRISPR-Cas12a amplification system, the proposed sensing platform exhibited high sensitivity and reached the limit of detection of ∼3 × 10^-6 μg/L (fluorescence method) or 1 × 10^-3 μg/L (lateral flow assay). In addition, the MC-LR-Casor showed excellent selectivity and good recovery rates, demonstrating their good applicability for real water sample analysis. During the whole assay, only two steps of incubation at a constant temperature were required and the results could be visualized when employing flow strips. Therefore, the proposed assay offered a simple and convenient alternative for in situ MC-LR monitoring, which may hold great promise for future environmental surveillance.

A novel CRISPR/Cas14a system integrated with 2D porphyrin metal-organic framework for microcystin-LR determination through a homogeneous competitive reaction

Selective and sensitive detection of microcystin-LR (MC-LR) is of vital importance because of its high toxicity and broad distribution. Herein, a novel and versatile fluorescence sensor (Cas14-pMOFs fluorescence sensor) was developed by combining the CRISPR/Cas14a system with a 2D porphyrin metal-organic framework nanosheets (2D-pMOFs) for MC-LR determination. The designed CRISPR/Cas14a system was activated by the unbound complementary DNA (cDNA), which was positively correlated with MC-LR concentration. Furthermore, the activated Cas14a protein was utilized to indiscriminately cleave the FAM-labeled single-stranded DNA (ssDNA-FAM), which was pre-absorbed on Cu-TCPP(Fe) nanosheets. Because of the desorption of the cleaved ssDNA-FAM, the pre-quenched fluorescence signal was recovered. Owing to the excellent performance in quantifying cDNA using this Cas14-pMOFs fluorescence sensor with a limit of detection (LOD) of 0.12 nM, this Cas14-pMOFs fluorescence sensor was able to detect MC-LR in a range from 50 pg/mL to 1 μg/mL with the LOD of 19 pg/mL. This work not only provided a new insight for the exploration of fluorescence sensors based on 2D-pMOFs coupled with CRISPR/Cas14a, but also, demonstrated its universality in both nucleic acid and non-nucleic acid targets determination.

The DNA-Cu nanocluster and exonuclease I integrated label-free reporting system for CRISPR/Cas12a-based SARS-CoV-2 detection with minimized background signal

CRISPR-driven biosensing is developing rapidly, but current works mostly adopt dye-labeled ssDNA as the signal reporter, which is costly and unstable. Herein, we developed a label-free and low-background reporter for...

VEGF aptamer/i-motif-grafted multi-functional SPION nanocarrier for chemotherapeutic/phototherapeutic synergistic research

Chemotherapeutic agents and photosensitizers often suffer from poor tumor selectivity, high side toxicity, or low water solubility. To address these problems, various drug delivery systems (DDS) have been explored but most of them are toxic, difficult to synthesize, or of single function. In order to design a highly biocompatible, conveniently prepared, multi-functional drug delivery system, herein, an aptamer of vascular endothelial growth factor (VEGF) and a cytosine (C)-DNA fragment were grafted on the surface of superparamagnetic iron oxide nanoparticles (SPION), and then a chemotherapeutic agent daunomycin (DNM) and a photosensitizer 5, 10, 15, 20-tetra (phenyl-4-N-methyl-4-pyridyl) porphyrin (TMPyP) were self-assembled with the hybridized VEGF-based DNA structure. By loading DNM and TMPyP, the DDS displayed strong chemotherapeutic/phototherapeutic capability against cancer cells via mechanisms such as mitochondrial dysfunction and ROS elevation, which triggered the apoptosis of the tumor cells. The dual delivery of chemotherapeutical agents and photosensitizers with aptamer/C-rich DNA successfully integrated the functions of pH stimuli-responsive drug release and chemotherapeutic/phototherapeutic modalities into one single system and thus could be considered as an ideal drug delivery vehicle with great potential in clinic.

Visible light-driven self-powered aptasensors for ultrasensitive Microcystin-LR detection based on the carrier density effect of N-doped graphene hydrogel/hematite Schottky junctions

In this work, a novel visible light-driven self-powered photoelectrochemical (PEC) platform was designed based on 3D N-doped graphene hydrogel/hematite nanocomposites (NGH/Fe₂O₃) via a facile one-pot hydrothermal route. The coupling NGH with Fe₂O₃ could generate a Schottky junction, which promoted the separation of charges. Moreover, Mott-Schottky measurements validated that the carrier concentration achieved by NGH/Fe₂O₃ was about 3.4 × 10³ times in comparison to that of pure Fe₂O₃, which was beneficial for efficient charge transfer. Owing to the carrier density effect and Schottky junction, the photocurrent of the as-fabricated NGH/Fe₂O₃ nanocomposites was 6.9-fold higher than that of pure Fe₂O₃. On the basis of such excellent Schottky junctions, an ultrasensitive visible light-induced self-powered PEC aptasensor was developed using a Microcystin-LR (MC-LR) aptamer. The as-fabricated PEC aptasensor displayed good analytical performance toward MC-LR detection in terms of wide linear range (1 pM-5 nM), low detection limit (0.23 pM, S/N = 3), excellent selectivity and high stability. This new strategy can provide a way for regulating nanostructures for more sensitive PEC sensors by increasing the carrier density.

VEGF aptamer/i-motif-based drug co-delivery system for combined chemotherapy and photodynamic therapy

BACKGROUND

Nucleic acids used as drug delivery systems (DDS) have gained attention because of their biosafety and effortless synthesis. G-quadruplex (G4) structured aptamer such as AS1411 was frequently employed to deliver photosensitizers or chemotherapeutic agents while other aptamers were seldomly reported in this field.

METHODS

Herein, a chemical anticancer drug daunomycin (DNM), and a photosensitizer 5, 10, 15, 20-tetra (phenyl-4-N-methyl-4-pyridyl) porphyrin (TMPyP) were physically assembled with a novel DNA structure composed of an aptamer of vascular endothelial growth factor (VEGF) and a cytosine (C)-rich DNA fragment (gc-34). Spectral and molecular mimicking methods were employed to research the drug loading/releasing process. The in vitro cytotoxicity was studied by MTT, ROS, cell cycle, and cell apoptotic assays and the in vivo anticancer efficiency was evaluated by the inhibitive effect on the cancerous growth of MCF-7 tumor-bearing nude mice.

RESULTS

The G4-structured VEGF aptamer delivered TMPyP successfully for the first time. The designed DDS displayed sensitive VEGF/pH controlled drug release. The co-delivery of DNM and TMPyP exhibited high ROS production, significant cell cycle arresting and evident cell apoptosis, and displayed superior cytotoxicity against tumor cells compared with individual agents in vitro. In vivo studies showed that the dual-drug loaded system can greatly inhibit tumor growth with chemotherapeutic/photodynamic synergistic effects.

CONCLUSION

The co-delivery of DNM and TMPyP with aptamer/C-rich DNA successfully integrates the functions of VEGF/pH stimuli-responsive drug release and chemotherapeutic/phototherapeutic modalities into one single system, and may have great potential in cancer treatment.

DNA Nanostructures in the Fight Against Infectious Diseases

Throughout history, humanity has been threatened by countless epidemic and pandemic outbreaks of infectious diseases, from the Justinianic Plague to the Spanish flu to COVID-19. While numerous antimicrobial and antiviral drugs have been developed over the last 200 years to face these threats, the globalized and highly connected world of the 21st century demands for an ever-increasing efficiency in the detection and treatment of infectious diseases. Consequently, the rapidly evolving field of nanomedicine has taken up the challenge and developed a plethora of strategies to fight infectious diseases with the help of various nanomaterials such as noble metal nanoparticles, liposomes, nanogels, and virus capsids. DNA nanotechnology represents a comparatively recent addition to the nanomedicine arsenal, which, over the past decade, has made great progress in the area of cancer diagnostics and therapy. However, the past few years have seen also an increasing number of DNA nanotechnology-related studies that particularly focus on the detection and inhibition of microbial and viral pathogens. Herein, a brief overview of this rather young research field is provided, successful concepts as well as potential challenges are identified, and promising directions for future research are highlighted.

Signal-Amplified Detection of the Tumor Biomarker FEN1 Based on Cleavage-Induced Ligation of a Dumbbell DNA Probe and Rolling Circle Amplification

Flap endonuclease 1 (FEN1), an endogenous nuclease with the ability to cleave the 5' overhang of branched dsDNA, is of significance in DNA replication and repair. The overexpression of FEN1 is common in cancer because of the ubiquitous upregulation of DNA replication; thus, FEN1 has been recognized as a potential biomarker in oncological investigations. However, few analytical methods targeting FEN1 with high sensitivity and simplicity have been developed. This work developed a signal-amplified detection of FEN1 based on the cleavage-induced ligation of a dumbbell DNA probe and rolling circle amplification (RCA). A flapped dumbbell DNA probe (FDP) was rationally designed with a FEN1 cleavable flap at the 5' end. The cleavage generated a nick site with juxtaposed 5' phosphate and 3' hydroxyl ends, which were linkable by T4 DNA ligase to form a closed dumbbell DNA probe (CDP) with a circular conformation. The CDP functioned as a template for RCA, which produced abundant DNA that could be probed using SYBR Green I. The highly sensitive detection of FEN1 with a limit of detection of 15 fM was achieved, and this method showed high specificity, which enabled the quantification of FEN1 in real samples. The inhibitory effects of chemicals on FEN1 were also evaluated. This study represents the first attempt to develop an FEN1 assay that involves signal amplification, and the novel biosensor method enriches the tools for FEN1-based diagnostics.

Impedimetric Microcystin-LR Aptasensor Prepared with Sulfonated Poly(2,5-dimethoxyaniline)–Silver Nanocomposite

This paper presents a novel impedimetric aptasensor for cyanobacterial microcystin-LR (L, l-leucine; R, l-arginine) (MC-LR) containing a 5′ thiolated 60-mer DNA aptamer (i.e., 5′-SH-(CH2)6GGCGCCAAACAGGACCACCATGACAATTACCCATACCACCTCATTATGCCCCATCT CCGC-3′). A nanocomposite electrode platform comprising biocompatible poly(2,5-dimethoxyaniline) (PDMA)-poly(vinylsulfonate) (PVS) and silver nanoparticle (Ag0) on a glassy carbon electrode (GCE), i.e., (GCE/PDMA–PVS–Ag0) was used in the biosensor development. Small-angle X-ray scattering (SAXS) spectroscopic analysis revealed that the PDMA–PVS–Ag0 nanocomposites were polydispersed and contained embedded Ag0. Electrochemical impedance spectroscopy (EIS) responses of the aptasensor gave a dynamic linear range (DLR) and limit of detection (LOD) values of 0.01–0.1 ng L−1 MC-LR and 0.003 ng L−1 MC-LR, respectively. The cross-reactivity studies, which was validated with enzyme-linked immunosorbent assay (ELISA), showed that the aptasensor possesses excellent selectivity for MC-LR.