An electrochemical supersandwich assay for sensitive and selective DNA detection in complex matrices.
Ontology highlight
ABSTRACT:
SUBMITTER: Xia F
PROVIDER: S-EPMC3082473 | biostudies-literature | 2010 Oct
REPOSITORIES: biostudies-literature
Publications
An electrochemical supersandwich assay for sensitive and selective DNA detection in complex matrices.
Xia Fan F White Ryan J RJ Zuo Xiaolei X Patterson Adriana A Xiao Yi Y Kang Di D Gong Xiong X Plaxco Kevin W KW Heeger Alan J AJ
Journal of the American Chemical Society 20101001 41
In a traditional sandwich assay, a DNA target hybridizes to a single copy of the signal probe. Here we employ a modified signal probe containing a methylene blue (a redox moiety) label and a "sticky end." When a DNA target hybridizes this signal probe, the sticky end remains free to hybridize another target leading to the creation of a supersandwich structure containing multiple labels. This leads to large signal amplification upon monitoring by voltammetry. ...[more]
Similar Datasets
Project description:BACKGROUND: In the context of a potential bioterrorist attack sensitive and fast detection of functionally active toxins such as ricin from complex matrices is necessary to be able to start timely countermeasures. One of the functional detection methods currently available for ricin is the endpoint cytotoxicity assay, which suffers from a number of technical deficits. METHODOLOGY/FINDINGS: This work describes a novel online cytotoxicity assay for the detection of active ricin and Ricinus communis agglutinin, that is based on a real-time cell electronic sensing system and impedance measurement. Characteristic growth parameters of Vero cells were monitored online and used as standardized viability control. Upon incubation with toxin the cell status and the cytotoxic effect were visualized using a characteristic cell index-time profile. For ricin, tested in concentrations of 0.06 ng/mL or above, a concentration-dependent decrease of cell index correlating with cytotoxicity was recorded between 3.5 h and 60 h. For ricin, sensitive detection was determined after 24 h, with an IC50 of 0.4 ng/mL (for agglutinin, an IC50 of 30 ng/mL was observed). Using functionally blocking antibodies, the specificity for ricin and agglutinin was shown. For detection from complex matrices, ricin was spiked into several food matrices, and an IC50 ranging from 5.6 to 200 ng/mL was observed. Additionally, the assay proved to be useful in detecting active ricin in environmental sample materials, as shown for organic fertilizer containing R. communis material. CONCLUSIONS/SIGNIFICANCE: The cell-electrode impedance measurement provides a sensitive online detection method for biologically active cytotoxins such as ricin. As the cell status is monitored online, the assay can be standardized more efficiently than previous approaches based on endpoint measurement. More importantly, the real-time cytotoxicity assay provides a fast and easy tool to detect active ricin in complex sample matrices.
| S-EPMC3330811 | biostudies-literature
Project description:Heavy metal contamination and its detrimental health effects are a growing concern globally. Several metal mitigation systems and regulatory approaches have been implemented to minimize the negative impacts on human health. However, none of these function at maximum efficiency, mainly due to the lack of accurate information about metal speciation. Therefore, there is a critical need to develop novel, cheap, efficient, and robust metal detecting sensors. In this study, we describe the application of a nanopipet based electrochemical sensor to detect aqueous Cd(ii) ions. The inner radius of our nanopipets is ∼300 nm, and the fundamental mechanism behind our sensor's response is ion transfer between two immiscible electrolyte solutions (ITIES). The absence of redox behavior makes ITIES an excellent, attractive electrochemical tool to study various ions in aqueous solutions. In this study, we used 1,10-phenanthroline as our ionophore in the organic phase (dichloroethane) to facilitate the transfer of Cd(ii) ions from the polar aqueous phase to the less polar organic phase. Unlike previous studies, we characterized our nanopipet in complicated matrices, including, but not limited to, tris buffer and artificial seawater. We performed quantitative assessments to determine our sensor's limit of detection, stability, sensitivity, and selectivity. We further show that our nanosensor can detect free Cd(ii) ions in the presence of strong complexing agents such as ethylenediaminetetraacetic acid, 2,3-dimercaptosuccinic acid, etc. We quantified the concentration of free Cd(ii) ions in a water sample collected from a local lagoon. Thus, we showcased the power of our nanopipets to act as a robust, accurate, and efficient speciation sensor to detect Cd(ii) ions in environmental samples.
| S-EPMC8978973 | biostudies-literature
Project description:This work proposes the concept of ratiometric electrochemical proximity assay (REPA), which can be used for one-step, highly sensitive and selective detection of protein. The assay strategy was achieved on a sensing interface that was formed by hybridization of methylene blue (MB)-labeled antibody-DNA probe (MB-DNA1-Ab1) with ferrocene (Fc)-labeled DNA capture probe (Fc-P) modified gold electrode. On the interface the target protein could trigger the formation of immunocomplex between MB-DNA1-Ab1 and detection antibody-DNA probe (Ab2-DNA2) and subsequently the proximity hybridization of DNA1-DNA2, which led to the departure of MB-DNA1-Ab1 from the interface. The remained Fc-P could form a hairpin structure to take Fc group to electrode surface. Therefore, the recognition of target protein to Ab1 and Ab2 resulted in both the "signal-off" of MB and the "signal-on" of Fc for dual-signal electrochemical ratiometric readout. The proposed REPA could be carried out in one-step with 40-min duration and showed a wide detection range from 0.05 to 100 ng/mL with pg/mL limit of detection, displaying great potential for convenient point-of-care testing and commercial application.
| S-EPMC3950580 | biostudies-literature
Project description:Botulinum neurotoxin (BoNT) intoxication can lead to the disease botulism, characterized by flaccid muscle paralysis that can cause respiratory failure and death. Due to the significant morbidity and mortality costs associated with BoNTs high toxicity, developing highly sensitive, rapid, and field-deployable assays are critically important to protect the nation's food supply against either accidental or intentional contamination. We report here that the B-cell based biosensor assay CANARY® (Cellular Analysis and Notification of Antigen Risks and Yields) Zephyr detects BoNT/A holotoxin at limits of detection (LOD) of 10.0 ± 2.5 ng/mL in assay buffer. Milk matrices (whole milk, 2% milk and non-fat milk) with BoNT/A holotoxin were detected at similar levels (7.4⁻7.9 ng/mL). BoNT/A complex was positive in carrot, orange, and apple juices at LODs of 32.5⁻75.0 ng/mL. The detection of BoNT/A complex in solid complex foods (ground beef, smoked salmon, green bean baby puree) ranged from 14.8 ng/mL to 62.5 ng/mL. Detection of BoNT/A complex in the viscous liquid egg matrix required dilution in assay buffer and gave a LOD of 171.9 ± 64.7 ng/mL. These results show that the CANARY® Zephyr assay can be a highly useful qualitative tool in environmental and food safety surveillance programs.
| S-EPMC6266793 | biostudies-literature
Project description:There is a need for point-of-care bacterial sensing and identification technologies that are rapid and simple to operate. Technologies that do not rely on growth cultures, nucleic acid amplification, step-wise reagent addition, and complex sample processing are the key for meeting this need. Herein, multiple materials technologies are integrated for overcoming the obstacles in creating rapid and one-pot bacterial sensing platforms. Liquid-infused nanoelectrodes are developed for reducing nonspecific binding on the transducer surface; bacterium-specific RNA-cleaving DNAzymes are used for bacterial identification; and redox DNA barcodes embedded into DNAzymes are used for binding-induced electrochemical signal transduction. The resultant single-step and one-pot assay demonstrates a limit-of-detection of 102 CFU mL-1 , with high specificity in identifying Escherichia coli amongst other Gram positive and negative bacteria including Klebsiella pneumoniae, Staphylococcus aureus, and Bacillus subtilis. Additionally, this assay is evaluated for analyzing 31 clinically obtained urine samples, demonstrating a clinical sensitivity of 100% and specify of 100%. When challenging this assay with nine clinical blood cultures, E. coli-positive and E. coli-negative samples can be distinguished with a probability of p < 0.001.
| S-EPMC10323635 | biostudies-literature
Project description:Rapid and specific quantitation of a variety of proteins over a wide concentration range is highly desirable for biosensing at the point-of-care, in clinical laboratories, and in research settings. Our recently developed electrochemical proximity assay (ECPA) is a target-flexible, DNA-directed, direct-readout protein quantitation method with detection limits in the low femtomolar range, making it particularly amenable to point-of-care detection. However, consistent quantitation in more complex matrices is required at the point-of-care, and improvements in measurement speed are needed for clinical and research settings. Here, we address these concerns with a reusable ECPA, where a gentle regeneration of the surface DNA monolayer (used to capture the proximity complex) is achieved enzymatically through a novel combination of molecular biology and electrochemistry. Strategically placed uracils in the DNA sequence trigger selective cleavage of the backbone, releasing the assembled proximity complex. This allows repeated protein quantitation by square-wave voltammetry (SWV)-as quickly as 3 min between runs. The process can be repeated up to 19 times on a single electrode without loss of assay sensitivity, and currents are shown to be highly repeatable with similar calibrations using seven different electrodes. The utility of reusable ECPA is demonstrated through two important applications in complex matrices: (1) direct, quantitative monitoring of hormone secretion in real time from as few as five murine pancreatic islets and (2) standard addition experiments in unspiked serum for direct quantitation of insulin at clinically relevant levels. Results from both applications distinguish ECPA as an exceptional tool in protein quantitation.
| S-EPMC4193296 | biostudies-literature
Project description:Prostate-specific antigen (PSA) is the most widely used biomarker for the early diagnosis of prostate cancer. Existing methods for PSA detection are burdened with some limitations and require improvement. Herein, we developed a novel microfluidic-electrochemical (μFEC) detection system for PSA detection. First, we constructed an electrochemical biosensor based on screen-printed electrodes (SPEs) with modification of gold nanoflowers (Au NFs) and DNA tetrahedron structural probes (TSPs), which showed great detection performance. Second, we fabricated microfluidic chips by DNA TSP-Au NF-modified SPEs and a PDMS layer with designed dense meandering microchannels. Finally, the μFEC detection system was achieved based on microfluidic chips integrated with the liquid automatic conveying unit and electrochemical detection platform. The μFEC system we developed acquired great detection performance for PSA detection in PBS solution. For PSA assays in spiked serum samples of the μFEC system, we obtained a linear dynamic range of 1-100 ng/mL with a limit of detection of 0.2 ng/mL and a total reaction time <25 min. Real serum samples of prostate cancer patients presented a strong correlation between the "gold-standard" chemiluminescence assays and the μFEC system. In terms of operation procedure, cost, and reaction time, our method was superior to the current methods for PSA detection and shows great potential for practical clinical application in the future.
| S-EPMC8433179 | biostudies-literature
Project description:Rapid, sensitive, and selective detection of viruses is critical for applications in medical diagnostics, biosecurity, and environmental safety. In this article, we report the application of a point-defect-coupled W1 photonic crystal (PhC) waveguide biosensor to label-free optical detection of viruses. Fabricated on a silicon-on-insulator (SOI) substrate using electron-beam (e-beam) lithography and reactive-ion-etching, the PhC sensing platform allows optical detection based on resonant mode shifts in response to ambient refractive index changes produced by infiltration of target biomaterial within the holes of the PhC structure. Finite difference time domain (FDTD) calculations were performed to assist with design of the sensor, and to serve as a theoretical benchmark against which experimental results could be compared. Using Human Papillomavirus virus-like particles (VLPs) spiked in 10% fetal bovine serum as a model system, we observed a limit of detection of 1.5 nM in simple (buffer only) or complex (10% serum) sample matrices. The use of anti-VLP antibodies specific for intact VLPs with the PhC sensors provided highly selective VLP detection.
| S-EPMC3596473 | biostudies-literature
Project description:Dengue fever is the most prevalent vector-borne disease in the world, with nearly 100 million people infected every year. Early diagnosis and identification of the pathogen are crucial steps for the treatment and for prevention of the disease, mainly in areas where the co-circulation of different serotypes is common, increasing the outcome of dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Due to the lack of fast and inexpensive methods available for the identification of dengue serotypes, herein we report the development of an electrochemical DNA biosensor for the detection of sequences of dengue virus serotype 3 (DENV-3). DENV-3 probe was designed using bioinformatics software and differential pulse voltammetry (DPV) was used for electrochemical analysis. The results showed that a 22-m sequence was the best DNA probe for the identification of DENV-3. The optimum concentration of the DNA probe immobilized onto the electrode surface is 500 nM and a low detection limit of the system (3.09 nM). Moreover, this system allows selective detection of DENV-3 sequences in buffer and human serum solutions. Therefore, the application of DNA biosensors for diagnostics at the molecular level may contribute to future advances in the implementation of specific, effective and rapid detection methods for the diagnosis dengue viruses.
| S-EPMC4541844 | biostudies-literature
Project description:A diboronic acid anthracene-based fluorescent system for detecting blood glucose could be used for 180 days. However, there has not yet been a boronic acid immobilized electrode to selectively detect glucose in a signal-increased way. Considering malfunctions of sensors at high sugar levels, the electrochemical signal should be increased proportionally to the glucose concentration. Therefore, we synthesized a new diboronic acid derivative and fabricated the derivative-immobilized electrodes for the selective detection of glucose. We performed cyclic voltammetry and electrochemical impedance spectroscopy with an Fe(CN)63-/4- redox pair for detecting glucose in the range of 0-500 mg/dL. The analysis revealed increased electron-transfer kinetics such as increased peak current and decreased semicircle radius of Nyquist plots as the glucose concentration increased. The cyclic voltammetry and impedance spectroscopy showed that the linear detection range of glucose was 40 to 500 mg/dL with limits of detection of 31.2 mg/dL and 21.5 mg/dL, respectively. We applied the fabricated electrode to detect glucose in artificial sweat and obtained 90% of the performance of the electrodes in PBS. Cyclic voltammetry measurements of other sugars such as galactose, fructose, and mannitol also showed linear increased peak currents proportional to the concentrations of the tested sugars. However, the slopes of the sugars were lower than that of glucose, indicating selectivity for glucose. These results proved the newly synthesized diboronic acid is a promising synthetic receptor for developing a long-term usable electrochemical sensor system.
| S-EPMC9954471 | biostudies-literature