Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Graphene oxide-assisted non-immobilized SELEX of okdaic acid aptamer and the analytical application of aptasensor.

ABSTRACT: Okadaic acid (OA) is a low-molecular-weight marine toxin from shellfish that causes abdominal pain, vomiting and diarrhea, i.e., diarrheic shellfish poisoning. In this study, a ssDNA aptamer that specifically binds to OA with high affinity was obtained via Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assisted by graphene oxide (GO). This aptamer was then applied to fabricate a novel direct competitive enzyme-linked aptamer assay (ELAA). At the optimized conditions, this ELAA method showed a low detection limit (LOD of 0.01 ng/mL), wide linear range (from 0.025 to 10 ng/mL), good recovery rate (92.86-103.34% in OA-spiked clam samples) and repeatability (RSD of 2.28-4.53%). The proposed method can be used to detect OA in seafood products with high sensitivity and can potentially be adapted for the determination of other small molecular analytes.

SUBMITTER: Gu H

PROVIDER: S-EPMC4761938 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Graphene oxide-assisted non-immobilized SELEX of okdaic acid aptamer and the analytical application of aptasensor.

Gu Huajie H Duan Nuo N Wu Shijia S Hao Liling L Xia Yu Y Ma Xiaoyuan X Wang Zhouping Z

Scientific reports 20160222

Okadaic acid (OA) is a low-molecular-weight marine toxin from shellfish that causes abdominal pain, vomiting and diarrhea, i.e., diarrheic shellfish poisoning. In this study, a ssDNA aptamer that specifically binds to OA with high affinity was obtained via Systematic Evolution of Ligands by Exponential Enrichment (SELEX) assisted by graphene oxide (GO). This aptamer was then applied to fabricate a novel direct competitive enzyme-linked aptamer assay (ELAA). At the optimized conditions, this ELAA ...[more]

PMID: 26898784

Similar Datasets

Aptasensor for multiplex detection of antibiotics based on FRET strategy combined with aptamer/graphene oxide complex.

Project description:The development of a multiplexed sensing platform is necessary for highly selective, sensitive, and rapid screening of specific antibiotics. In this study, we designed a novel multiplex aptasensor for antibiotics by fluorescence resonance energy transfer (FRET) strategy using DNase I-assisted cyclic enzymatic signal amplification (CESA) method combined with aptamer/graphene oxide complex. The aptamers specific for sulfadimethoxine, kanamycin, and ampicillin were conjugated with Cyanine 3 (Cy3), 6-Carboxyfluorescein (FAM), and Cyanine 5 (Cy5), respectively, and graphene oxide (GO) was adopted to quench the fluorescence of the three different fluorophores with the efficiencies of 94.36%, 93.94%, and 96.97% for Cy3, FAM, and Cy5, respectively. CESA method was used for sensitive detection, resulting in a 2.1-fold increased signal compared to those of unamplified method. The aptasensor rapidly detected antibiotics in solution with limit of detection of 1.997, 2.664, and 2.337 ng/mL for sulfadimethoxine, kanamycin, and ampicillin, respectively. In addition, antibiotics dissolved in milk were efficiently detected with similar sensitivities. Multiplexed detection test proved that the fluorescently modified aptamers could work separately from each other. The results indicate that the aptasensor offers high specificity for each antibiotic and enables simultaneous and multicolor sensing for rapid screening of multiple antibiotics at the same time.

| S-EPMC6529438 | biostudies-literature

Graphene oxide quantum dots immobilized on mesoporous silica: preparation, characterization and electroanalytical application.

Project description:Because of its high surface area and combination of various functional groups, graphene oxide (GO) is currently one of the most actively studied materials for electroanalytical applications. It is not practical to utilize self-supported GO on its own and thus it is commonly integrated with different supporting carriers. Having a large lateral size, GO can only wrap the particles of the support and thus can significantly reduce the surface area of porous materials. To achieve synergy from the high surface area and polyfunctional nature of GO, and the rigid structure of a porous support, the lateral size of GO must essentially be decreased. Recently reported graphene oxide quantum dots (GOQDs) can fulfil this task. Here we report the successful preparation of an SiO2-GOQDs hybrid, where GOQDs have been incorporated into the mesoporous network of silica. The SiO2-GOQDs emit a strong luminescence with a band maximum at 404 nm. The Raman spectrum of SiO2-GOQDs shows two distinct peaks at 1585 cm-1 (G-peak) and 1372 cm-1 (D-peak), indicating the presence of a graphene ordered basal plane with aromatic sp2-domains and a disordered oxygen-containing structure. Covalent immobilization of GOQDs onto aminosilica via such randomly structured oxygen fragments was proven with the help of Fourier transform infrared spectroscopy, solid-state cross-polarization magic angle spinning 13C nuclear magnetic resonance, and X-ray photoelectron spectroscopy. SiO2-GOQDs were used as a modifier of a carbon paste electrode for differential pulse voltammetry determination of two antibiotics (sulfamethoxazole and trimethoprim) and two endocrine disruptors (diethylstilbestrol (DES) and estriol (EST)). The modified electrodes demonstrated a significant signal enhancement for EST (370%) and DES (760%), which was explained by a π-π stacking interaction between GOQDs and the aromatic system of the analytes.

| S-EPMC9056381 | biostudies-literature

Albuminuria detection using graphene oxide-mediated fluorescence quenching aptasensor.

Project description:A simple and sensitive graphene oxide-mediated fluorescence quenching aptasensor is developed to quantify albuminuria in urine samples. The developed aptasensor used the specific target binding property of aptamer and fluorescence quenching property of graphene oxide to determine the concentration of human serum albumin in urine. The limit of detection of the developed platform is 0.05 µg.mL-1 and the detection range is 0.1-600 µg.mL-1, which covers the albuminuria concentration range present in normal human urine and the urine of the patient with chronic kidney disease. This approach can be modified to measure albuminuria using a high-throughput quantification platform and portable point of care testing. In addition, the production cost for one reaction is cheaper than those for the standard automated method. Therefore, this aptasensor has significant potential for commercialization and public use.•Our protocol is customized by using the fluorescence quenching property of graphene oxide and specific binding property of human serum albumin aptamer to detect human serum albumin in urine sample•The limit of detection of our developed platform is 0.05 µg.mL-1•The detection range of our aptasensor is 0.1-600 µg.mL-1.

| S-EPMC7644748 | biostudies-literature

Selection of Aptamers Specific for DEHP Based on ssDNA Library Immobilized SELEX and Development of Electrochemical Impedance Spectroscopy Aptasensor.

Project description:A selection of aptamers specific for di(2-ethylhexyl) phthalate (DEHP) and development of electrochemical impedance spectroscopy (EIS) aptasensor are described in this paper. The aptamers were selected from an immobilized ssDNA library using the systematic evolution of ligands by exponential enrichment (SELEX). The enrichment was monitored using real-time quantitative PCR (Q-PCR), and the aptamers were identified by high-throughput sequencing (HTS), gold nanoparticles (AuNPs) colorimetric assay, and localized surface plasmon resonance (LSPR). The EIS aptasensor was developed to detect DEHP in water samples. After eight rounds of enrichment, HTS, AuNPs colorimetric assay, and LSPR analysis indicated that four aptamers had higher binding activity, and aptamer 31 had the highest affinity (Kd = 2.26 ± 0.06 nM). The EIS aptasensor had a limit of detection (LOD) of 0.103 pg/mL with no cross-reactivity to DEHP analogs and a mean recovery of 76.07% to 141.32% for detection of DEHP in water samples. This aptamer is novel with the highest affinity and sensitivity.

| S-EPMC7038136 | biostudies-literature

Graphene oxide assisted light-up aptamer selection against Thioflavin T for label-free detection of microRNA.

Project description:We selected an aptamer against a fluorogenic dye called Thioflavin T (ThT). Aptamers are single-stranded DNA that can bind a specific target. We selected the ThT aptamer using graphene oxide assisted SELEX and a low-cost Open qPCR instrument. We optimized, minimized, and characterized the best aptamer candidate against ThT. The aptamer, ThT dye, and the enzymatic strand displacement amplification (SDA) were used in a label-free approach to detect the micro RNA miR-215 in saliva and serum. The aptamer confers higher specificity than intercalating dyes but without expensive covalently modified DNA probes. This isothermal, low-cost, simple method can detect both DNA and RNA. The target, miR-215, was detected with a limit of detection of 2.6 nM.

| S-EPMC7900183 | biostudies-literature

AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from its Application.

Project description:Systematic Evolution of Ligands by EXponential Enrichment (SELEX) is a well established experimental procedure to identify aptamers - synthetic single-stranded (ribo)nucleic molecules that bind to a given molecular target. Recently, new sequencing technologies have revolutionized the SELEX protocol by allowing for deep sequencing of the selection pools after each cycle. The emergence of High Throughput SELEX (HT-SELEX) has opened the field to new computational opportunities and challenges that are yet to be addressed. To aid the analysis of the results of HT-SELEX and to advance the understanding of the selection process itself, we developed AptaCluster. This algorithm allows for an efficient clustering of whole HT-SELEX aptamer pools; a task that could not be accomplished with traditional clustering algorithms due to the enormous size of such datasets. We performed HT-SELEX with Interleukin 10 receptor alpha chain (IL-10RA) as the target molecule and used AptaCluster to analyze the resulting sequences. AptaCluster allowed for the first survey of the relationships between sequences in different selection rounds and revealed previously not appreciated properties of the SELEX protocol. As the first tool of this kind, AptaCluster enables novel ways to analyze and to optimize the HT-SELEX procedure. Our AptaCluster algorithm is available as a very fast multiprocessor implementation upon request.

| S-EPMC4281958 | biostudies-literature

A simple label-free electrochemical sensor for sensitive detection of alpha-fetoprotein based on specific aptamer immobilized platinum nanoparticles/carboxylated-graphene oxide.

Project description:A label-free electrochemical aptamer-based sensor has been fabricated for alpha-fetoprotein (AFP) detection. Platinum nanoparticles on carboxylated-graphene oxide (PtNPs/GO-COOH) modified screen-printed graphene-carbon paste electrode (SPGE) was utilized as an immobilization platform, and the AFP aptamer was employed as a bio-recognition element. The synthesized GO-COOH helps to increase the surface area and amounts of the immobilized aptamer. Subsequently, PtNPs are decorated on GO-COOH to enhance electrical conductivity and an oxidation current of the hydroquinone electrochemical probe. The aptamer selectively interacts with AFP, causing a decrease in the peak current of the hydroquinone because the binding biomolecules on the electrode surface hinder the electron transfer of the redox probe. Effects of aptamer concentration and AFP incubation time were studied, and the current changes of the redox probe before and after AFP binding were investigated by square wave voltammetry. The developed aptasensor provides a linear range from 3.0-30 ng mL-1 with a detection limit of 1.22 ng mL-1. Moreover, the aptamer immobilized electrode offers high selectivity to AFP molecules, good stability, and sensitive determination of AFP in human serum samples with high recoveries.

| S-EPMC8263621 | biostudies-literature

Insulin-binding aptamer-conjugated graphene oxide for insulin detection.

Project description:This paper describes a simple and sensitive aptamer/graphene oxide (GO) based assay for insulin detection. GO can protect DNA from nuclease cleavage, but aptamers can be detached from the GO surface by specific target binding. This exposes the aptamers to enzymatic cleavage and releases the target for a new cycle. Cycling of targets leads to significant signal amplification and low LOD.

| S-EPMC5508966 | biostudies-literature

Screening and Evaluation of Thiamethoxam Aptamer Based on Pressurized GO-SELEX and Its Sensor Application

Project description:Thiamethoxam, a nicotinic pesticide used worldwide, can cause great harm to the environment and even to human health, and aptamers, known as chemical antibodies, have high affinity and specificity for the target, as well as great potential in detecting small molecules such as pesticides. In this paper, we report a highly sensitive biosensor system for thiamethoxam residue detection based on aptamer technology. After 15 rounds of screening with the pressurized GO-SELEX technology, we found that the aptamer libraries of the 5th and 9th rounds showed high affinity by the capture method. Four candidate aptamers were obtained by high-throughput sequencing and secondary structure prediction. Among them, the aptamer named Thi-5R-18 from the 5th round was demonstrated to possess the highest affinity by isothermal titration calorimetry, with a dissociation constant (Kd) of 4.935 × 10−5 M. The results of molecular docking showed that thiamethoxam and Thi-5R-18 were combined with bases G-15, A-19, and T-71 through hydrogen bonding and π–π interaction.Thi-5R-18 was used as a recognition element to construct a AuNPs colorimetric aptasensor, achieving an ultralow detection limit of 0.37 nM. More importantly, this colorimetric aptasensor can be used for quantitative detection of thiamethoxam on tea leaves, with a recovery of 96.94%~105.86%. This study provides a highly sensitive biosensor for detection of thiamethoxam residue.

| S-EPMC9953353 | biostudies-literature

Topical Application of Nano-sized Graphene Oxide Cream Ameliorates Acute Skin Inflammation in Mice

Project description:We have previously shown that nano-sized graphene oxide (NGO) displays anti-inflammatory activities against natural killer T (NKT) cell-mediated sepsis. To address whether NGO could be applied to treat acute skin inflammation. We developed a conventional skin Cetaphil® cream containing NGO (NGO cream) for topical application to skin lesions and investigated its therapeutic efficacy by employing the tape-stripping-induced acute skin inflammation model. Topical application of NGO cream to the wounded area significantly reduced skin lesions compared with the control cream. Moreover, NGO cream treatment prevented the tape-stripping-elicited infiltration of and IL1β production by skin neutrophils and dendritic cells (DCs). Furthermore, such anti-inflammatory effects of NGO cream were attributed to decreased infiltration of IL12-producing DCs and IFNγ-producing cells (e.g., CD4+ T, CD8+ T, γδ T, NK, and NKT cells) into the skin. In addition, topical NGO cream administration enhanced the expression of suppressive molecules such as FR4 on skin regulatory T cells. Through RNA sequencing analysis, we found that the preventive effect of NGO cream on acute skin inflammation may be correlated with the activation of keratinocytes located in the epidermis. Our results support NGO cream as a therapeutic option to control acute skin inflammation.

2024-08-20 | GSE272008 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data