Browse
Submit Data
Databases
API
Help

Dataset Information

18 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Target-induced activation of DNAzyme for highly sensitive colorimetric detection of bleomycin via DNA scission.

ABSTRACT: In this work, a label-free and sensitive colorimetric sensing strategy for the detection of bleomycin (BLM) was developed on the basis of BLM-mediated activation of G-quadruplex DNAzyme via DNA strand scission. A G-quadruplex based hairpin probe (G4HP) containing the scission site (5'-GT-3') of BLM at the loop region and guanine (G)-rich sequences at its 5'-end was employed in this protocol. In the presence of BLM, it may cleave the 5'-GT-3' site of the hairpin probe with Fe(ii) as a cofactor, releasing the G-tetrads DNA fragment, which may further bind hemin to form a catalytic G-quadruplex-hemin DNAzyme. The resultant G-quadruplex DNAzyme has notable peroxidase-like activity, which effectively catalyzes the oxidation of 2,2'-azino-bis(3-ethylbenzothiozoline-6-sulfonic acid) (ABTS) by H₂O₂ to produce the blue-green-colored free-radical cation (ABTS^·+). Therefore, the detection of BLM can be achieved by observing the color transition with the naked eye or measuring the absorbance at a wavelength of 420 nm using a UV-Vis spectrophotometer. Attributing to the specific BLM-induced DNA strand scission and the effective locking of G-tetrads in the stem of the G4HP, the colorimetric sensing strategy exhibits high sensitivity and selectivity for detection of BLM in human serum samples, which might hold great promise for BLM assay in biomedical and clinical research.

SUBMITTER: Liao X

PROVIDER: S-EPMC9215162 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A simple and highly sensitive colorimetric detection method for gaseous formaldehyde.

Project description:A colorimetric detection method using amine-functionalized polymer films doped with a pH indicator has been developed for the rapid, sensitive, and quantitative detection of gaseous formaldehyde at concentrations well below the immediately dangerous to life or health (IDLH) limit. In 1 min, visible color changes are easily observed, even down to the permissible exposure limit (PEL) at 750 ppb. The limit of detection is below 50 ppb (7% of the PEL) after 10 min of exposure. This sensor is essentially unaffected by changes in humidity or temperature (4 to 50 degrees C) and is not sensitive to common interferents.

| S-EPMC2854577 | biostudies-literature

Label-Free Isothermal Amplification Assay for Specific and Highly Sensitive Colorimetric miRNA Detection.

Project description:We describe a new method for the detection of miRNA in biological samples. This technology is based on the isothermal nicking enzyme amplification reaction and subsequent hybridization of the amplification product with gold nanoparticles and magnetic microparticles (barcode system) to achieve naked-eye colorimetric detection. This platform was used to detect a specific miRNA (miRNA-10b) associated with breast cancer, and attomolar sensitivity was demonstrated. The assay was validated in cell culture lysates from breast cancer cells and in serum from a mouse model of breast cancer.

| S-EPMC5046170 | biostudies-literature

Highly sensitive and selective colorimetric sensors for uranyl (UO2(2+)): development and comparison of labeled and label-free DNAzyme-gold nanoparticle systems.

Project description:Colorimetric uranium sensors based on uranyl (UO2(2+)) specific DNAzyme and gold nanoparticles (AuNP) have been developed and demonstrated using both labeled and label-free methods. In the labeled method, a uranyl-specific DNAzyme was attached to AuNP, forming purple aggregates. The presence of uranyl induced disassembly of the DNAzyme functionalized AuNP aggregates, resulting in red individual AuNPs. Once assembled, such a "turn-on" sensor is highly stable, works in a single step at room temperature, and has a detection limit of 50 nM after 30 min of reaction time. The label-free method, on the other hand, utilizes the different adsorption properties of single-stranded and double-stranded DNA on AuNPs, which affects the stability of AuNPs in the presence of NaCl. The presence of uranyl resulted in cleavage of substrate by DNAzyme, releasing a single stranded DNA that can be adsorbed on AuNPs and protect them from aggregation. Taking advantage of this phenomenon, a "turn-off" sensor was developed, which is easy to control through reaction quenching and has 1 nM detection limit after 6 min of reaction at room temperature. Both sensors have excellent selectivity over other metal ions and have detection limits below the maximum contamination level of 130 nM for UO2(2+) in drinking water defined by the U.S. Environmental Protection Agency (EPA). This study represents the first direct systematic comparison of these two types of sensor methods using the same DNAzyme and AuNPs, making it possible to reveal advantages, disadvantages, versatility, limitations, and potential applications of each method. The results obtained not only allow practical sensing application for uranyl but also serve as a guide for choosing different methods for designing colorimetric sensors for other targets.

| S-EPMC2667950 | biostudies-literature

An allosteric dual-DNAzyme unimolecular probe for colorimetric detection of copper(II).

Project description:An effective dual-DNAzyme-based unimolecular probe design employing intramolecular signal transduction is demonstrated. The probe is composed of three domains: a DNA-cleaving DNAzyme, a substrate, and an HRP-mimicking DNAzyme. When the probe meets its target, cleavage of the substrate by the DNA-cleaving DNAzyme activates the HRP-mimicking DNAzyme, producing a colorimetric signal. The Cu(2+)-dependent DNAzyme engineered to demonstrate this design revealed a sensitivity corresponding to 65 ppb, which is sufficient to detect Cu(2+) in drinking water. The new probe has excellent selectivity toward Cu(2+). This three-component design is simple and easy to engineer. It may provide the basis for future development of other nucleic acid-based probes for toxicological and environmental monitoring.

| S-EPMC2764326 | biostudies-literature

Highly Sensitive and Selective Colorimetric Detection of Methylmercury Based on DNA Functionalized Gold Nanoparticles.

Project description:A new colorimetric detection of methylmercury (CH?Hg?) was developed, which was based on the surface deposition of Hg enhancing the catalytic activity of gold nanoparticles (AuNPs). The AuNPs were functionalized with a specific DNA strand (HT7) recognizing CH?Hg?, which was used to capture and separate CH?Hg? by centrifugation. It was found that the CH?Hg? reduction resulted in the deposition of Hg onto the surface of AuNPs. As a result, the catalytic activity of the AuNPs toward the chromogenic reaction of 3,3,5,5-tetramethylbenzidine (TMB)-H?O? was remarkably enhanced. Under optimal conditions, a limit of detection of 5.0 nM was obtained for CH?Hg? with a linear range of 10?200 nM. We demonstrated that the colorimetric method was fairly simple with a low cost and can be conveniently applied to CH?Hg? detection in environmental samples.

| S-EPMC6111283 | biostudies-literature

A Sensitive DNAzyme-Based Chiral Sensor for Lead Detection.

Project description:A DNAzyme-based sensor for the determination and quantification of lead ions (Pb2+) has been established, which combines the recognition and catalysis of DNAzyme with the optical properties of nanomaterials. Circular dichroism (CD) signals were obtained by a DNAzyme-based assembly of asymmetric silver nanoparticle (AgNPs) dimers. A good linear relationship between CD signals and Pb2+ concentration was obtained ranging from 0.05 ng∙mL-1 to 10 ng∙mL-1 with a limit of detection (LOD) of 0.02 ng∙mL-1. The specificity of this sensor in lead ion detection was excellent, and a satisfactory recovery was obtained in the analysis of tap water samples. The proposed technique possesses both high sensitivity and good specificity, giving it great potential for the analysis of Pb2+ in water.

| S-EPMC5452787 | biostudies-literature

Highly sensitive colorimetric detection of 17β-estradiol using split DNA aptamers immobilized on unmodified gold nanoparticles.

Project description:Gold nanoparticle (AuNP) based colorimetric aptasensor have been developed for many analytes recently largely because of the ease of detection, high sensitivity, and potential for high-throughput analysis. Most of the target aptamers for detection have short sequences. However, the approach shows poor performance in terms of detection sensitivity for most of the long-sequence aptamers. To address this problem, for the first time, we split the 76 mer aptamer of 17β-estradiol into two short pieces to improve the AuNP based colorimetric sensitivity. Our results showed that the split P1 + P2 still retained the original 76 mer aptamer's affinity and specificity but increased the detection limit by 10-fold, demonstrating that as low as 0.1 ng/mL 17β-estradiol could be detected. The increased sensitivity may be caused by lower aptamer adsorption concentration and a lower affinity to the AuNPs of a short single-strand DNA (ssDNA) sequence. Our study provided a new way to use long-sequence aptamers to develop a highly sensitive AuNP-based colorimetric aptasensor.

| S-EPMC4271257 | biostudies-other

Dual-Surfactant-Capped Ag Nanoparticles as a Highly Selective and Sensitive Colorimetric Sensor for Citrate Detection.

Project description:A colorimetric sensor for the detection of citrate ions is reported here using dual-surfactant-capped Ag nanoparticles (dual-AgNP sensor). A mixture of cetyl trimethyl ammonium bromide and a newly prepared gemini nonionic (GFEO) surfactant was used as a capping agent to synthesize dual-surfactant-capped Ag NPs for selective and sensitive citrate detection. The GFEO surfactant was designed with a specific chemical structure to provide strong binding with citrate for selective and sensitive detection. The developed dual-AgNP sensor showed extremely high selectivity toward citrate even in the presence of interfering species. Quantitative detection of citrate was carried out based on the changes in UV-vis absorbance and naked-eye readout. After optimization, the dual-AgNP sensor exhibited a visual detection limit of 25 μM and a low limit of detection of 4.05 nM with a UV-vis spectrometer. The developed citrate sensor performed well with a urine sample, with a high recovery of 99.6%. The prepared solution sensor was constructed on a paper-based analytical device.

| S-EPMC7240824 | biostudies-literature

Highly Sensitive and Selective Colorimetric Detection of Creatinine Based on Synergistic Effect of PEG/Hg2+-AuNPs.

Project description:A colorimetric sensor, based on the synergistic coordination effect on a gold nanoparticle (AuNP) platform has been developed for the determination of creatinine. The sensor selects citrate stabilized AuNPs as a platform, polyethylene glycol (PEG) as a decorator, and Hg2+ as a linkage to form a colorimetric probe system (PEG/Hg2--AuNPs). By forming hydrogen bond between the oxygen-containing functional groups of PEG and citrate ions on the surface of AuNPs, this probe shows good stability. PEG coordinated with Hg2+ synergistically and specifically on the surface of dispersed AuNPs, and the existence of creatinine could induce the aggregation of AuNPs with a corresponding color change and an obvious absorption peak shift within 5 min. This PEG/Hg2+-AuNPs probe towards creatinine shows high sensitivity, and a good linear relationship (R2 = 0.9948) was obtained between A620-522 nm and creatinine concentration, which can achieve the quantitative calculations of creatinine. The limit of detection (LOD) of this PEG/Hg2+-AuNPs probe was estimated to be 9.68 nM, lower than that of many other reported methods (Supplementary Materials Table S3). Importantly, the sensitive probe can be successfully applied in a urine simulating fluid sample and a bovine serum sample. The unique synergistic coordination sensing mechanism applied in the designation of this probe further improves its high selectivity and specificity for the detection of creatinine. Thus, the proposed probe may give new inspirations for colorimetric detection of creatinine and other biomolecules.

| S-EPMC6835235 | biostudies-literature

Multiple ligation-Assisted recombinase polymerase amplification for highly sensitive and selective colorimetric detection of SARS-CoV-2.

Project description:In this paper we present a new method for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), targeting a specific region "N gene." Under isothermal reaction conditions, we integrated ligation (Lig; high selectivity) and recombinase polymerase amplification (RPA; high sensitivity) processes, obtaining a robust method of detection. For point-of-care testing, we incorporated our laboratory-produced pyrophosphate ion (PPi)-sensing probe (PK-probe) for colorimetric analysis of the reaction. The total detection system was efficient and effective at diagnosing this RNA virus-mediated disease rapidly (30 min). In a full-genome SARS-CoV-2 study, our PK-probe/Lig-RPA system functioned with a limit of detection of 1160 copies/ml, with a single-mismatch level of selectively, and it was highly selective even in the presence of bacterial genomes commonly found in the human mouth and nose. This robust, straightforward, selective, efficient, and ultrasensitive colorimetric detection method, with potential for point-of-care analysis, should also be effective in detecting a diverse range of other RNA-based diseases.

| S-EPMC9375730 | biostudies-literature

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