Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Graphene-DNAzyme Junctions: A Platform for Direct Metal Ion Detection with Ultrahigh Sensitivity.

ABSTRACT: Many metal ions are present in biology and in the human body in trace amounts. Despite numerous efforts, metal sensors with ultrahigh sensitivity (< a few picomolar) are rarely achieved. Here, we describe a platform method that integrates a Cu2+-dependent DNAzyme into graphene-molecule junctions and its application for direct detection of paramagnetic Cu2+ with femtomolar sensitivity and high selectivity. Since DNAzymes specific for other metal ions can be obtained through in vitro selection, the method demonstrated here can be applied to the detection of a broad range of other metal ions.

SUBMITTER: Gao L

PROVIDER: S-EPMC4583199 | biostudies-literature | 2015 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Graphene-DNAzyme Junctions: A Platform for Direct Metal Ion Detection with Ultrahigh Sensitivity.

Gao Li L Li Le-Le LL Wang Xiaolong X Wu Peiwen P Cao Yang Y Liang Bo B Li Xin X Lin Yuanwei Y Lu Yi Y Guo Xuefeng X

Chemical science 20150205 4

Many metal ions are present in biology and in the human body in trace amounts. Despite numerous efforts, metal sensors with ultrahigh sensitivity (< a few picomolar) are rarely achieved. Here, we describe a platform method that integrates a Cu<sup>2+</sup>-dependent DNAzyme into graphene-molecule junctions and its application for direct detection of paramagnetic Cu<sup>2+</sup> with femtomolar sensitivity and high selectivity. Since DNAzymes specific for other metal ions can be obtained through ...[more]

PMID: 26417425

Similar Datasets

Ultrahigh humidity sensitivity of graphene oxide.

Project description:Humidity sensors have been extensively used in various fields, and numerous problems are encountered when using humidity sensors, including low sensitivity, long response and recovery times, and narrow humidity detection ranges. Using graphene oxide (G-O) films as humidity sensing materials, we fabricate here a microscale capacitive humidity sensor. Compared with conventional capacitive humidity sensors, the G-O based humidity sensor has a sensitivity of up to 37800% which is more than 10 times higher than that of the best one among conventional sensors at 15%-95% relative humidity. Moreover, our humidity sensor shows a fast response time (less than 1/4 of that of the conventional one) and recovery time (less than 1/2 of that of the conventional one). Therefore, G-O appears to be an ideal material for constructing humidity sensors with ultrahigh sensitivity for widespread applications.

| S-EPMC3776968 | biostudies-literature

Graphene field-effect transistor biosensor for detection of biotin with ultrahigh sensitivity and specificity.

Project description:Because avidin and biotin molecules exhibit the most specific and strongest non-covalent interaction, avidin-biotin technology is widely used in ELISA (enzyme-linked immunosorbent assay) kits for the detection of different bio-macromolecules linked to different diseases including cancer and influenza. Combining the outstanding electrical conductivity (200,000 cm2V-1s-1) of graphene with the unique avidin and biotin interaction, we demonstrate a novel graphene field-effect transistor (GFET) biosensor for the quantitative detection of bio-macromolecules. The GFET consists of six pairs of interdigital Cr/Au electrodes supported on Si/SiO2 substrate with an avidin immobilized single layer graphene channel as the sensing platform. By monitoring the real time current change upon the addition of biotin solution in bovine serum albumin (BSA) in the silicone pool preformed onto the GFET, the lowest detectable biotin concentration is estimated to be 90 fg/ml (0.37 pM). The specificity of the GFET is confirmed both by controlled and real sample measurements. From the magnitude of current change upon the addition of different concentrations of biotin solutions, the dissociation constant Kd is estimated to be 1.6 × 10-11 M. Since biotin is capable of conjugating with proteins, nucleotides and other bio-macromolecules without altering their properties, the present GFET sensor with its ultra-high sensitivity (0.37 pM) and specificity can be tailored to the rapid point-of-care detection of different types of desired biomolecules at very low concentration level through biotinylation as well as the exogenous biotin in blood serum.

| S-EPMC7272179 | biostudies-literature

Multicolor Phenylenediamine Carbon Dots for Metal-Ion Detection with Picomolar Sensitivity.

Project description:Carbon dots keep attracting attention in multidisciplinary fields, motivating the development of new compounds. Phenylenediamine C6H4(NH2)2 dots are known to exhibit colorful emission, which depends on size, composition, and the functional surface groups, forming those structures. While quite a few fabrication protocols have been developed, the quantum yield of phenylenediamine dots still does not exceed 50% owing to undesired fragment formation during carbonization. Here, we demonstrate that an ethylene glycol-based environment allows obtaining multicolor high-quantum-yield phenylenediamine carbon dots. In particular, a kinetic realization of solvothermal synthesis in acidic environments enhances carbonization reaction yield for meta phenylenediamine compounds and leads to quantum yields, exciting 60%. Reaction yield after the product's purification approaches 90%. Furthermore, proximity of metal ions (Nd3+, Co3+, La3+) can either enhance or quench the emission, depending on the concentration. Optical monitoring of the solution allows performing an accurate detection of ions at picomolar concentrations. An atomistic model of carbon dots was developed to confirm that the functional surface group positioning within the molecular structure has a major impact on dots' physicochemical properties. The high performance of new carbon dots paves the way toward their integration in numerous applications, including imaging, sensing, and therapeutics.

| S-EPMC8488935 | biostudies-literature

Dissecting metal ion-dependent folding and catalysis of a single DNAzyme.

Project description:Protein metalloenzymes use various modes for functions for which metal-dependent global conformational change is required in some cases but not in others. In contrast, most ribozymes require a global folding that almost always precedes enzyme reactions. Herein we studied metal-dependent folding and cleavage activity of the 8-17 DNAzyme using single-molecule fluorescence resonance energy transfer. Addition of Zn2+ and Mg2+ induced folding of the DNAzyme into a more compact structure followed by a cleavage reaction, which suggests that the DNAzyme may require metal-dependent global folding for activation. In the presence of Pb2+, however, the cleavage reaction occurred without a precedent folding step, which suggests that the DNAzyme may be prearranged to accept Pb2+ for the activity. Neither ligation reaction of the cleaved substrates nor dynamic changes between folded and unfolded states was observed. These features may contribute to the unusually fast Pb2+-dependent reaction of the DNAzyme. These results suggest that DNAzymes can use all modes of activation that metalloproteins use.

| S-EPMC4376948 | biostudies-literature

Enhanced Thermoelectricity in Metal-[60]Fullerene-Graphene Molecular Junctions.

Project description:The thermoelectric properties of molecular junctions consisting of a metal Pt electrode contacting [60]fullerene derivatives covalently bound to a graphene electrode have been studied by using a conducting-probe atomic force microscope (c-AFM). The [60]fullerene derivatives are covalently linked to the graphene via two meta-connected phenyl rings, two para-connected phenyl rings, or a single phenyl ring. We find that the magnitude of the Seebeck coefficient is up to nine times larger than that of Au-C60-Pt molecular junctions. Moreover, the sign of the thermopower can be either positive or negative depending on the details of the binding geometry and on the local value of the Fermi energy. Our results demonstrate the potential of using graphene electrodes for controlling and enhancing the thermoelectric properties of molecular junctions and confirm the outstanding performance of [60]fullerene derivatives.

| S-EPMC10103166 | biostudies-literature

Ultrahigh Sensitivity PTR-MS Instrument with a Well-Defined Ion Chemistry.

Project description:Proton-transfer-reaction mass spectrometry (PTR-MS) is widely used for measuring organic trace gases in air. In traditional PTR-MS, both nonpolar and polar analytes are ionized with unit efficiency, as predicted from ion-molecule collision theories. This well-defined ion chemistry allows for direct quantification of analytes without prior calibration and therefore is an important characteristic of PTR-MS. In an effort to further increase the sensitivity, recently developed ultrahigh sensitivity chemical ionization mass spectrometry (CIMS) analyzers have, however, been reported to have sacrificed unit ionization efficiency for selected analytes or classes of analytes. We herein report on the development of a novel ultrasensitive PTR-MS instrument, the FUSION PTR-TOF 10k, which exhibits the same universal unit response as conventional PTR-MS analyzers. The core component of this analyzer is the newly designed FUSION ion-molecule reactor, which is a stack of concentric ring electrodes generating a static longitudinal electric field superimposed by a focusing transversal radiofrequency (RF) field. The FUSION PTR-TOF 10k instrument is equipped with an improved ion source, capable of switching between different reagent ions (H3O+, O2+, NO+, NH4+) in less than one second. The improved time-of-flight mass spectrometer analyzes m/z signals with a mass resolution in the 10000-15000 range. FUSION PTR-TOF 10k achieves sensitivities up to 80000 cps ppbV-1 and detection limits down to 0.5 pptV for a 1 s measurement time. We show time-series of naphthalene and 13C-napthalene as measured in ambient air in Innsbruck for demonstrating the sub-pptV detection capability of this novel FUSION PTR-TOF 10k.

| S-EPMC10433242 | biostudies-literature

Intelligent demethylase-driven DNAzyme sensor for highly reliable metal-ion imaging in living cells.

Project description:The accurate intracellular imaging of metal ions requires an exquisite site-specific activation of metal-ion sensors, for which the pervasive epigenetic regulation strategy can serve as an ideal alternative thanks to its orthogonal control feature and endogenous cell/tissue-specific expression pattern. Herein, a simple yet versatile demethylation strategy was proposed for on-site repairing-to-activating the metal-ion-targeting DNAzyme and for achieving the accurate site-specific imaging of metal ions in live cells. This endogenous epigenetic demethylation-regulating DNAzyme system was prepared by modifying the DNAzyme with an m6A methylation group that incapacitates the DNAzyme probe, thus eliminating possible off-site signal leakage, while the cell-specific demethylase-mediated removal of methylation modification could efficiently restore the initial catalytic DNAzyme for sensing metal ions, thus allowing a high-contrast bioimaging in live cells. This epigenetic repair-to-activate DNAzyme strategy may facilitate the robust visualization of disease-specific biomarkers for in-depth exploration of their biological functions.

| S-EPMC8635203 | biostudies-literature

Designing a Biostable L-DNAzyme for Lead(II) Ion Detection in Practical Samples.

Project description:A promising biosensor for effectively lead (II) ion detection in practical applications was developed by constructing a Pb2+-specific L-DNAzyme, the enantiomer of the natural nucleic acid-constructed D-DNAzyme. This fluorescent sensor contains the L-enzyme strand with a quencher at the 3' end, and the L-substrate strand with a fluorophore at the 5' and a quencher at the 3' ends that formed a complex. In the presence of Pb2+, the L-substrate is cut into two fragments, leading to the recovery of fluorescence. The sensor shows high sensitivity and selectivity for Pb2+ detection with a linear response in the range of 5-100 nM and a detection limit of 3 nM in aqueous solution. Importantly, based on that L-DNAzyme consists of non-natural nucleic acids, which is insensitive to nuclease digestion, protein adsorption and D-DNA hybridization, our sensor shows specific response to Pb2+ in practical water and serum samples. Therefore, it is expected that our L-DNAzyme-based strategy may offer a new method for developing simple, rapid and sensitive sensors in complex systems.

| S-EPMC5650247 | biostudies-literature

Brownian-dynamics simulations of metal-ion binding to four-way junctions.

Project description:Four-way junctions (4Hs) are important intermediates in DNA rearrangements such as genetic recombination. Under the influence of multivalent cations these molecules undergo a conformational change, from an extended planar form to a quasi-continuous stacked X-structure. Recently, a number of X-ray structures and a nuclear magnetic resonance (NMR) structure of 4Hs have been reported and in three of these the position of multivalent cations is revealed. These structures belong to two main families, characterized by the angle between the two co-axial stacked helices, which is either around +40 to +55 degrees or around -70 to -80 degrees. To investigate the role of metal-ion binding on the conformation of folded 4Hs we performed Brownian-dynamics simulations on the set of available structures. The simulations confirm the proposed metal-ion binding sites in the NMR structure and in one of the X-ray structures. Furthermore, the calculations suggest positions for metal-ion binding in the other X-ray structures. The results show a striking dependence of the ion density on the helical environment (B-helix or A-helix) and the structural family.

| S-EPMC99837 | biostudies-literature

Avidin-Biotin Technology in Gold Nanoparticle-Decorated Graphene Field Effect Transistors for Detection of Biotinylated Macromolecules with Ultrahigh Sensitivity and Specificity.

Project description:The strong and specific noncovalent interaction between avidin and biotin is widely exploited in different types of enzyme-linked immunosorbent assay kits, labeled immunosensors, and polymer-based sensing devices for the detection of different biomarkers specific to different diseases such as cancer and influenza. Here, we employed the avidin-biotin technology in a novel gold nanoparticle-decorated graphene field-effect transistor (AuNP-GFET) and demonstrated the specific detection of the biotinylated macromolecules such as biotinylated proteins and nucleotides in the sub-picomolar (pM) range. The AuNP-GFET was constructed by fabricating six pairs of interdigital electrodes on graphene transferred on a SiO2/Si substrate. The sensing performance of AuNP-GFET was characterized by the real-time two-terminal electrical current measurement upon injection of the analyte solution into a silicone pool preattached onto the electrodes. Avidin, a tetrameric biotin-binding protein with strong affinity and specificity, immobilized on AuNP-decorated single-layer graphene, was used as the sensing platform and transduced the electrical signal upon binding to the analyte macromolecules. The sensing capability of the AuNP-GFET was tested with the biotinylated protein A. Sensitivity of the present biosensor was estimated to be ∼0.4 pM. The specificity and applicability of the biosensor were confirmed using both synthetic and real samples. Because the biotin label can retain its binding capability to avidin with strong affinity and specificity even after conjugating with varieties of proteins and nucleotides, the present AuNP-GFET biosensor is expected to promote the research in developing different biosensors.

| S-EPMC7689884 | 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