Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Two color DNA barcode detection in photoluminescence suppressed silicon nitride nanopores.

ABSTRACT: Optical sensing of solid-state nanopores is a relatively new approach that can enable high-throughput, multicolor readout from a collection of nanopores. It is therefore highly attractive for applications such as nanopore-based DNA sequencing and genotyping using DNA barcodes. However, to date optical readout has been plagued by the need to achieve sufficiently high signal-to-noise ratio (SNR) for single fluorophore sensing, while still maintaining millisecond resolution. One of the main factors degrading the optical SNR in solid-state nanopores is the high photoluminescence (PL) background emanating from the silicon nitride (SiNx) membrane in which pores are commonly fabricated. Focusing on the optical properties of SiNx nanopores we show that the local membrane PL intensity is substantially reduced, and its spectrum is shifted toward shorter wavelengths with increasing e-beam dose. This phenomenon, which is correlated with a marked photocurrent enhancement in these nanopores, is utilized to perform for the first time single molecule fluorescence detection using both green and red laser excitations. Specifically, the reduction in PL and the concurrent measurement of the nanopore photocurrent enhancement allow us to maximize the background suppression and to detect a dual color, five-unit DNA barcode with high SNR levels.

SUBMITTER: Assad ON

PROVIDER: S-EPMC4296929 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

K(+) , Na(+) , and Mg(2+) on DNA translocation in silicon nitride nanopores.

Project description:In this work, we report on how salt concentration and cation species affect DNA translocation in voltage-biased silicon nitride nanopores. The translocation of dsDNA in linear, circular, and supercoiled forms was measured in salt solutions containing KCl, NaCl, and MgCl(2) . As the KCl concentrations were decreased from 1 to 0.1 M, the time taken by a DNA molecule to pass through a nanopore was shorter and the frequency of the translocation in a folded configuration was reduced, suggesting an increase in DNA electrophoretic mobility and DNA persistence length. When the salt concentration was kept at 1 M, but replacing K(+) with Na(+) , longer DNA translocation times (t(d) ) were observed. The addition of low concentrations of MgCl(2) with 1.6 M KCl resulted in longer t(d) and an increased frequency of supercoiled DNA molecules in a branched form. These observations were consistent with the greater counterion charge screening ability of Na(+) and Mg(2+) as compared to K(+) . In addition, we demonstrated that dsDNA molecules indeed translocated through a ?10 nm nanopore by PCR amplification and gel electrophoresis. We also compared the dependence of DNA mobility and conformation on KCl concentration and cation species measured at single molecule level by silicon nitride nanopores with existing bulk-based experimental results and theoretical predictions.

| S-EPMC3514626 | biostudies-literature

Photoluminescence and electronic transitions in cubic silicon nitride.

Project description:A spectroscopic study of cubic silicon nitride (?-Si3N4) at cryogenic temperatures of 8?K in the near IR - VUV range of spectra with synchrotron radiation excitation provided the first experimental evidence of direct electronic transitions in this material. The observed photoluminescence (PL) bands were assigned to excitons and excited and centers formed after the electron capture by neutral structural defects. The excitons are weakly quenched on neutral and strongly on charged defects. The fundamental band-gap energy of 5.05?±?0.05?eV and strong free exciton binding energy ~0.65?eV were determined. The latter value suggests a high efficiency of the electric power transformation in light in defect-free crystals. Combined with a very high hardness and exceptional thermal stability in air, our results indicate that ?-Si3N4 has a potential for fabrication of robust and efficient photonic emitters.

| S-EPMC4698759 | biostudies-literature

Optical Gating of Photoluminescence from Color Centers in Hexagonal Boron Nitride.

Project description:We report on multicolor excitation experiments with color centers in hexagonal boron nitride at cryogenic temperatures. We demonstrate controllable optical switching between bright and dark states of color centers emitting around 2 eV. Resonant, or quasi-resonant, excitation of photoluminescence also pumps the color center, via a two-photon process, into a dark state, where it becomes trapped. Repumping back into the bright state has a step-like spectrum with a defect-dependent threshold between 2.25 and 2.6 eV. This behavior is consistent with photoionization and charging between optically bright and dark states of the defect. Furthermore, a second zero phonon line, detuned by +0.4 eV, is observed in absorption with orthogonal polarization to the emission, evidencing an additional energy level in the color center.

| S-EPMC7304068 | biostudies-literature

Surveying silicon nitride nanopores for glycomics and heparin quality assurance.

Project description:Polysaccharides have key biological functions and can be harnessed for therapeutic roles, such as the anticoagulant heparin. Their complexity-e.g., >100 monosaccharides with variety in linkage and branching structure-significantly complicates analysis compared to other biopolymers such as DNA and proteins. More, and improved, analysis tools have been called for, and here we demonstrate that solid-state silicon nitride nanopore sensors and tuned sensing conditions can be used to reliably detect native polysaccharides and enzymatic digestion products, differentiate between different polysaccharides in straightforward assays, provide new experimental insights into nanopore electrokinetics, and uncover polysaccharide properties. We show that nanopore sensing allows us to easily differentiate between a clinical heparin sample and one spiked with the contaminant that caused deaths in 2008 when its presence went undetected by conventional assays. The work reported here lays a foundation to further explore polysaccharide characterization and develop assays using thin-film solid-state nanopore sensors.

| S-EPMC6095881 | biostudies-other

Covalent Modification of Silicon Nitride Nanopore by Amphoteric Polylysine for Short DNA Detection.

Project description:In this work, we demonstrate a chemical modification approach, by means of covalent-bonding amphoteric poly-l-lysine (PLL) on the interior nanopore surface, which could intensively protect the pore from etching when exposed in the electrolyte under various pH conditions (from pH 4 to 12). Nanopore was generated via simple current dielectric breakdown methodology, covalent modification was performed in three steps, and the functional nanopore was fully characterized in terms of chemical structure, hydrophilicity, and surface morphology. I-V curves were recorded under a broad range of pH stimuli to evaluate the stability of the chemical bonding layer; the plotted curves demonstrated that nanopore with a covalent bonding layer has good pH tolerance and showed apparent reversibility. In addition, we have also measured the conductance of modified nanopore with varied KCl concentration (from 0.1 mM to 1 M) at different pH conditions (pHs 5, 7, 9, and 11). The results suggested that the surface charge density does not fluctuate with variation in salt concentration, which inferred that the SiN x nanopore was fully covered by PLL. Moreover, the PLL functionalized nanopore has realized the detection of single-stranded DNA homopolymer translocation under bias voltage of 500 mV, and the 20 nt homopolymers could be evidently differentiated in terms of the current amplitude and dwell time at pHs 5, 8, and 11.

| S-EPMC6645049 | biostudies-literature

Evolution of nanopores in hexagonal boron nitride.

Project description:The engineering of atomically-precise nanopores in two-dimensional materials presents exciting opportunities for both fundamental science studies as well as applications in energy, DNA sequencing, and quantum information technologies. The exceptional chemical and thermal stability of hexagonal boron nitride (h-BN) suggest that exposed h-BN nanopores will retain their atomic structure even when subjected to extended periods of time in gas or liquid environments. Here we employ transmission electron microscopy to examine the time evolution of h-BN nanopores in vacuum and in air and find, even at room temperature, dramatic geometry changes due to atom motion and edge contamination adsorption, for timescales ranging from one hour to one week. The discovery of nanopore evolution contrasts with general expectations and has profound implications for nanopore applications of two-dimensional materials.

| S-EPMC10241886 | biostudies-literature

Computational investigation of DNA detection using graphene nanopores.

Project description:Nanopore-based single-molecule detection and analysis have been pursued intensively over the past decade. One of the most promising applications in this regard is DNA sequencing achieved through DNA translocation-induced blockades in ionic current. Recently, nanopores fabricated in graphene sheets were used to detect double-stranded DNA. Due to its subnanometer thickness, graphene nanopores show great potential to realize DNA sequencing at single-base resolution. Resolving at the atomic level electric field-driven DNA translocation through graphene nanopores is crucial to guide the design of graphene-based sequencing devices. Molecular dynamics simulations, in principle, can achieve such resolution and are employed here to investigate the effects of applied voltage, DNA conformation, and sequence as well as pore charge on the translocation characteristics of DNA. We demonstrate that such simulations yield current characteristics consistent with recent measurements and suggest that under suitable bias conditions A-T and G-C base pairs can be discriminated using graphene nanopores.

| S-EPMC3222720 | biostudies-literature

Detection of DNA hybridizations using solid-state nanopores.

Project description:We report an experimental study of using DNA translocation through solid-state nanopores to detect the sequential arrangement of two double-stranded 12-mer hybridization segments on a single-stranded DNA molecule. The sample DNA is a trimer molecule formed by hybridizing three single-stranded oligonucleotides. A polystyrene bead is attached to the end of the trimer DNA, providing a mechanism in slowing down the translocation and suppressing the thermal diffusion, thereby allowing the detection of short features of DNA by standard patch-clamp electronics. The electrical signature of the translocation of a trimer molecule through a nanopore has been identified successfully in the temporal traces of ionic current. The results reported here represent the first successful attempt in using a solid-state nanopore as an ionic scanning device in resolving individual hybridization segments (or 'probes') on a DNA molecule.

| S-EPMC4811674 | biostudies-literature

Silicon vacancy color center photoluminescence enhancement in nanodiamond particles by isolated substitutional nitrogen on {100} surfaces.

Project description:Fluorescent nanodiamonds were produced by incorporation of silicon-vacancy (Si-V) defect centers in as-received diamonds of averaged size ∼255 nm using microwave plasma chemical vapor deposition. The potential for further enhancement of Si-V emission in nanodiamonds (NDs) is demonstrated through controlled nitrogen doping by adding varying amounts of N(2) in a H(2) + CH(4) feedgas mixture. Nitrogen doping promoted strong narrow-band (FWHM ∼ 10 nm) emission from the Si-V defects in NDs, as confirmed by room temperature photoluminescence. At low levels, isolated substitutional nitrogen in {100} growth sectors is believed to act as a donor to increase the population of optically active (Si-V)(-) at the expense of optically inactive Si-V defects, thus increasing the observed luminescence from this center. At higher levels, clustered nitrogen leads to deterioration of diamond quality with twinning and increased surface roughness primarily on {111} faces, leading to a quenching of the Si-V luminescence. Enhancement of the Si-V defect through controlled nitrogen doping offers a viable alternative to nitrogen-vacancy defects in biolabeling/sensing applications involving sub-10 nm diamonds for which luminescent activity and stability are reportedly poor.

| S-EPMC3568091 | biostudies-other

DNA profiling using solid-state nanopores: detection of DNA-binding molecules.

Project description:We present a novel single-molecule method for rapidly evaluating small-molecule binding to individual DNA molecules using nanopores fabricated in ultrathin silicon membranes. A measurable shift in the residual ion current through a approximately 3.5 nm pore results from threading of a dye-intercalated DNA molecule, as compared to the typical residual current of native DNA. The average level of the residual current can be used to directly quantify the fraction of bound molecules to DNA, providing a new way to determine binding isotherms. Spatial sensitivity is also demonstrated by designing a two-segment DNA molecule that contains small-molecule binding sites in one of its two segments. Translocations of such molecules exhibit two current levels upon incubation with a DNA-binding dye, caused by selectively bound dye in one of the DNA segments. Our results, as shown here with four different dyes, coincide well with bulk fluorescence measurements performed under identical conditions. The nanopore approach for "reading-out" molecular binding along a DNA molecule, combined with the miniscule amounts of DNA required and the potential for scalability using nanopore arrays, provide a novel platform for future applications in analytical drug screening.

| S-EPMC2871189 | 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