Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley.

ABSTRACT: Proteins adhere to DNA at locations and with strengths that depend on the protein conformation, the underlying DNA sequence and the ionic content of the solution. A facile technique to probe the positions and strengths of protein-DNA binding would aid in understanding these important interactions. Here, we describe a 'DNA pulley' for position-resolved nano-mechanical measurements of protein-DNA interactions. A molecule of ? DNA is tethered by one end to a glass surface, and by the other end to a magnetic bead. The DNA is stretched horizontally by a magnet, and a nanoscale knife made of silicon nitride is manipulated to contact, bend and scan along the DNA. The mechanical profile of the DNA at the contact with the knife is probed via nanometer-precision optical tracking of the magnetic bead. This system enables detection of protein bumps on the DNA and localization of their binding sites. We study theoretically the technical requirements to detect mechanical heterogeneities in the DNA itself.

SUBMITTER: Shon MJ

PROVIDER: S-EPMC4705685 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Nano-mechanical measurements of protein-DNA interactions with a silicon nitride pulley.

Shon Min Ju MJ Cohen Adam E AE

Nucleic acids research 20150903 1

Proteins adhere to DNA at locations and with strengths that depend on the protein conformation, the underlying DNA sequence and the ionic content of the solution. A facile technique to probe the positions and strengths of protein-DNA binding would aid in understanding these important interactions. Here, we describe a 'DNA pulley' for position-resolved nano-mechanical measurements of protein-DNA interactions. A molecule of λ DNA is tethered by one end to a glass surface, and by the other end to a ...[more]

PMID: 26338777

Similar Datasets

Optical diffraction for measurements of nano-mechanical bending.

Project description:We explore and exploit diffraction effects that have been previously neglected when modelling optical measurement techniques for the bending of micro-mechanical transducers such as cantilevers for atomic force microscopy. The illumination of a cantilever edge causes an asymmetric diffraction pattern at the photo-detector affecting the calibration of the measured signal in the popular optical beam deflection technique (OBDT). The conditions that avoid such detection artefacts conflict with the use of smaller cantilevers. Embracing diffraction patterns as data yields a potent detection technique that decouples tilt and curvature and simultaneously relaxes the requirements on the illumination alignment and detector position through a measurable which is invariant to translation and rotation. We show analytical results, numerical simulations and physiologically relevant experimental data demonstrating the utility of the diffraction patterns. We offer experimental design guidelines and quantify possible sources of systematic error in OBDT. We demonstrate a new nanometre resolution detection method that can replace OBDT, where diffraction effects from finite sized or patterned cantilevers are exploited. Such effects are readily generalized to cantilever arrays, and allow transmission detection of mechanical curvature, enabling instrumentation with simpler geometry. We highlight the comparative advantages over OBDT by detecting molecular activity of antibiotic Vancomycin.

| S-EPMC4891711 | biostudies-literature

Lifetime and Stability of Silicon Nitride Nanopores and Nanopore Arrays for Ionic Measurements.

Project description:Nanopores are promising for many applications including DNA sequencing and molecular filtration. Solid-state nanopores are preferable over their biological counterparts for applications requiring durability and operation under a wider range of external parameters, yet few studies have focused on optimizing their robustness. We report the lifetime and durability of pores and porous arrays in 10 to 100 nm-thick, low-stress silicon nitride (SiNx) membranes. Pores are fabricated using a transmission electron microscope (TEM) and/or electron beam lithography (EBL) and reactive ion etching (RIE), with diameters from 2 to 80 nm. We store them in various electrolyte solutions (KCl, LiCl, MgCl2) and record open pore conductance over months to quantify pore stability. Pore diameters increase with time, and diameter etch rate increases with electrolyte concentration from Δd/Δt ∼ 0.2 to ∼ 3 nm/day for 0.01 to 3 M KCl, respectively. TEM confirms the range of diameter etch rates from ionic measurements. Using electron energy loss spectroscopy (EELS), we observe a N-deficient region around the edges of TEM-drilled pores. Pore expansion is caused by etching of the Si/SiO2 pore walls, which resembles the dissolution of silicon found in minerals such as silica (SiO2) in salty ocean water. The etching process occurs where the membrane was exposed to the electron beam and can result in pore formation. However, coating pores with a conformal 1 nm-thick hafnium oxide layer prevents expansion in 1 M KCl, in stark contrast to bare SiNx pores (∼ 1.7 nm/day). EELS data reveal the atomic composition of bare and HfO2-coated pores.

| S-EPMC9547353 | biostudies-literature

A polypeptide-DNA hybrid with selective linking capability applied to single molecule nano-mechanical measurements using optical tweezers.

Project description:Many applications in biosensing, biomaterial engineering and single molecule biophysics require multiple non-covalent linkages between DNA, protein molecules, and surfaces that are specific yet strong. Here, we present a novel method to join proteins and dsDNA molecule at their ends, in an efficient, rapid and specific manner, based on the recently developed linkage between the protein StrepTactin (STN) and the peptide StrepTag II (ST). We introduce a two-step approach, in which we first construct a hybrid between DNA and a tandem of two STs peptides (tST). In a second step, this hybrid is linked to polystyrene bead surfaces and Maltose Binding Protein (MBP) using STN. Furthermore, we show the STN-tST linkage is more stable against forces applied by optical tweezers than the commonly used biotin-Streptavidin (STV) linkage. It can be used in conjunction with Neutravidin (NTV)-biotin linkages to form DNA tethers that can sustain applied forces above 65 pN for tens of minutes in a quarter of the cases. The method is general and can be applied to construct other surface-DNA and protein-DNA hybrids. The reversibility, high mechanical stability and specificity provided by this linking procedure make it highly suitable for single molecule mechanical studies, as well as biosensing and lab on chip applications.

| S-EPMC3545873 | biostudies-literature

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

Project description: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.

| S-EPMC4296929 | biostudies-literature

An interpretable deep learning approach for designing nanoporous silicon nitride membranes with tunable mechanical properties.

Project description:The high permeability and strong selectivity of nanoporous silicon nitride (NPN) membranes make them attractive in a broad range of applications. Despite their growing use, the strength of NPN membranes needs to be improved for further extending their biomedical applications. In this work, we implement a deep learning framework to design NPN membranes with improved or prescribed strength values. We examine the predictions of our framework using physics-based simulations. Our results confirm that the proposed framework is not only able to predict the strength of NPN membranes with a wide range of microstructures, but also can design NPN membranes with prescribed or improved strength. Our simulations further demonstrate that the microstructural heterogeneity that our framework suggests for the optimized design, lowers the stress concentration around the pores and leads to the strength improvement of NPN membranes as compared to conventional membranes with homogenous microstructures.

| S-EPMC10221757 | biostudies-literature

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

Transparent polycrystalline cubic silicon nitride.

Project description:Glasses and single crystals have traditionally been used as optical windows. Recently, there has been a high demand for harder and tougher optical windows that are able to endure severe conditions. Transparent polycrystalline ceramics can fulfill this demand because of their superior mechanical properties. It is known that polycrystalline ceramics with a spinel structure in compositions of MgAl2O4 and aluminum oxynitride (γ-AlON) show high optical transparency. Here we report the synthesis of the hardest transparent spinel ceramic, i.e. polycrystalline cubic silicon nitride (c-Si3N4). This material shows an intrinsic optical transparency over a wide range of wavelengths below its band-gap energy (258 nm) and is categorized as one of the third hardest materials next to diamond and cubic boron nitride (cBN). Since the high temperature metastability of c-Si3N4 in air is superior to those of diamond and cBN, the transparent c-Si3N4 ceramic can potentially be used as a window under extremely severe conditions.

| S-EPMC5355983 | biostudies-literature

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

Facile synthesis of silicon nitride nanowires with flexible mechanical properties and with diameters controlled by flow rate.

Project description:Ultralong Si3N4 nanowires (NWs) were successfully synthesized with size controlled in N2 gas by using an efficient method. The diameters of the Si3N4 NWs increased when the flow rate of N2 gas increased, with average diameters of 290 nm from flow rates of 100 ml/min, 343 nm from flow rates of 200 ml/min and 425 nm from flow rates of 400 ml/min. Young's modulus was found to rely strongly on the diameters of the Si3N4 NWs, decreasing from approximately 526.0 GPa to 321.9 GPa; as the diameters increased from 360 nm to 960 nm. These findings provide a promising method for tailoring these mechanical properties of the NWs in a controlled manner over a wide range of Young's modulus values. Vapour-liquid-solid (VLS) mechanisms were used to model the growth of Si3N4 NWs on the inner wall of an alumina crucible and on the surface of the powder mixture. Alumina may be an effective mediator of NW growth that plays an important role in controlling the concentrations of Si-containing reactants to support the growth of NWs on the inner wall of the alumina crucible. This approach offers a valuable means for preparing ultralong Si3N4 NWs doped with Al with unique properties.

| S-EPMC5368666 | biostudies-literature

Quantum limit of quality factor in silicon micro and nano mechanical resonators.

Project description:Micromechanical resonators are promising replacements for quartz crystals for timing and frequency references owing to potential for compactness, integrability with CMOS fabrication processes, low cost, and low power consumption. To be used in high performance reference application, resonators should obtain a high quality factor. The limit of the quality factor achieved by a resonator is set by the material properties, geometry and operating condition. Some recent resonators properly designed for exploiting bulk-acoustic resonance have been demonstrated to operate close to the quantum mechanical limit for the quality factor and frequency product (Q-f). Here, we describe the physics that gives rise to the quantum limit to the Q-f product, explain design strategies for minimizing other dissipation sources, and present new results from several different resonators that approach the limit.

| S-EPMC3832850 | biostudies-other

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