Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Resistive Pulse Analysis of Microgel Deformation During Nanopore Translocation.

ABSTRACT: Deformation of 570-nm radius poly(N-isopropylacrylamide-co-acrylic acid) microgels passing through individual 375- to 915-nm radius nanopores in glass has been investigated by the resistive-pulse method. Particle translocation through nanopores of dimensions smaller than the microgel yields electrical signatures reflecting the dynamics of microgel deformation. Translocation rates, and event duration and peak shape, are functions of the conductivities of microgel and electrolyte. Our results demonstrate that nanopore resistive-pulse methods provide new fundamental insights into microgel permeation through porous membranes.

SUBMITTER: Holden DA

PROVIDER: S-EPMC4920357 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Resistive Pulse Analysis of Microgel Deformation During Nanopore Translocation.

Holden Deric A DA Hendrickson Grant G Lyon L Andrew LA White Henry S HS

The journal of physical chemistry. C, Nanomaterials and interfaces 20110127 7

Deformation of 570-nm radius poly(N-isopropylacrylamide-co-acrylic acid) microgels passing through individual 375- to 915-nm radius nanopores in glass has been investigated by the resistive-pulse method. Particle translocation through nanopores of dimensions smaller than the microgel yields electrical signatures reflecting the dynamics of microgel deformation. Translocation rates, and event duration and peak shape, are functions of the conductivities of microgel and electrolyte. Our results demo ...[more]

PMID: 27347278

Similar Datasets

Magnetic microbead transport during resistive pulse sensing.

Project description:Tunable resistive pulse sensing (TRPS) experiments have been used to quantitatively study the motion of 1 μm superparamagnetic beads in a variable magnetic field. Closed-form theory has been developed to interpret the experiments, incorporating six particle transport mechanisms which depend on particle position in and near a conical pore. For our experiments, calculations indicate that pressure-driven flow dominates electrophoresis and magnetism by a factor of ∼100 in the narrowest part of the pore, but that magnetic force should dominate further than ∼1 mm from the membrane. As expected, the observed resistive pulse rate falls as the magnet is moved closer to the pore, while the increase in pulse duration suggests that trajectories in the half space adjacent to the pore opening are important. Aggregation was not observed, consistent with the high hydrodynamic shear near the pore constriction and the high magnetization of aggregates. The theoretical approach is also used to calculate the relative importance of transport mechanisms over a range of geometries and experimental conditions extending well beyond our own experiments. TRPS is emerging as a versatile form of resistive pulse sensing, while magnetic beads are widely used in biotechnology and sensing applications.

| S-EPMC3855170 | biostudies-other

Multistep protein unfolding during nanopore translocation.

Project description:Cells are divided into compartments and separated from the environment by lipid bilayer membranes. Essential molecules are transported back and forth across the membranes. We have investigated how folded proteins use narrow transmembrane pores to move between compartments. During this process, the proteins must unfold. To examine co-translocational unfolding of individual molecules, we tagged protein substrates with oligonucleotides to enable potential-driven unidirectional movement through a model protein nanopore, a process that differs fundamentally from extension during force spectroscopy measurements. Our findings support a four-step translocation mechanism for model thioredoxin substrates. First, the DNA tag is captured by the pore. Second, the oligonucleotide is pulled through the pore, causing local unfolding of the C terminus of the thioredoxin adjacent to the pore entrance. Third, the remainder of the protein unfolds spontaneously. Finally, the unfolded polypeptide diffuses through the pore into the recipient compartment. The unfolding pathway elucidated here differs from those revealed by denaturation experiments in solution, for which two-state mechanisms have been proposed.

| S-EPMC4830145 | biostudies-literature

Plastic deformation, wrinkling, and recovery in microgel multilayers.

Project description:Microgel multi-layer films assembled from anionic particles and linear polycation were prepared on elastomeric substrates and their self-healing properties studied. Dried films were imaged in situ during mechanical deformation and were determined to undergo plastic deformation in response to linear strain, leading to film buckling upon strain relaxation. Hydration leads to rapid reorganization of the film building blocks, permitting recovery of the film to the undamaged state. Additionally, films were determined to heal in the presence of high relative humidity environments, suggesting that film swelling and hydration is a major factor in the restoration of film integrity, and that full immersion in solvent is not required for healing. Films prepared from microgels with lower levels of acid content and/or polycation length, factors strongly connected to the charge density and presumably the connectivity of the film, also display self-healing characteristics.

| S-EPMC3891675 | biostudies-literature

Characterization of hepatitis B virus capsids by resistive-pulse sensing.

Project description:We report characterization of hepatitis B virus (HBV) capsids by resistive-pulse sensing through single track-etched conical nanopores formed in poly(ethylene terephthalate) membranes. The pores were ?40 nm in diameter at the tip, and the pore surface was covalently modified with triethylene glycol to reduce surface charge density, minimize adsorption of the virus capsids, and suppress electroosmotic flow in the pore. The HBV capsids were assembled in vitro from Cp149, the assembly domain of HBV capsid protein. Assembled T = 3 (90 Cp149 dimer) and T = 4 (120 dimer) capsids are 31 and 36 nm in diameter, respectively, and were easily discriminated by monitoring the change in current as capsids passed through an electrically biased pore. The ratio of the number of T = 3 to T = 4 capsids transiting a pore did not reflect actual concentrations, but favored transport of smaller T = 3 capsids. These results combined with longer transit times for the T = 4 capsids indicated that the capsids must overcome an entropic barrier to enter a pore.

| S-EPMC3096690 | biostudies-literature

Quantitative analysis of the nanopore translocation dynamics of simple structured polynucleotides.

Project description:Nanopore translocation experiments are increasingly applied to probe the secondary structures of RNA and DNA molecules. Here, we report two vital steps toward establishing nanopore translocation as a tool for the systematic and quantitative analysis of polynucleotide folding: 1), Using ?-hemolysin pores and a diverse set of different DNA hairpins, we demonstrate that backward nanopore force spectroscopy is particularly well suited for quantitative analysis. In contrast to forward translocation from the vestibule side of the pore, backward translocation times do not appear to be significantly affected by pore-DNA interactions. 2), We develop and verify experimentally a versatile mesoscopic theoretical framework for the quantitative analysis of translocation experiments with structured polynucleotides. The underlying model is based on sequence-dependent free energy landscapes constructed using the known thermodynamic parameters for polynucleotide basepairing. This approach limits the adjustable parameters to a small set of sequence-independent parameters. After parameter calibration, the theoretical model predicts the translocation dynamics of new sequences. These predictions can be leveraged to generate a baseline expectation even for more complicated structures where the assumptions underlying the one-dimensional free energy landscape may no longer be satisfied. Taken together, backward translocation through ?-hemolysin pores combined with mesoscopic theoretical modeling is a promising approach for label-free single-molecule analysis of DNA and RNA folding.

| S-EPMC3250678 | biostudies-literature

Finite Element Modelling Simulated Meniscus Translocation and Deformation during Locomotion of the Equine Stifle.

Project description:We developed a finite element model (FEM) of the equine stifle joint to identify pressure peaks and simulate translocation and deformation of the menisci. A series of sectional magnetic resonance images (1.5 T) of the stifle joint of a 23 year old Shetland pony gelding served as basis for image segmentation. Based on the 3D polygon models of femur, tibia, articular cartilages, menisci, collateral ligaments and the meniscotibial ligaments, an FEM model was generated. Tissue material properties were assigned based on data from human (Open knee(s) project) and bovine femoro-tibial joint available in the literature. The FEM model was tested across a range of motion of approximately 30°. Pressure load was overall higher in the lateral meniscus than in the medial. Accordingly, the simulation showed higher translocation and deformation in the lateral compared to the medial meniscus. The results encourage further refinement of this model for studying loading patterns on menisci and articular cartilages as well as the resulting mechanical stress in the subchondral bone (femur and tibia). A functional FEM model can not only help identify segments in the stifle which are predisposed to injury, but also to better understand the progression of certain stifle disorders, simulate treatment/surgery effects and to optimize implant/transplant properties.

| S-EPMC6720206 | biostudies-literature

DNAzyme Sensor for the Detection of Ca2+ Using Resistive Pulse Sensing.

Project description:DNAzymes are DNA oligonucleotides that can undergo a specific chemical reaction in the presence of a cofactor. Ribonucleases are a specific form of DNAzymes where a tertiary structure undergoes cleavage at a single ribonuclease site. The cleavage is highly specificity to co-factors, which makes them excellent sensor recognition elements. Monitoring the change in structure upon cleavage has given rise to many sensing strategies; here we present a simple and rapid method of following the reaction using resistive pulse sensors, RPS. To demonstrate this methodology, we present a sensor for Ca2+ ions in solution. A nanoparticle was functionalised with a Ca2+ DNAzyme, and it was possible to follow the cleavage and rearrangement of the DNA as the particles translocate the RPS. The binding of Ca2+ caused a conformation change in the DNAzyme, which was monitored as a change in translocation speed. A 30 min assay produced a linear response for Ca2+ between 1-9 μm, and extending the incubation time to 60 min allowed for a concentration as low as 0.3 μm. We demonstrate that the signal is specific to Ca2+ in the presence of other metal ions, and we can quantify Ca2+ in tap and pond water samples.

| S-EPMC7589696 | biostudies-literature

Enzyme-modulated DNA translocation through a nanopore.

Project description:We present a Langevin dynamics simulation study of enzyme-modulated translocation of a single-stranded DNA molecule through a cylindrical nanopore. The toroidal-shaped enzyme placed along the axis of the pore, threads a DNA molecule at a constant rate. As a result of this controlled release process, the length of DNA available for translocation varies with time. We examine the effect of time-dependent conformational entropy of the DNA on the translocation process. In addition, we also examine the effects of both the separation between the exonuclease and the pore, and the rate at which DNA is released by the enzyme. Our results indicate that the separation distance primarily influences the entry of the DNA into the pore. The length of the DNA released by the exonuclease that is most likely to enter the pore is nearly equal to separation distance between the pore and the exonuclease despite the flexibility of the polymer. However, the speed at which the DNA translocates through the nanopore is solely determined by the rate at which the exonuclease releases the DNA. We find that the translocation velocity is directly proportional to the rate of release.

| S-EPMC2797554 | biostudies-literature

Analysis of exosome purification methods using a model liposome system and tunable-resistive pulse sensing.

Project description:Exosomes are vesicles which have garnered interest due to their diagnostic and therapeutic potential. Isolation of pure yields of exosomes from complex biological fluids whilst preserving their physical characteristics is critical for downstream applications. In this study, we use 100 nm-liposomes from 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and cholesterol as a model system as a model system to assess the effect of exosome isolation protocols on vesicle recovery and size distribution using a single-particle analysis method. We demonstrate that liposome size distribution and ζ-potential are comparable to extracted exosomes, making them an ideal model for comparison studies. Four different purification protocols were evaluated, with liposomes robustly isolated by three of them. Recovered yields varied and liposome size distribution was unaltered during processing, suggesting that these protocols do not induce particle aggregation. This leads us to conclude that the size distribution profile and characteristics of vesicles are stably maintained during processing and purification, suggesting that reports detailing how exosomes derived from tumour cells differ in size to those from normal cells are reporting a real phenomenon. However, we hypothesize that larger particles present in most purified exosome samples represent co-purified contaminating non-exosome debris. These isolation techniques are therefore likely nonspecific and may co-isolate non-exosome material of similar physical properties.

| S-EPMC4648344 | biostudies-other

Pulse-modulated multilevel data storage in an organic ferroelectric resistive memory diode.

Project description:We demonstrate multilevel data storage in organic ferroelectric resistive memory diodes consisting of a phase-separated blend of P(VDF-TrFE) and a semiconducting polymer. The dynamic behaviour of the organic ferroelectric memory diode can be described in terms of the inhomogeneous field mechanism (IFM) model where the ferroelectric components are regarded as an assembly of randomly distributed regions with independent polarisation kinetics governed by a time-dependent local field. This allows us to write and non-destructively read stable multilevel polarisation states in the organic memory diode using controlled programming pulses. The resulting 2-bit data storage per memory element doubles the storage density of the organic ferroelectric resistive memory diode without increasing its technological complexity, thus reducing the cost per bit.

| S-EPMC4832143 | 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