Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribosome Fingerprinting with a Solid-State Nanopore.

ABSTRACT: Nanopores hold great potential for the analysis of complex biological molecules at the single-entity level. One particularly interesting macromolecular machine is the ribosome, responsible for translating mRNAs into proteins. In this study, we use a solid-state nanopore to fingerprint 80S ribosomes and polysomes from a human neuronal cell line andDrosophila melanogaster cultured cells and ovaries. Specifically, we show that the peak amplitude and dwell time characteristics of 80S ribosomes are distinct from polysomes and can be used to discriminate ribosomes from polysomes in mixed samples. Moreover, we are able to distinguish large polysomes, containing more than seven ribosomes, from those containing two to three ribosomes, and demonstrate a correlation between polysome size and peak amplitude. This study highlights the application of solid-state nanopores as a rapid analytical tool for the detection and characterization of ribosomal complexes.

SUBMITTER: Raveendran M

PROVIDER: S-EPMC7706116 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Ribosome Fingerprinting with a Solid-State Nanopore.

Raveendran Mukhil M Leach Anna Rose AR Hopes Tayah T Aspden Julie L JL Actis Paolo P

ACS sensors 20201028 11

Nanopores hold great potential for the analysis of complex biological molecules at the single-entity level. One particularly interesting macromolecular machine is the ribosome, responsible for translating mRNAs into proteins. In this study, we use a solid-state nanopore to fingerprint 80S ribosomes and polysomes from a human neuronal cell line and<i>Drosophila melanogaster</i> cultured cells and ovaries. Specifically, we show that the peak amplitude and dwell time characteristics of 80S ribosome ...[more]

PMID: 33111519

Similar Datasets

Monitoring tetracycline through a solid-state nanopore sensor.

Project description:Antibiotics as emerging environmental contaminants, are widely used in both human and veterinary medicines. A solid-state nanopore sensing method is reported in this article to detect Tetracycline, which is based on Tet-off and Tet-on systems. rtTA (reverse tetracycline-controlled trans-activator) and TRE (Tetracycline Responsive Element) could bind each other under the action of Tetracycline to form one complex. When the complex passes through nanopores with 8 ~ 9 nanometers in diameter, we could detect the concentrations of Tet from 2 ng/mL to 2000 ng/mL. According to the Logistic model, we could define three growth zones of Tetracycline for rtTA and TRE. The slow growth zone is 0-39.5 ng/mL. The rapid growth zone is 39.5-529.7 ng/mL. The saturated zone is > 529.7 ng/mL. Compared to the previous methods, the nanopore sensor could detect and quantify these different kinds of molecule at the single-molecule level.

| S-EPMC4910080 | biostudies-literature

Back-Side Polymer-Coated Solid-State Nanopore Sensors.

Project description:We systematically investigated the influence of polymer coating on temporal resolution of solid-state nanopores. We fabricated a Si3N4 nanopore integrated with a polyimide sheet partially covering the substrate surface. Upon detecting the nanoparticles dispersed in an electrolyte buffer by ionic current measurements, we observed a larger resistive pulse height along with a faster current decay at the tails under larger coverage of the polymeric layer, thereby suggesting a prominent role of the water-touching Si3N4 thin film as a significant capacitor serving to retard the ionic current response to the ion blockade by fast translocation of particles through the nanopores. From this, we came up with back-side polymer-coated chip designs and demonstrated improved pore sensor temporal resolution by developing a nanopore with a thick polymethyl-methacrylate layer laminated on the bottom surface. The present findings may be useful in developing integrated solid-state nanopore sensors with embedded nanochannels and nanoelectrodes.

| S-EPMC6682124 | biostudies-literature

Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores.

Project description:Nucleic acid nanoparticles (NANPs) are an emerging class of programmable structures with tunable shape and function. Their promise as tools for fundamental biophysics studies, molecular sensing, and therapeutic applications necessitates methods for their detection and characterization at the single-particle level. In this work, we study electrophoretic transport of individual ring-shaped and cube-shaped NANPs through solid-state nanopores. In the optimal nanopore size range, the particles must deform to pass through, which considerably increases their residence time within the pore. Such anomalously long residence times permit detection of picomolar amounts of NANPs when nanopore measurements are carried out at a high transmembrane bias. In the case of a NANP mixture, the type of individual particle passing through nanopores can be efficiently determined from analysis of a single electrical pulse. Molecular dynamics simulations provide insight into the mechanical barrier to transport of the NANPs and corroborate the difference in the signal amplitudes observed for the two types of particles. Our study serves as a basis for label-free analysis of soft programmable-shape nanoparticles.

| S-EPMC5959297 | biostudies-literature

Effect of charge patterns along a solid-state nanopore on polyelectrolyte translocation.

Project description:We investigate the effectiveness of charge patterns along a nanopore on translocation dynamics of a flexible polyelectrolyte. We perform a three dimensional Langevin dynamics simulation of a uniformly charged flexible polyelectrolyte translocating under uniform external electric field through a solid-state nanopore. We maintain the total charge along the pore to be constant, while varying its distribution by placing alternate charged and uncharged sections of different lengths along the pore length. Longest average translocation time is observed for a pattern corresponding to an optimum section length, with a major delay in the translocation time during the pore ejection stage. This optimum section length is independent of lengths of polyelectrolyte and pore within the range studied. A theory based on the Fokker-Planck formalism is found to successfully describe the observed trends with reasonable quantitative agreement.

| S-EPMC3976468 | biostudies-other

Recapturing and trapping single molecules with a solid-state nanopore.

Project description:The development of solid-state nanopores, inspired by their biological counterparts, shows great potential for the study of single macromolecules. Applications such as DNA sequencing and the exploration of protein folding require control of the dynamics of the molecule's interaction with the pore, but DNA capture by a solid-state nanopore is not well understood. By recapturing individual molecules soon after they pass through a nanopore, we reveal the mechanism by which double-stranded DNA enters the pore. The observed recapture rates and times agree with solutions of a drift-diffusion model. Electric forces draw DNA to the pore over micrometer-scale distances, and upon arrival at the pore, molecules begin translocation almost immediately. Repeated translocation of the same molecule improves measurement accuracy, offers a way to probe the chemical transformations and internal dynamics of macromolecules on sub-millisecond time and sub-micrometre length scales, and demonstrates the ability to trap, study and manipulate individual macromolecules in solution.

| S-EPMC3174059 | biostudies-literature

Electrical characterization of protein molecules by a solid-state nanopore.

Project description:The authors measured ionic current blockages caused by protein translocation through voltage-biased silicon nitride nanopores in ionic solution. By calculating the mean amplitude, time duration, and the integral of current blockages, they estimated the relative charge and size of protein molecules at a single molecule level. The authors measured the change in protein charge of bovine serum albumin (BSA) protein induced by pH variation. They also confirmed that BSA molecules indeed traverse nanopores using an improved chemiluminescent analysis. They demonstrated that a larger protein fibrinogen could be distinguished from BSA by a solid-state nanopore measurement.

| S-EPMC2288568 | biostudies-literature

Single-molecule bonds characterized by solid-state nanopore force spectroscopy.

Project description:Weak molecular interactions drive processes at the core of living systems, such as enzyme-substrate interactions, receptor-ligand binding, and nucleic acid replication. Single-molecule force spectroscopy is a remarkable tool for revealing molecular scale energy landscapes of noncovalent bonds, by exerting a mechanical force directly on an individual molecular complex and tracking its survival as a function of time and applied force. In principle, force spectroscopy methods can also be used for highly specific molecular recognition assays, by directly characterizing the strength of bonds between probe and target molecules. However, complexity and low throughput of conventional force spectroscopy techniques render such biosensing applications impractical. Here we demonstrate a straightforward single-molecule approach, suitable for both biophysical studies and molecular recognition assays, in which a approximately 3 nm silicon nitride nanopore is used to determine the bond lifetime spectrum of the biotin-neutravidin complex. Thousands of individual molecular complexes are captured and dissociated in the solid-state nanopore under constant applied forces, ranging from 400 to 900 mV, allowing us to extract the location of the energy barrier that governs the interaction, mapped at Deltax approximately 0.5 nm. These results highlight the capacity of a solid-state nanopore to detect and characterize intermolecular interactions and demonstrate how this could be applied to rapid, highly specific molecular detection assays.

| S-EPMC2800075 | biostudies-literature

Probing RNA Conformations Using a Polymer-Electrolyte Solid-State Nanopore.

Project description:Nanopore systems have emerged as a leading platform for the analysis of biomolecular complexes with single-molecule resolution. The conformation of biomolecules, such as RNA, is highly dependent on the electrolyte composition, but solid-state nanopore systems often require high salt concentration to operate, precluding analysis of macromolecular conformations under physiologically relevant conditions. Here, we report the implementation of a polymer-electrolyte solid-state nanopore system based on alkali metal halide salts dissolved in 50% w/v poly(ethylene) glycol (PEG) to augment the performance of our system. We show that polymer-electrolyte bath governs the translocation dynamics of the analyte which correlates with the physical properties of the salt used in the bath. This allowed us to identify CsBr as the optimal salt to complement PEG to generate the largest signal enhancement. Harnessing the effects of the polymer-electrolyte, we probed the conformations of the Chikungunya virus (CHIKV) RNA genome fragments under physiologically relevant conditions. Our system was able to fingerprint CHIKV RNA fragments ranging from ∼300 to ∼2000 nt length and subsequently distinguish conformations between the co-transcriptionally folded and the natively refolded ∼2000 nt CHIKV RNA. We envision that the polymer-electrolyte solid-state nanopore system will further enable structural and conformational analyses of individual biomolecules under physiologically relevant conditions.

| S-EPMC9798860 | biostudies-literature

Structure-flexible DNA origami translocation through a solid-state nanopore.

Project description:Nanopore detection is a label-free detection method designed to analyze single molecules by comparing specific translocation events with high signal-to-noise ratios. However, it is still challenging to understand the influences of structural flexibility of 100 nm DNA origami on nanopore translocations. Here, we used solid-state nanopores to characterize the translocation of "nunchaku" origami structures, the flexibility of which can be regulated by introducing specific DNA strands and streptavidin protein. The structural changes can result in significant variations in the translocation signals and distributions. It is anticipated that such a method of the flexible DNA origami translocation through a solid-state nanopore will find further applications in molecular detection as well as biosensing.

| S-EPMC9036576 | biostudies-literature

Pressure-voltage trap for DNA near a solid-state nanopore.

Project description:We report the formation of a tunable single DNA molecule trap near a solid-state nanopore in an electrolyte solution under conditions where an electric force and a pressure-induced viscous flow force on the molecule are nearly balanced. Trapped molecules can enter the pore multiple times before escaping the trap by passing through the pore or by diffusing away. Statistical analysis of many individually trapped molecules yields a detailed picture of the fluctuation phenomena involved, which are successfully modeled by a one-dimensional first passage approach.

| S-EPMC4131299 | 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