Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

MoS₂ nanopore identifies single amino acids with sub-1 Dalton resolution.

ABSTRACT: The sequencing of single protein molecules using nanopores is faced with a huge challenge due to the lack of resolution needed to resolve single amino acids. Here we report the direct experimental identification of single amino acids in nanopores. With atomically engineered regions of sensitivity comparable to the size of single amino acids, MoS₂ nanopores provide a sub-1 Dalton resolution for discriminating the chemical group difference of single amino acids, including recognizing the amino acid isomers. This ultra-confined nanopore system is further used to detect the phosphorylation of individual amino acids, demonstrating its capability for reading post-translational modifications. Our study suggests that a sub-nanometer engineered pore has the potential to be applied in future chemical recognition and de novo protein sequencing at the single-molecule level.

SUBMITTER: Wang F

PROVIDER: S-EPMC10199900 | biostudies-literature | 2023 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

MoS2 nanopore identifies single amino acids with sub-1 Dalton resolution.

Wang Fushi F Zhao Chunxiao C Zhao Pinlong P Chen Fanfan F Qiao Dan D Feng Jiandong J

Nature communications 20230520 1

The sequencing of single protein molecules using nanopores is faced with a huge challenge due to the lack of resolution needed to resolve single amino acids. Here we report the direct experimental identification of single amino acids in nanopores. With atomically engineered regions of sensitivity comparable to the size of single amino acids, MoS2 nanopores provide a sub-1 Dalton resolution for discriminating the chemical group difference of single amino acids, including recognizing th ...[more]

PMID: 37210427

Similar Datasets

High-resolution discrimination of homologous and isomeric proteinogenic amino acids in nanopore sensors with ultrashort single-walled carbon nanotubes.

Project description:The hollow and tubular structure of single-walled carbon nanotubes (SWCNTs) makes them ideal candidates for making nanopores. However, the heterogeneity of SWCNTs hinders the fabrication of robust and reproducible carbon-based nanopore sensors. Here we develop a modified density gradient ultracentrifugation approach to separate ultrashort (≈5-10 nm) SWCNTs with a narrow conductance range and construct high-resolution nanopore sensors with those tubes inserted in lipid bilayers. By conducting ionic current recordings and fluorescent imaging of Ca2+ flux through different nanopores, we prove that the ion mobilities in SWCNT nanopores are 3-5 times higher than the bulk mobility. Furthermore, we employ SWCNT nanopores to discriminate homologue or isomeric proteinogenic amino acids, which are challenging tasks for other nanopore sensors. These successes, coupled with the building of SWCNT nanopore arrays, may constitute a crucial part of the recently burgeoning protein sequencing technologies.

| S-EPMC10169846 | biostudies-literature

Molecular Transport across the Ionic Liquid-Aqueous Electrolyte Interface in a MoS2 Nanopore.

Project description:Nanopore sequencing of DNA has been enabled by the use of a biological enzyme to thread DNA through an engineered biological nanopore while recording the ionic current flowing through the nanopore. Efforts to realize a similar concept using a solid-state nanopore have been met with several technical challenges, one of which is the high speed of DNA translocation and the other the low ionic current contrast among individual nucleotides. A promising avenue to addressing both problems is using an ionic liquid to slow DNA translocation and a tiny nanopore in the MoS2 membrane to distinguish individual nucleotides. The physical mechanisms enabling these technical advances have remained elusive. Here, we characterize the ion and DNA transport through the ionic liquid/aqueous electrolyte interface, with and without a MoS2 nanopore, using the all-atom molecular dynamics method. We find that the partial miscibility of the ionic liquid and the aqueous electrolyte considerably alters the physics of the nanopore translocation process. Thus, the interface of the two phases generates a contact potential of 600 mV, the ionic current is dominated by the motion of ionic liquid molecules through the aqueous solution phase, and the DNA nucleotides exhibit preferential partitioning into the aqueous electrolyte, which leads to spontaneous transport of DNA polymers from the ionic liquid to the aqueous solution compartment in the absence of external voltage bias. The complex physics of the two-phase nanopore system offers a multitude of opportunities for extending the functionality of nanopore-sensing platforms.

| S-EPMC7292782 | biostudies-literature

Integrated nanopore sensing platform with sub-microsecond temporal resolution.

Project description:Nanopore sensors have attracted considerable interest for high-throughput sensing of individual nucleic acids and proteins without the need for chemical labels or complex optics. A prevailing problem in nanopore applications is that the transport kinetics of single biomolecules are often faster than the measurement time resolution. Methods to slow down biomolecular transport can be troublesome and are at odds with the natural goal of high-throughput sensing. Here we introduce a low-noise measurement platform that integrates a complementary metal-oxide semiconductor (CMOS) preamplifier with solid-state nanopores in thin silicon nitride membranes. With this platform we achieved a signal-to-noise ratio exceeding five at a bandwidth of 1 MHz, which to our knowledge is the highest bandwidth nanopore recording to date. We demonstrate transient signals as brief as 1 ?s from short DNA molecules as well as current signatures during molecular passage events that shed light on submolecular DNA configurations in small nanopores.

| S-EPMC3648419 | biostudies-literature

Enabling nanopore technology for sensing individual amino acids by a derivatization strategy.

Project description:Nanopore technology holds remarkable promise for sequencing proteins and peptides. To achieve this, it is necessary to establish a characteristic profile for each individual amino acid through the statistical description of its translocation process. However, the subtle molecular differences among all twenty amino acids along with their unpredictable conformational changes at the nanopore sensing region result in very low distinguishability. Here we report the electrical sensing of individual amino acids using an α-hemolysin nanopore based on a derivatization strategy. Using derivatized amino acids as detection surrogates not only prolongs their interactions with the sensing region, but also improves their conformational variation. Furthermore, we show that distinct characteristics including current blockades and dwell times can be observed among all three classes of amino acids after 2,3-naphthalenedicarboxaldehyde (NDA)- and 2-naphthylisothiocyanate (NITC)-derivatization, respectively. These observable characteristics were applied towards the identification and differentiation of 9 of the 20 natural amino acids using their NITC derivatives. The method demonstrated herein will pave the way for the identification of all amino acids and further protein and peptide sequencing.

| S-EPMC7429270 | biostudies-literature

Electrical recognition of the twenty proteinogenic amino acids using an aerolysin nanopore.

Project description:Efforts to sequence single protein molecules in nanopores1-5 have been hampered by the lack of techniques with sufficient sensitivity to discern the subtle molecular differences among all twenty amino acids. Here we report ionic current detection of all twenty proteinogenic amino acids in an aerolysin nanopore with the help of a short polycationic carrier. Application of molecular dynamics simulations revealed that the aerolysin nanopore has a built-in single-molecule trap that fully confines a polycationic carrier-bound amino acid inside the sensing region of the aerolysin. This structural feature means that each amino acid spends sufficient time in the pore for sensitive measurement of the excluded volume of the amino acid. We show that distinct current blockades in wild-type aerolysin can be used to identify 13 of the 20 natural amino acids. Furthermore, we show that chemical modifications, instrumentation advances and nanopore engineering offer a route toward identification of the remaining seven amino acids. These findings may pave the way to nanopore protein sequencing.

| S-EPMC7008938 | biostudies-literature

Aerolysin nanopore-based identification of proteinogenic amino acids using a bipolar peptide probe.

Project description:Nanopore technology has attracted extensive attention due to its rapid, highly sensitive, and label-free performance. In this study, we aimed to identify proteinogenic amino acids using a wild-type aerolysin nanopore. Specifically, bipolar peptide probes were synthesised by linking four aspartic acid residues to the N-terminal and five arginine residues to the C-terminal of individual amino acids. With the help of the bipolar peptide carrier, 9 proteinogenic amino acids were reliably recognised based on current blockade and dwell time using an aerolysin nanopore. Furthermore, by changing the charge of the peptide probe, two of the five unrecognized amino acids above mentioned were identified. These findings promoted the application of aerolysin nanopores in proteinogenic amino acid recognition.

| S-EPMC9470019 | biostudies-literature

A single-molecule nanopore device detects DNA polymerase activity with single-nucleotide resolution.

Project description:The ability to monitor DNA polymerase activity with single-nucleotide resolution has been the cornerstone of a number of advanced single-molecule DNA sequencing concepts. Toward this goal, we report the first observation of the base-by-base DNA polymerase activity with single-base resolution at the single-molecule level. We describe the design and characterization of a supramolecular nanopore device capable of detecting up to nine consecutive DNA polymerase-catalyzed single-nucleotide primer extensions with high sensitivity and spatial resolution (<or=2.4 A). The device is assembled in a suspended lipid membrane by threading and mechanically capturing a single strand of DNA-PEG copolymer inside an alpha-hemolysin protein pore. Single-nucleotide primer extensions result in successive displacements of the template DNA strand within the protein pore, which can be monitored by the corresponding stepped changes in the ion current flowing through the pore under an applied transmembrane potential. The system described thus represents a promising advance toward nanopore-mediated single-molecule DNA sequencing concept and, in addition, might be applicable to studying a number of other biopolymer-protein interactions and dynamics.

| S-EPMC2453067 | biostudies-literature

A Single-Step Route to Single-Crystal Molybdenum Disulphide (MoS2) Monolayer domains.

Project description:We report a simple, single-cycle synthetic method for forming highly-crystalline, micron-sized monolayer domains of phase-pure MoS2. This method combines liquid chemistry with discrete, layer-by-layer deposition from a novel Mo precursor. Single-crystalline MoS2 with domain sizes up to 100 μm have been obtained and characterised by optical and electron microscopy as well as Raman and photoluminescence spectroscopy.

| S-EPMC6411997 | biostudies-literature

A Biaxial Strain Sensor Using a Single MoS2 Grating.

Project description:In this paper, we report a new type of MoS2-based grating sensor for in-plane biaxial strain gauges with a precision limit of ~ 1‰. The MoS2 grating is numerically simulated with different biaxial strains up to 5%. Our first-principles calculations reveal that the strain sensitivity of the MoS2 reflectance spectrum can be considered an additional strain sensor integrated with the grating structure, enabling the mapping of in-plane biaxial strains. Our experimental studies on a prototype MoS2-grating sensor further confirm that a strain component perpendicular to the grating period can cause intensity peak shifts in the grating's first-order diffraction patterns. This work opens a new path towards the sensing of in-plane biaxial strain within a single-grating device. Our new approach is applicable for other materials that have predictable reflectance response under biaxial strains and the capacity to form a two-dimensional single-crystal layer.

| S-EPMC7876191 | biostudies-literature

N-Terminal Derivatization-Assisted Identification of Individual Amino Acids Using a Biological Nanopore Sensor.

Project description:Nanopore technology has been employed as a powerful tool for DNA sequencing and analysis. To extend this method to peptide sequencing, a necessary step is to profile individual amino acids (AAs) through their nanopore stochastic signals, which remains a great challenge because of the low signal-to-noise ratio and unpredictable conformational changes of AAs during their translocation through nanopores. We showed that the combination of an N-terminal derivatization strategy of AAs with nanopore technology could lead to effective in situ differentiation of AAs. Four different derivatization reactions have been tested with five selected AAs: Ala, Phe, Tyr, His, and Asp. Using an α-hemolysin nanopore, we demonstrated the feasibility of derivatization-assisted identification of AAs regardless of their charge composition and polarity. The method was further applied to discriminate each individual AA in testing data sets using their established nanopore profiles from training data sets. We envision that this proof-of-concept study will not only pave a way for identification of individual AAs but also lead to future applications in protein/peptide sequencing using the nanopore technology.

| S-EPMC7978492 | biostudies-literature