Browse
Submit Data
Databases
API
Help

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular Combing of a Flexible Polymer Chain by Simple Spin-Casting.

ABSTRACT: If polymer chains could be fixed on a substrate as a fully elongated chain, a procedure known as "molecular combing", the chain structure could be analyzed more precisely than has been possible with the characterization techniques available today. Although the molecular combing of a rigid biomolecule, DNA, has been attained for the mapping of genetic information, that of flexible chains has never been achieved as yet. We show here that poly(n-nonyl acrylate) (PNA) can be molecularly combed on mica by a simple spin-casting method, and that the chain lengths were in good agreement with that of the all-trans conformation. One of the key factors for successful molecular combing was found to be the weak adsorption of PNA on mica, indicating that flexible polymers may be molecularly combed by adjusting their affinity to the substrate. The molecular combing of polymer chains may open a new way not only to characterize the chain structures more precisely but also to fabricate new nanomaterials based on polymers.

SUBMITTER: Shimanuki C

PROVIDER: S-EPMC6641330 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Molecular Combing of a Flexible Polymer Chain by Simple Spin-Casting.

Shimanuki Chisato C Matsuta Yuuma Y Fujita Ryo R Kumaki Jiro J

ACS omega 20180410 4

If polymer chains could be fixed on a substrate as a fully elongated chain, a procedure known as "<i>molecular combing</i>", the chain structure could be analyzed more precisely than has been possible with the characterization techniques available today. Although the molecular combing of a rigid biomolecule, DNA, has been attained for the mapping of genetic information, that of flexible chains has never been achieved as yet. We show here that poly(<i>n</i>-nonyl acrylate) (PNA) can be molecularl ...[more]

PMID: 31458636

Similar Datasets

Flexible and active self-powered pressure, shear sensors based on freeze casting ceramic-polymer composites.

Project description:Self-powered flexible electronics are of particular interest and important for next generation electronics due to their light weight, flexible and self-sustainable properties. Many self-powered sensors made from piezoelectric composite materials are either inflexible or possess low piezoelectricity. In this work, we demonstrate self-powered flexible and highly active pressure and shear sensors based on freeze casting ceramic-polymer structures. A lamellar lead zirconate titanate (PZT) structure is initially developed via freeze-casting and the piezoelectric composites are formed by impregnating a polydimethylsiloxane (PDMS) matrix into the aligned pore channels. The structured PZT-PDMS composites exhibited a high effective longitudinal piezoelectric coefficient (d 33*) of 750 pC N-1, which is higher than that of the monolithic ceramic due to the combination of bending and flexural effects. The use of freeze casting enables the manufacture of complex and arbitrary shaped 3D piezoelectric architectures, along with the unique advantages of low-cost and ease of fabrication. A 14 × 14 mm2 PZT-PDMS pressure sensor was able to bend to a small radius of 8 mm and maintain a high d 33. Furthermore, the manufactured self-powered sensors are demonstrated in a range of applications, such as acceleration, strain and touch sensors that use the d 33, d 31 and d 15 coefficients to detect longitudinal, transverse and shear loads. This work expands on the potential applications of freeze casting and provides new opportunities for the manufacture of future electronic sensors.

| S-EPMC6333270 | biostudies-literature

Telomere Length Measurement by Molecular Combing.

Project description:Telomeres are repetitive regions of DNA bound by specialized proteins at the termini of linear chromosomes that prevent the natural chromosome ends from being recognized as DNA double strand breaks. Telomeric DNA is gradually eroded with each round of cell division, resulting in the accumulation of critically short or dysfunctional telomeres that eventually trigger cellular senescence. Consequently, telomere length is indicative of the proliferative capacity of a cell. Multiple methods exist to measure telomere length and telomere content, but a simple and reliable technique to accurately measure individual telomere lengths is currently lacking. We have developed the Telomere length Combing Assay (TCA) to measure telomere length on stretched DNA fibers. We used TCA to measure telomere erosion in primary human fibroblasts, and to detect telomere lengthening in response to activation of telomere maintenance pathways. TCA was also used to accurately measure telomere length in healthy individuals, and to identify critically short telomeres in patients with telomere biology disorders. TCA is performed on isolated DNA, negating the need for cycling cells. TCA is amenable to semi-automated image analysis, and can be fully automated using the Genomic Vision molecular combing platform. This not only precludes sampling bias, but also provides the potential for high-throughput applications and clinical development. TCA is a simple and versatile technique to measure the distribution of individual telomere lengths in a cell population, offering improved accuracy, and more detailed biological insight for telomere length measurement applications.

| S-EPMC7308456 | biostudies-literature

Controlled Deposition of Nanosize and Microsize Particles by Spin-Casting.

Project description:The deposition of nanosize and microsize spherical particles on planar solid substrates by hydrodynamic-evaporative spin-casting is studied. The particles are dispersed in a volatile liquid, which evaporates during the process, and the particles are finally deposited on the substrate. Their coverage, Γ, depends on the processing parameters (concentration by weight, particles size, etc.). The behavior of the particles during the spin-casting process and their final Γ values are investigated. It is found that for up to particle diameters of a few micrometers, particle deposition can be described by a theoretical approach developed for the spin-casting of polymer solutions (Karpitschka, S.; Weber, C. M.; Riegler, H. Chem. Eng. Sci. 2015, 129, 243-248. Danglad-Flores, J.; Eickelmann, S.; Riegler, H. Chem. Eng. Sci. 2018, 179, 257-264). For large particles, this basic theory fails. The causes of this failure are analyzed, and a corrected, more general theoretical approach is presented. It takes into account particle size effects as well as particle sedimentation. In summary, we present new insights into the spin-cast process of particle dispersions, analyze the contributions affecting the final particle coverage, and present a theoretical approach which describes and explains the experimental findings.

| S-EPMC6728089 | biostudies-literature

DNA molecular combing-based replication fork directionality profiling

Project description:The replication strategy of metazoan genomes is still unclear, mainly because definitive maps of replication origins are missing. High-throughput methods are based on population average and thus may exclusively identify efficient initiation sites, whereas ineffective origins go undetected. Single-molecule analyses of specific loci can detect both common and rare initiation events along the targeted regions. However, these usually concentrate on positioning individual events, which only gives an overview of the replication dynamics. Here, we computed the replication fork directionality (RFD) profiles of two large genes in different transcriptional states in chicken DT40 cells, namely untranscribed and transcribed DMD and CCSER1 expressed at WT levels or overexpressed, by aggregating hundreds of oriented replication tracks detected on individual DNA fibres stretched by molecular combing. These profiles reconstituted RFD domains composed of zones of initiation flanking a zone of termination originally observed in mammalian genomes and were highly consistent with independent population-averaging profiles generated by Okazaki fragment sequencing (OK-seq). Importantly, we demonstrate that inefficient origins do not manifest as detectable RFD shifts, explaining why dispersed initiation has remained invisible to population-based assays. Our method can both generate quantitative profiles and identify discrete events, thereby constituting a comprehensive approach to study metazoan genome replication.

2021-03-16 | GSE164252 | GEO

Molecular Recognition-Mediated Transformation of Single-Chain Polymer Nanoparticles into Crosslinked Polymer Films.

Project description:We describe single-chain polymer nanoparticles (SCNPs) possessing intramolecular dynamic covalent crosslinks that can transform into polymer films through a molecular recognition-mediated crosslinking process. The SCNPs utilise molecular recognition with surface-immobilised proteins to concentrate upon a substrate, bringing the SCNPs into close spatial proximity with one another and allowing their dynamic covalent crosslinkers to undergo intra- to interpolymer chain crosslinking leading to the formation of polymeric film. SCNPs must possess both the capacity for specific molecular recognition and a dynamic nature to their intramolecular crosslinkers to form polymer films, and an investigation of the initial phase of film formation indicates it proceeds from features which form upon the surface then grow predominantly in the xy directions. This approach to polymer film formation presents a potential method to "wrap" surfaces displaying molecular recognition motifs-which could potentially include viral, cellular and bacterial surfaces or artificial surfaces displaying multivalent recognition motifs-within a layer of polymer film.

| S-EPMC5656938 | biostudies-literature

Simple and scalable growth of AgCl nanorods by plasma-assisted strain relaxation on flexible polymer substrates.

Project description:Implementing nanostructures on plastic film is indispensable for highly efficient flexible optoelectronic devices. However, due to the thermal and chemical fragility of plastic, nanostructuring approaches are limited to indirect transfer with low throughput. Here, we fabricate single-crystal AgCl nanorods by using a Cl2 plasma on Ag-coated polyimide. Cl radicals react with Ag to form AgCl nanorods. The AgCl is subjected to compressive strain at its interface with the Ag film because of the larger lattice constant of AgCl compared to Ag. To minimize strain energy, the AgCl nanorods grow in the [200] direction. The epitaxial relationship between AgCl (200) and Ag (111) induces a strain, which leads to a strain gradient at the periphery of AgCl nanorods. The gradient causes a strain-induced diffusion of Ag atoms to accelerate the nanorod growth. Nanorods grown for 45?s exhibit superior haze up to 100% and luminance of optical device increased by up to 33%.

| S-EPMC5461508 | biostudies-literature

DNA molecular combing-based replication fork directionality profiling.

Project description:The replication strategy of metazoan genomes is still unclear, mainly because definitive maps of replication origins are missing. High-throughput methods are based on population average and thus may exclusively identify efficient initiation sites, whereas inefficient origins go undetected. Single-molecule analyses of specific loci can detect both common and rare initiation events along the targeted regions. However, these usually concentrate on positioning individual events, which only gives an overview of the replication dynamics. Here, we computed the replication fork directionality (RFD) profiles of two large genes in different transcriptional states in chicken DT40 cells, namely untranscribed and transcribed DMD and CCSER1 expressed at WT levels or overexpressed, by aggregating hundreds of oriented replication tracks detected on individual DNA fibres stretched by molecular combing. These profiles reconstituted RFD domains composed of zones of initiation flanking a zone of termination originally observed in mammalian genomes and were highly consistent with independent population-averaging profiles generated by Okazaki fragment sequencing. Importantly, we demonstrate that inefficient origins do not appear as detectable RFD shifts, explaining why dispersed initiation has remained invisible to population-based assays. Our method can both generate quantitative profiles and identify discrete events, thereby constituting a comprehensive approach to study metazoan genome replication.

| S-EPMC8266662 | biostudies-literature

Surface-Controlled Molecular Self-Alignment in Polymer Actuators for Flexible Microrobot Applications.

Project description:Polymer actuators are important components in lab-on-a-chip and micromechanical systems because of the inherent properties that result from their large and fast mechanical responses induced by molecular-level deformations (e.g., isomerization). They typically exhibit bending movements via asymmetric contraction or expansion with respect to changes in environmental conditions. To enhance the mechanical properties of actuators, a strain gradient should be introduced by regulating the molecular alignment; however, the miniaturization of polymer actuators for microscale systems has raised concerns regarding the complexity of such molecular control. Herein, a novel method for the fabrication of micro-actuators using a simple molecular self-alignment method is presented. Amphiphilic molecules that consist of azobenzene mesogens were located between the hydrophilic and hydrophobic surfaces, which resulted in a splayed alignment. Thereafter, molecular isomerization on the surface induced a large strain gradient and bending movement of the actuator under ultraviolet-light irradiation. Moreover, the microelectromechanical systems allowed for the variation of the actuator size below the micron scale. The mechanical properties of the fabricated actuators such as the bending direction, maximum angle, and response time were evaluated with respect to their thicknesses and lengths. The derivatives of the polymer actuator microstructure may contribute to the development of novel applications in the micro-robotics field.

| S-EPMC6523470 | biostudies-literature

Long Range Polymer Chain Dynamics of Highly Flexible Polysiloxane in Solution Probed by Pyrene Excimer Fluorescence.

Project description:A poly(dimethylsiloxane-co-(3-aminopropyl)methylsiloxane) polymer (PDMS with 20.3 mol % of (3-aminopropyl)methyl siloxane monomer) has been labeled randomly with 1-pyreneacetyl groups to generate a series of polysiloxanes (Py-PDMS) with pyrenyl contents ranging from 0.7 mol % to 5.2 mol % of the total number of structural units. The remainder of the amino groups were acetylated to avoid intra-chain quenching of the excited singlet states of pyrene via exciplex formation with free amino groups while allowing the formation of excimers to proceed. The fluorescence spectra and temporal decays of the Py-PDMS samples were acquired in tetrahydrofuran (THF), N,N-dimethylformamide (DMF), and dioxane. <kMF>blob, the average rate constant for intra-chain pyrene excimer formation, was determined from the analysis of the fluorescence decays. <kMF>blob was found to equal 1.16 (±0.13) × 10⁸, 1.14 (±0.12) × 10⁸, and 0.99 (±0.10) × 10⁸ s-1 in THF, DMF, and dioxane, respectively, at room temperature. They are the largest values found to date for any polymeric backbone in these solvents. The qualitative relationship found here between <kMF>blob and the chemical structures of the polymers indicates that the luminescence characteristics of randomly labeled polymers is a very useful method to probe the long range dynamics of chains of almost any polymer that is amenable to substitution by a lumophore.

| S-EPMC6414900 | biostudies-literature

Quantum spin transistor with a Heisenberg spin chain.

Project description:Spin chains are paradigmatic systems for the studies of quantum phases and phase transitions, and for quantum information applications, including quantum computation and short-distance quantum communication. Here we propose and analyse a scheme for conditional state transfer in a Heisenberg XXZ spin chain which realizes a quantum spin transistor. In our scheme, the absence or presence of a control spin excitation in the central gate part of the spin chain results in either perfect transfer of an arbitrary state of a target spin between the weakly coupled input and output ports, or its complete blockade at the input port. We also discuss a possible proof-of-concept realization of the corresponding spin chain with a one-dimensional ensemble of cold atoms with strong contact interactions. Our scheme is generally applicable to various implementations of tunable spin chains, and it paves the way for the realization of integrated quantum logic elements.

| S-EPMC5062499 | 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