Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Elongated unique DNA strand deposition on microstructured substrate by receding meniscus assembly and capillary force.

ABSTRACT: Ordered deposition of elongated DNA molecules was achieved by the forced dewetting of a DNA solution droplet over a microstructured substrate. This technique allows trapping, uncoiling, and deposition of DNA fragments without the need of a physicochemical anchoring of the molecule and results in the combing of double stranded DNA from the edge of microwells on a polydimethylsiloxane (PDMS) substrate. The technique involves scanning a droplet of DNA solution caught between a movable blade and a PDMS substrate containing an array of microwells. The deposition and elongation appears when the receding meniscus dewets microwells, the latter acting here as a perturbation in the dewetting line forcing the water film to break locally. Thus, DNA molecules can be deposited in an ordered manner and elongated conformation based solely on a physical phenomenon, allowing uncoiled DNA molecules to be observed in all their length. However, the exact mechanism that governs the deposition of DNA strands is not well understood. This paper is an analysis of the physical phenomenon occurring in the deposition process and is based on observations made with the use of high frame/second rate video microscopy.

SUBMITTER: Charlot B

PROVIDER: S-EPMC3977786 | biostudies-other | 2014 Jan

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Bioinspired inner microstructured tube controlled capillary rise.

Project description:Effective, long-range, and self-propelled water elevation and transport are important in industrial, medical, and agricultural applications. Although research has grown rapidly, existing methods for water film elevation are still limited. Scaling up for practical applications in an energy-efficient way remains a challenge. Inspired by the continuous water cross-boundary transport on the peristome surface of Nepenthes alata, here we demonstrate the use of peristome-mimetic structures for controlled water elevation by bending biomimetic plates into tubes. The fabricated structures have unique advantages beyond those of natural pitcher plants: bulk water diode transport behavior is achieved with a high-speed passing state (several centimeters per second on a milliliter scale) and a gating state as a result of the synergistic effect between peristome-mimetic structures and tube curvature without external energy input. Significantly, on further bending the peristome-mimetic tube into a "candy cane"-shaped pipe, a self-siphon with liquid diode behavior is achieved. Such a transport mechanism should inspire the design of next generation water transport devices.

| S-EPMC6600971 | biostudies-literature

The meniscus-guided deposition of semiconducting polymers.

Project description:The electronic devices that play a vital role in our daily life are primarily based on silicon and are thus rigid, opaque, and relatively heavy. However, new electronics relying on polymer semiconductors are opening up new application spaces like stretchable and self-healing sensors and devices, and these can facilitate the integration of such devices into our homes, our clothing, and even our bodies. While there has been tremendous interest in such technologies, the widespread adoption of these organic electronics requires low-cost manufacturing techniques. Fortunately, the realization of organic electronics can take inspiration from a technology developed since the beginning of the Common Era: printing. This review addresses the critical issues and considerations in the printing methods for organic electronics, outlines the fundamental fluid mechanics, polymer physics, and deposition parameters involved in the fabrication process, and provides future research directions for the next generation of printed polymer electronics.

| S-EPMC5803241 | biostudies-literature

Capillary Force Lithography Pattern-Directed Self-Assembly (CFL-PDSA) of Phase-Separating Polymer Blend Thin Films.

Project description:We report capillary force lithography pattern-directed self-assembly (CFL-PDSA), a facile technique for patterning immiscible polymer blend films of polystyrene (PS)/poly(methyl methacrylate) (PMMA), resulting in a highly ordered phase-separated morphology. The pattern replication is achieved by capillary force lithography (CFL), by annealing the film beyond the glass transition temperature of both the constituent polymers, while confining it between a patterned cross-linked poly(dimethyl siloxane) (PDMS) stamp and the silicon substrate. As the pattern replication takes place because of rise of the polymer meniscus along the confining stamp walls, higher affinity of PMMA toward the oxide-coated silicon substrate and of PS toward cross-linked PDMS leads to well-controlled vertically patterned phase separation of the two constituent polymers during thermal annealing. Although a perfect negative replica of the stamp pattern is obtained in all cases, the phase-separated morphology of the films under pattern confinement is strongly influenced by the blend composition and annealing time. The phase-separated domains coarsen with time because of migration of the two components into specific areas, PS into an elevated mesa region and PMMA toward the substrate, because of preferential wetting. We show that a well-controlled, phase-separated morphology is achieved when the blend ratio matches the volume ratio of the elevated region to the base region in the patterned films. The proposed top-down imprint patterning of blends can be easily made roll-to-roll-compatible for industrial adoption.

| S-EPMC6641379 | biostudies-literature

Calcium deposition in osteoarthritic meniscus and meniscal cell culture.

Project description:IntroductionCalcium crystals exist in the knee joint fluid of up to 65% of osteoarthritis (OA) patients and the presence of these calcium crystals correlates with the radiographic evidence of hyaline cartilaginous degeneration. This study sought to examine calcium deposition in OA meniscus and to investigate OA meniscal cell-mediated calcium deposition. The hypothesis was that OA meniscal cells may play a role in pathological meniscal calcification.MethodsStudies were approved by our human subjects Institutional Review Board. Menisci were collected during joint replacement surgeries for OA patients and during limb amputation surgeries for osteosarcoma patients. Calcium deposits in menisci were examined by alizarin red staining. Expression of genes involved in biomineralization in OA meniscal cells was examined by microarray and real-time RT-PCR. Cell-mediated calcium deposition in monolayer culture of meniscal cells was examined using an ATP-induced (45)calcium deposition assay.ResultsCalcium depositions were detected in OA menisci but not in normal menisci. The expression of several genes involved in biomineralization including ENPP1 and ANKH was upregulated in OA meniscal cells. Consistently, ATP-induced calcium deposition in the monolayer culture of OA meniscal cells was much higher than that in the monolayer culture of control meniscal cells.ConclusionsCalcium deposition is common in OA menisci. OA meniscal cells calcify more readily than normal meniscal cells. Pathological meniscal calcification, which may alter the biomechanical properties of the knee meniscus, is potentially an important contributory factor to OA.

| S-EPMC2888206 | biostudies-literature

DNA polymerase ε relies on a unique domain for efficient replisome assembly and strand synthesis.

Project description:DNA polymerase epsilon (Pol ε) is required for genome duplication and tumor suppression. It supports both replisome assembly and leading strand synthesis; however, the underlying mechanisms remain to be elucidated. Here we report that a conserved domain within the Pol ε catalytic core influences both of these replication steps in budding yeast. Modeling cancer-associated mutations in this domain reveals its unexpected effect on incorporating Pol ε into the four-member pre-loading complex during replisome assembly. In addition, genetic and biochemical data suggest that the examined domain supports Pol ε catalytic activity and symmetric movement of replication forks. Contrary to previously characterized Pol ε cancer variants, the examined mutants cause genome hyper-rearrangement rather than hyper-mutation. Our work thus suggests a role of the Pol ε catalytic core in replisome formation, a reliance of Pol ε strand synthesis on a unique domain, and a potential tumor-suppressive effect of Pol ε in curbing genome re-arrangements.

| S-EPMC7228970 | biostudies-literature

Capillary-Force-Assisted Optical Tuning of Coupled Plasmons.

Project description:An ultrathin (few nanometer) polymer spacer layer is softened by local optical heating and restructured by strong capillary forces, which increase the gap between the plasmonic metal components. This results in a continuous blue-shift of the coupled plasmon from near infrared to visible with a tuning range of >150 nm that can be tightly controlled by adjusting either irradiation time or power.

| S-EPMC4768643 | biostudies-literature

Periodically microstructured composite films made by electric- and magnetic-directed colloidal assembly.

Project description:Living organisms often combine soft and hard anisotropic building blocks to fabricate composite materials with complex microstructures and outstanding mechanical properties. An optimum design and assembly of the anisotropic components reinforces the material in specific directions and sites to best accommodate multidirectional external loads. Here, we fabricate composite films with periodic modulation of the soft-hard microstructure by simultaneously using electric and magnetic fields. We exploit forefront directed-assembly approaches to realize highly demanded material microstructural designs and showcase a unique example of how one can bridge colloidal sciences and composite technology to fabricate next-generation advanced structural materials. In the proof-of-concept experiments, electric fields are used to dictate the position of the anisotropic particles through dielectrophoresis, whereas a rotating magnetic field is used to control the orientation of the particles. By using such unprecedented control over the colloidal assembly process, we managed to fabricate ordered composite microstructures with up to 2.3-fold enhancement in wear resistance and unusual site-specific hardness that can be locally modulated by a factor of up to 2.5.

| S-EPMC4855575 | biostudies-literature

Analysis of diverse double-strand break synapsis with Polλ reveals basis for unique substrate specificity in nonhomologous end-joining.

Project description:DNA double-strand breaks (DSBs) threaten genomic stability, since their persistence can lead to loss of critical genetic information, chromosomal translocations or rearrangements, and cell death. DSBs can be repaired through the nonhomologous end-joining pathway (NHEJ), which processes and ligates DNA ends efficiently to prevent or minimize sequence loss. Polymerase λ (Polλ), one of the Family X polymerases, fills sequence gaps of DSB substrates with a strict specificity for a base-paired primer terminus. There is little information regarding Polλ's approach to engaging such substrates. We used in vitro polymerization and cell-based NHEJ assays to explore the contributions of conserved loop regions toward DSB substrate specificity and utilization. In addition, we present multiple crystal structures of Polλ in synapsis with varying biologically relevant DSB end configurations, revealing how key structural features and hydrogen bonding networks work in concert to stabilize these tenuous, potentially cytotoxic DNA lesions during NHEJ.

| S-EPMC9249759 | biostudies-literature

Advances in enzyme substrate analysis with capillary electrophoresis.

Project description:Capillary electrophoresis provides a rapid, cost-effective platform for enzyme and substrate characterization. The high resolution achievable by capillary electrophoresis enables the analysis of substrates and products that are indistinguishable by spectroscopic techniques alone, while the small volume requirement enables analysis of enzymes or substrates in limited supply. Furthermore, the compatibility of capillary electrophoresis with various detectors makes it suitable for KM determinations ranging from nanomolar to millimolar concentrations. Capillary electrophoresis fundamentals are discussed with an emphasis on the separation mechanisms relevant to evaluate sets of substrate and product that are charged, neutral, and even chiral. The basic principles of Michaelis-Menten determinations are reviewed and the process of translating capillary electrophoresis electropherograms into a Michaelis-Menten curve is outlined. The conditions that must be optimized in order to couple off-line and on-line enzyme reactions with capillary electrophoresis separations, such as incubation time, buffer pH and ionic strength, and temperature, are examined to provide insight into how the techniques can be best utilized. The application of capillary electrophoresis to quantify enzyme inhibition, in the form of KI or IC50 is detailed. The concept and implementation of the immobilized enzyme reactor is described as a means to increase enzyme stability and reusability, as well as a powerful tool for screening enzyme substrates and inhibitors. Emerging techniques focused on applying capillary electrophoresis as a rapid assay to obtain structural identification or sequence information about a substrate and in-line digestions of peptides and proteins coupled to mass spectrometry analyses are highlighted.

| S-EPMC6098732 | biostudies-literature

Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein.

Project description:Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed 'clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length.

| S-EPMC4458895 | 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