Browse
Submit Data
Databases
API
Help

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Convex lens-induced nanoscale templating.

ABSTRACT: We demonstrate a new platform, convex lens-induced nanoscale templating (CLINT), for dynamic manipulation and trapping of single DNA molecules. In the CLINT technique, the curved surface of a convex lens is used to deform a flexible coverslip above a substrate containing embedded nanotopography, creating a nanoscale gap that can be adjusted during an experiment to confine molecules within the embedded nanostructures. Critically, CLINT has the capability of transforming a macroscale flow cell into a nanofluidic device without the need for permanent direct bonding, thus simplifying sample loading, providing greater accessibility of the surface for functionalization, and enabling dynamic manipulation of confinement during device operation. Moreover, as DNA molecules present in the gap are driven into the embedded topography from above, CLINT eliminates the need for the high pressures or electric fields required to load DNA into direct-bonded nanofluidic devices. To demonstrate the versatility of CLINT, we confine DNA to nanogroove and nanopit structures, demonstrating DNA nanochannel-based stretching, denaturation mapping, and partitioning/trapping of single molecules in multiple embedded cavities. In particular, using ionic strengths that are in line with typical biological buffers, we have successfully extended DNA in sub-30-nm nanochannels, achieving high stretching (90%) that is in good agreement with Odijk deflection theory, and we have mapped genomic features using denaturation analysis.

SUBMITTER: Berard DJ

PROVIDER: S-EPMC4169971 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Standalone interferometry-based calibration of convex lens-induced confinement microscopy with nanoscale accuracy.

Project description:Strongly confined environments (confined dimensions between 1-100 nm) represent unique challenges and opportunities for understanding and manipulating molecular behavior due to the significant effects of electric double layers, high surface-area to volume ratios, and other phenomena at the nanoscale. Convex Lens-induced Confinement (CLiC) can be used to analyze the dynamics of individual molecules or particles confined in a planar slit geometry with continuously varying gap thickness. We describe an interferometry-based method for precise measurement of the slit pore geometry. Specifically, this approach permitted accurate characterization of separation distances as small as 5 nm, with 1 nm precision, without a priori knowledge or assumptions about the contact geometry, as well as a greatly simplified experimental setup that required only a lens, coverslip, and inverted microscope. The interferometry-based measurement of gap height offered a distinct advantage over conventional fluorescent dye-based methods; e.g., accurate interferometric height measurements were made at low gap heights regardless of solution conditions, while the concentration of fluorescent dye was significantly impacted by solution conditions such as ionic strength or pH. The accuracy of the interferometric measurements was demonstrated by comparing the experimentally measured concentration of a charged fluorescent dye as a function of gap thickness with dye concentration profiles calculated using Debye-Hückel theory. Accurate characterization of nanoscale gap thickness will enable researchers to study a variety of practical and biologically relevant systems within the CLiC geometry.

| S-EPMC6779313 | biostudies-literature

Convex lens-induced confinement for imaging single molecules.

Project description:Fluorescence imaging is used to study the dynamics of a wide variety of single molecules in solution or attached to a surface. Two key challenges in this pursuit are (1) to image immobilized single molecules in the presence of a high level of fluorescent background and (2) to image freely diffusing single molecules for long times. Strategies that perform well by one measure often perform poorly by the other. Here, we present a simple modification to a wide-field fluorescence microscope that addresses both challenges and dramatically improves single-molecule imaging. The technique of convex lens-induced confinement (CLIC) restricts molecules to a wedge-shaped gap of nanoscale depth, formed between a plano-convex lens and a planar coverslip. The shallow depth of the imaging volume leads to 20-fold greater rejection of background fluorescence than is achieved with total internal reflection fluorescence (TIRF) imaging. Elimination of out-of-plane diffusion leads to an approximately 10,000-fold longer diffusion-limited observation time per molecule than is achieved with confocal fluorescence correlation spectroscopy. The CLIC system also provides a new means to determine molecular size. The CLIC system does not require any nanofabrication, nor any custom optics, electronics, or computer control.

| S-EPMC3172322 | biostudies-literature

Nanoscale Magnetic Arrays through Block Copolymer Templating of Polyoxometalates.

Project description:Magnetic nanoarrays promise to enable new energy-efficient computations based on spintronics or magnonics. In this work, we present a block copolymer-assisted strategy for fabricating ordered magnetic nanostructures on silicon and permalloy substrates. Block copolymer micelle-like structures were used as a template in which polyoxometalate (POM) clusters could assemble in an opal-like structure. A combination of microscopy and scattering techniques was used to confirm the structural and organizational features of the fabricated materials. The magnetic properties of these materials were investigated by polarized neutron reflectometry, nuclear magnetic resonance, and magnetometry measurements. The data show that a magnetic structural design was achieved and that a thin layer of patterned POMs strongly influenced an underlying permalloy layer. This work demonstrates that the bottom-up pathway is a potentially viable method for patterning magnetic substrates on a sub-100 nm scale, toward the magnetic nanostructures needed for spintronic or magnonic crystal devices.

| S-EPMC10885194 | biostudies-literature

Nanoscale self-templating for oxide epitaxy with large symmetry mismatch.

Project description:Direct observations using scanning transmission electron microscopy unveil an intriguing interfacial bi-layer that enables epitaxial growth of a strain-free, monoclinic, bronze-phase VO2(B) thin film on a perovskite SrTiO3 (STO) substrate. We observe an ultrathin (2-3 unit cells) interlayer best described as highly strained VO2(B) nanodomains combined with an extra (Ti,V)O2 layer on the TiO2 terminated STO (001) surface. By forming a fully coherent interface with the STO substrate and a semi-coherent interface with the strain-free epitaxial VO2(B) film above, the interfacial bi-layer enables the epitaxial connection of the two materials despite their large symmetry and lattice mismatch.

| S-EPMC5133589 | biostudies-literature

The role of nanoscale architecture in supramolecular templating of biomimetic hydroxyapatite mineralization.

Project description:Understanding and mimicking the hierarchical structure of mineralized tissue is a challenge in the field of biomineralization and is important for the development of scaffolds to guide bone regeneration. Bone is a remarkable tissue with an organic matrix comprised of aligned collagen bundles embedded with nanometer-sized inorganic hydroxyapatite (HAP) crystals that exhibit orientation on the macroscale. Hybrid organic-inorganic structures mimic the composition of mineralized tissue for functional bone scaffolds, but the relationship between morphology of the organic matrix and orientation of mineral is poorly understood. Herein the mineralization of supramolecular peptide amphiphile templates, that are designed to vary in nanoscale morphology by altering the amino acid sequence, is reported. It is found that 1D cylindrical nanostructures direct the growth of oriented HAP crystals, while flatter nanostructures fail to guide the orientation found in biological systems. The geometric constraints associated with the morphology of the nanostructures may effectively control HAP nucleation and growth. Additionally, the mineralization of macroscopically aligned bundles of the nanoscale assemblies to create hierarchically ordered scaffolds is explored. Again, it is found that only aligned gel templates of cylindrical nanostructures lead to hierarchical control over hydroxyapatite orientation across multiple length scales as found in bone.

| S-EPMC3400347 | biostudies-literature

A microfluidically controlled concave-convex membrane lens using an addressing operation system.

Project description:Electrical control toolkits for microlens arrays are available to some extent, but for applications in environments with strong electromagnetic fields, radiation, or deep water, non-electrical actuation and control strategies are more appropriate. An integrated digital microfluidic zoom actuating unit with a logic addressing unit for a built-in membrane lens array, e.g., a flexible bionic compound eye, is developed and studied in this article. A concave-convex membrane fluidic microvalve, which is the component element of the logic gate, actuator, and microlens, is proposed to replace the traditional solenoid valve. The functions of pressure regulation and decoding can be obtained by incorporating microvalves into fluidic networks according to equivalent circuit designs. The zoom actuating unit contains a pressure regulator to adjust the focal length of lenses with three levels, and the logic addressing unit contains a decoder to choose a typical lens from a hexagonal lens array. The microfluidic chip control system is connected flexibly to the actuating part, a membrane lens array. It is shown from a simulation and experimental demonstration that the designed and fabricated system, which is composed of a whole microfluidic zoom unit, addressing technology, and a microlens array, works well. Because these components are constructed in the same fabrication process and operate with the same work media and driving source, the system can be made highly compatible and lightweight for applications such as human-machine interfaces and soft robots.

| S-EPMC8433168 | biostudies-literature

Templating hydrogels.

Project description:Templating processes for creating polymerized hydrogels are reviewed. The use of contact photonic crystals and of non-contact colloidal crystalline arrays as templates are described and applications to chemical sensing and device fabrication are illustrated. Emulsion templating is illustrated in the formation of microporous membranes, and templating on reverse emulsions and double emulsions is described. Templating in solutions of macromolecules and micelles is discussed and then various applications of hydrogel templating on surfactant liquid crystalline mesophases are illustrated, including a nanoscale analogue of colloidal crystalline array templating, except that the bead array in this case is a cubic array of nonionic micelles. The use of particles as templates in making core-shell and hollow microgel beads is described, as is the use of membrane pores as another illustration of confinement templating.

| S-EPMC2755765 | biostudies-other

Algebraic signatures of convex and non-convex codes.

Project description:A convex code is a binary code generated by the pattern of intersections of a collection of open convex sets in some Euclidean space. Convex codes are relevant to neuroscience as they arise from the activity of neurons that have convex receptive fields. In this paper, we use algebraic methods to determine if a code is convex. Specifically, we use the neural ideal of a code, which is a generalization of the Stanley-Reisner ideal. Using the neural ideal together with its standard generating set, the canonical form, we provide algebraic signatures of certain families of codes that are non-convex. We connect these signatures to the precise conditions on the arrangement of sets that prevent the codes from being convex. Finally, we also provide algebraic signatures for some families of codes that are convex, including the class of intersection-complete codes. These results allow us to detect convexity and non-convexity in a variety of situations, and point to some interesting open questions.

| S-EPMC6750060 | biostudies-literature

Lens-induced uveitis: an update.

Project description:Ocular inflammation resulting from a lens pathology is rare in the absence of a cataract or lens trauma because of the lens' immune privilege. The lens can be a source of ocular inflammation when the capsule is broken or when lens proteins leak out through an intact capsule. These uveitides are termed lens-induced uveitis (LIU) and are often associated with advanced cataracts. Cataracts are part of the normal aging process, and in today's world, cataract surgery is a safe and affordable means of vision restoration in the developed world. In patients with neglected cataracts and in the developing world where cataract surgery rates are lower, LIU rates are higher together with the associated complications. In this literature review, we intend to equip the armamentarium of the practicing ophthalmologist with an updated knowledge on the demographic features, clinical characteristics, treatment options, and outcomes of LIU. This is to highlight the need for timely management of cataracts before the development of advanced cataracts and LIU.

| S-EPMC7223998 | biostudies-literature

MOF-Based Nanotubes to Hollow Nanospheres through Protein-Induced Soft-Templating Pathways.

Project description:A controllable and facile strategy is established for constructing metal-organic frameworks-based (MOF-based) hollow composites via a protein-induced soft-templating pathway. Using metal-sodium deoxycholate hydrogel as soft-template, nanotubes are gained while the protein is absent. With the presence of protein, hollow nanospheres structure are prepared by changing the amount of protein. To verify the universality of the proposed pathway, two kinds of proteins (Burkholderia cepacia lipase and penicillin G acylase) and three kinds of MOF (ZIF-8, ZIF-67, and Fe-MOF) are adopted as model proteins and materials, and the obtained protein-containing composites (named protein@H-MOF) possess high bioactivity and stability. This proposed strategy provides a facile method for preparing MOF-based composites under mild conditions, facilitating the applications of MOF in the fields of biocatalyst construction, biomolecule encapsulation, and drug delivery.

| S-EPMC6425429 | 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