Browse
Submit Data
Databases
API
Help

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Biomimetic Molecular Signaling using DNA Walkers on Microparticles.

ABSTRACT: We report the release of catalytic DNA walkers from hydrogel microparticles and the detection of those walkers by substrate-coated microparticles. This might be considered a synthetic biology analog of molecular signal release and reception. One type of particles was coated with components of a DNA one-step strand displacement (OSD) reaction to release the walker. A second type of particle was coated with substrate (or "track") for the molecular walker. We distinguish these particle types using fluorescence barcoding: we synthesized and distinguished multiple particle types with multicolor fluorescence microscopy and automated image analysis software. This represents a step toward amplified, multiplex, and microscopically localized detection based on DNA nanotechnology.

SUBMITTER: Damase TR

PROVIDER: S-EPMC5481426 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Biomimetic Molecular Signaling using DNA Walkers on Microparticles.

Damase Tulsi Ram TR Spencer Adam A Samuel Bamidele B Allen Peter B PB

Scientific reports 20170622 1

We report the release of catalytic DNA walkers from hydrogel microparticles and the detection of those walkers by substrate-coated microparticles. This might be considered a synthetic biology analog of molecular signal release and reception. One type of particles was coated with components of a DNA one-step strand displacement (OSD) reaction to release the walker. A second type of particle was coated with substrate (or "track") for the molecular walker. We distinguish these particle types using ...[more]

PMID: 28642488

Similar Datasets

Therapeutic microparticles functionalized with biomimetic cardiac stem cell membranes and secretome.

Project description:Stem cell therapy represents a promising strategy in regenerative medicine. However, cells need to be carefully preserved and processed before usage. In addition, cell transplantation carries immunogenicity and/or tumourigenicity risks. Mounting lines of evidence indicate that stem cells exert their beneficial effects mainly through secretion (of regenerative factors) and membrane-based cell-cell interaction with the injured cells. Here, we fabricate a synthetic cell-mimicking microparticle (CMMP) that recapitulates stem cell functions in tissue repair. CMMPs carry similar secreted proteins and membranes as genuine cardiac stem cells do. In a mouse model of myocardial infarction, injection of CMMPs leads to the preservation of viable myocardium and augmentation of cardiac functions similar to cardiac stem cell therapy. CMMPs (derived from human cells) do not stimulate T-cell infiltration in immuno-competent mice. In conclusion, CMMPs act as 'synthetic stem cells' which mimic the paracrine and biointerfacing activities of natural stem cells in therapeutic cardiac regeneration.

| S-EPMC5512648 | biostudies-literature

Programming in situ accelerated DNA walkers in diffusion-limited microenvironments.

Project description:Macromolecule diffusion in cellular microenvironments dictates the kinetics of biochemical processes, yet inevitably limiting the assembly and operation of biomimetic motors. Herein we program in situ accelerated DNA walkers in diffusion-limited microenvironments such as molecularly crowded solutions and cytoplasm. All DNA components, including single-foot walkers, chemically damaged tracks and calibration elements, are anchored on individual gold nanoparticles. Two endogenous enzymes participating in base repair pathways are used to actuate on-particle walking via a base excision/hydrolyzation coupled reaction. The walkers are in situ driven without requiring external drivers and accelerated several times. They also avoid low-efficiency diffusion/assembly procedures and respond to heterogeneous cellular milieus with calibration function. We further regulated the walking kinetics via DNA densities and sets of enzymes, and demonstrated cytoplasmic behaviors of three kinds of walkers. They were utilized to profile DNA repair pathways and monitor enzyme catalysis in living cells.

| S-EPMC6432271 | biostudies-literature

Controlling the preferential motion of chiral molecular walkers on a surface.

Project description:Molecular walkers standing on two or more "feet" on an anisotropic periodic potential of a crystal surface may perform a one-dimensional Brownian motion at the surface-vacuum interface along a particular direction in which their mobility is the largest. In thermal equilibrium the molecules move with equal probabilities both ways along this direction, as expected from the detailed balance principle, well-known in chemical reactivity and in the theory of molecular motors. For molecules that possess an asymmetric potential energy surface (PES), we propose a generic method based on the application of a time-periodic external stimulus that would enable the molecules to move preferentially in a single direction thereby acting as Brownian ratchets. To illustrate this method, we consider a prototypical synthetic chiral molecular walker, 1,3-bis(imidazol-1-ylmethyl)-5(1-phenylethyl)benzene, diffusing on the anisotropic Cu(110) surface along the Cu rows. As unveiled by our kinetic Monte Carlo simulations based on the rates calculated using ab initio density functional theory, this molecule moves to the nearest equivalent lattice site via the so-called inchworm mechanism in which it steps first with the rear foot and then with the front foot. As a result, the molecule diffuses via a two-step mechanism, and due to its inherent asymmetry, the corresponding PES is also spatially asymmetric. Taking advantage of this fact, we show how the external stimulus can be tuned to separate molecules of different chirality, orientation and conformation. The consequences of these findings for molecular machines and the separation of enantiomers are also discussed.

| S-EPMC6582760 | biostudies-literature

Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers.

Project description:DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers' small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s-1) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps.

| S-EPMC5249260 | biostudies-literature

Light-Fueled Microscopic Walkers.

Project description:The first microscopic artificial walker equipped with liquid-crystalline elastomer muscle is reported. The walker is fabricated by direct laser writing, is smaller than any known living terrestrial creatures, and is capable of several autonomous locomotions on different surfaces.

| S-EPMC4660875 | biostudies-other

Sequence walkers: a graphical method to display how binding proteins interact with DNA or RNA sequences.

Project description:A graphical method is presented for displaying how binding proteins and other macromolecules interact with individual bases of nucleotide sequences. Characters representing the sequence are either oriented normally and placed above a line indicating favorable contact, or upside-down and placed below the line indicating unfavorable contact. The positive or negative height of each letter shows the contribution of that base to the average sequence conservation of the binding site, as represented by a sequence logo. These sequence 'walkers' can be stepped along raw sequence data to visually search for binding sites. Many walkers, for the same or different proteins, can be simultaneously placed next to a sequence to create a quantitative map of a complex genetic region. One can alter the sequence to quantitatively engineer binding sites. Database anomalies can be visualized by placing a walker at the recorded positions of a binding molecule and by comparing this to locations found by scanning the nearby sequences. The sequence can also be altered to predict whether a change is a polymorphism or a mutation for the recognizer being modeled.

| S-EPMC147041 | biostudies-other

Biomimetic mineralization using matrix vesicle nanofragments.

Project description:In vitro synthesis of bone tissue has been paid attention in recent years; however, current methods to fabricate bone tissue are still ineffective due to some remaining gaps in the understanding of real in vivo bone formation process, and application of the knowledge in bone synthesis. Therefore, the objectives of this study were first, to perform a systematic and ultrastructural investigation of the initial mineral formation during intramembranous ossification of mouse calvaria from a material scientists' viewpoint, and to develop novel mineralization methods based on the in vivo findings. First, the very initial mineral deposition was found to occur at embryonic day E14.0 in mouse calvaria. Analysis of the initial bone formation process showed that it involved the following distinct steps: collagen secretion, matrix vesicle (MV) release, MV mineralization, MV rupture, and collagen fiber mineralization. Next, we performed in vitro mineralization experiments using MVs and hydrogel scaffolds. Intact MVs embedded in collagen gel did not mineralize, whereas, interestingly, MV nanofragments obtained by ultrasonication could promote rapid mineralization. These results indicate that mechanically ruptured MV membrane can be a promising material for in vitro bone tissue synthesis. © 2019 The Authors. journal Of Biomedical Materials Research Part A Published By Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 1021-1030, 2019.

| S-EPMC6594056 | biostudies-literature

On-chip microfluidic biosensor using superparamagnetic microparticles.

Project description:In this paper, an integrated solution towards an on-chip microfluidic biosensor using the magnetically induced motion of functionalized superparamagnetic microparticles (SMPs) is presented. The concept of the proposed method is that the induced velocity on SMPs in suspension, while imposed to a magnetic field gradient, is inversely proportional to their volume. Specifically, a velocity variation of suspended functionalized SMPs inside a detection microchannel with respect to a reference velocity, specified in a parallel reference microchannel, indicates an increase in their non-magnetic volume. This volumetric increase of the SMPs is caused by the binding of organic compounds (e.g., biomolecules) to their functionalized surface. The new compounds with the increased non-magnetic volume are called loaded SMPs (LSMPs). The magnetic force required for the manipulation of the SMPs and LSMPs is produced by current currying conducting microstructures, driven by a programmable microcontroller. Experiments were carried out as a proof of concept. A promising decrease in the velocity of the LSMPs in comparison to that of the SMPs was measured. Thus, it is the velocity variation which determines the presence of the organic compounds in the sample fluid.

| S-EPMC3820637 | biostudies-other

Smartphone-Based Inertial Odometry for Blind Walkers.

Project description:Pedestrian tracking systems implemented in regular smartphones may provide a convenient mechanism for wayfinding and backtracking for people who are blind. However, virtually all existing studies only considered sighted participants, whose gait pattern may be different from that of blind walkers using a long cane or a dog guide. In this contribution, we present a comparative assessment of several algorithms using inertial sensors for pedestrian tracking, as applied to data from WeAllWalk, the only published inertial sensor dataset collected indoors from blind walkers. We consider two situations of interest. In the first situation, a map of the building is not available, in which case we assume that users walk in a network of corridors intersecting at 45° or 90°. We propose a new two-stage turn detector that, combined with an LSTM-based step counter, can robustly reconstruct the path traversed. We compare this with RoNIN, a state-of-the-art algorithm based on deep learning. In the second situation, a map is available, which provides a strong prior on the possible trajectories. For these situations, we experiment with particle filtering, with an additional clustering stage based on mean shift. Our results highlight the importance of training and testing inertial odometry systems for assisted navigation with data from blind walkers.

| S-EPMC8230905 | biostudies-literature

Biomimetic Stress Sensitive Hydrogel Controlled by DNA Nanoswitches.

Project description:One of the most intriguing and important aspects of biological supramolecular materials is its ability to adapt macroscopic properties in response to environmental cues for controlling cellular processes. Recently, bulk matrix stiffness, in particular, stress sensitivity, has been established as a key mechanical cue in cellular function and development. However, stress-stiffening capacity and the ability to control and exploit this key characteristic is relatively new to the field of biomimetic materials. In this work, DNA-responsive hydrogels, composed of semiflexible PIC polymers equipped with DNA cross-linkers, were engineered to create mimics of natural biopolymer networks that capture these essential elastic properties and can be controlled by external stimuli. We show that the elastic properties are governed by the molecular structure of the cross-linker, which can be readily varied providing access to a broad range of highly tunable soft hydrogels with diverse stress-stiffening regimes. By using cross-linkers based on DNA nanoswitches, responsive to pH or ligands, internal control elements of mechanical properties are implemented that allow for dynamic control of elastic properties with high specificity. The work broadens the current knowledge necessary for the development of user defined biomimetic materials with stress stiffening capacity.

| S-EPMC5665546 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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