Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A quantitative assessment of the dynamic modification of lipid-DNA probes on live cell membranes.

ABSTRACT: Synthetic lipid-DNA probes have recently attracted much attention for cell membrane analysis, transmembrane signal transduction, and regulating intercellular networks. These lipid-DNA probes can spontaneously insert onto plasma membranes simply after incubation. The highly precise and controllable DNA interactions have further allowed the programmable manipulation of these membrane-anchored functional probes. However, we still have quite limited understanding of how these lipid-DNA probes interact with cell membranes and also what parameters determine this process. In this study, we have systematically studied the dynamic process of cell membrane modification with a group of lipid-DNA probes. Our results indicated that the hydrophobicity of the lipid-DNA probes is strongly correlated with their membrane insertion and departure rates. Most cell membrane insertion stems from the monomeric form of probes, rather than the aggregates. Lipid-DNA probes can be removed from cell membranes through either endocytosis or direct outflow into the solution. As a result, long-term probe modifications on cell membranes can be realized in the presence of excess probes in the solution and/or endocytosis inhibitors. For the first time, we have successfully improved the membrane persistence of lipid-DNA probes to more than 24 h. Our quantitative data have dramatically improved our understanding of how lipid-DNA probes dynamically interact with cell membranes. These results can be further used to allow a broad range of applications of lipid-DNA probes for cell membrane analysis and regulation.

SUBMITTER: Bagheri Y

PROVIDER: S-EPMC7003967 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

DNA probes for monitoring dynamic and transient molecular encounters on live cell membranes.

Project description:Cells interact with the extracellular environment through molecules expressed on the membrane. Disruption of these membrane-bound interactions (or encounters) can result in disease progression. Advances in super-resolution microscopy have allowed membrane encounters to be examined, however, these methods cannot image entire membranes and cannot provide information on the dynamic interactions between membrane-bound molecules. Here, we show a novel DNA probe that can transduce transient membrane encounter events into readable cumulative fluorescence signals. The probe, which translocates from one anchor site to another, mimicking motor proteins, is realized through a toehold-mediated DNA strand displacement reaction. Using this probe, we successfully monitored rapid encounter events of membrane lipid domains using flow cytometry and fluorescence microscopy. Our results show a preference for encounters within the same lipid domains.

| S-EPMC5507702 | biostudies-literature

Imaging organelle membranes in live cells at the nanoscale with lipid-based fluorescent probes.

Project description:Understanding how organelles interact, exchange materials, assemble, disassemble, and evolve as a function of space, time, and environment is an exciting area at the very forefront of chemical and cell biology. Here, we bring attention to recent progress in the design and application of lipid-based tools to visualize and interrogate organelles in live cells, especially at super resolution. We highlight strategies that rely on modification of natural lipids or lipid-like small molecules ex cellula, where organelle specificity is provided by the structure of the chemically modified lipid, or in cellula using cellular machinery, where an enzyme labels the lipid in situ. We also describe recent improvements to the chemistry upon which lipid probes rely, many of which have already begun to broaden the scope of biological questions that can be addressed by imaging organelle membranes at the nanoscale.

| S-EPMC9904808 | biostudies-literature

DNA modification of live cell surface.

Project description:We report a novel approach for the attachment of DNA fragments to the surface of live cells. By using fluorescence microscopy and flow cytometry we demonstrated that our synthetic conjugates of fatty acid with oligonucleotides can be incorporated in plasma membrane and then hybridized with complementary sequences at the cell surface. Method permits to control amount of immobilized DNA on the cell surface. All procedures can be completed within minutes and do not alter cell viability. Using this approach we tethered floating myeloid HL-60 cells to adherent A431 epitheliocytes in a sequence specific fashion. Thus, this method allows rapid and simple DNA multicoding of the cell surface and, therefore, opens new opportunities in manipulating with cell-cell interactions.

| S-EPMC2651772 | biostudies-literature

Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes.

Project description:Lipid-anchored DNA can attach functional cargo to bilayer membranes in DNA nanotechnology, synthetic biology, and cell biology research. To optimize DNA anchoring, an understanding of DNA-membrane interactions in terms of binding strength, extent, and structural dynamics is required. Here we use experiments and molecular dynamics (MD) simulations to determine how the membrane binding of cholesterol-modified DNA depends on electrostatic and steric factors involving the lipid headgroup charge, duplexed or single-stranded DNA, and the buffer composition. The experiments distinguish between free and membrane vesicle-bound DNA and thereby reveal the surface density of anchored DNA and its binding affinity, something which had previously not been known. The Kd values range from 8.5 ± 4.9 to 466 ± 134 μM whereby negatively charged headgroups led to weak binding due to the electrostatic repulsion with respect to the negatively charged DNA. Atomistic MD simulations explain the findings and elucidate the dynamic nature of anchored DNA such as the mushroom-like conformation of single-stranded DNA hovering over the bilayer surface in contrast to a straight-up conformation of double-stranded DNA. The biophysical insight into the binding strength to membranes as well as the molecular accessibility of DNA for hybridization to molecular cargo is expected to facilitate the creation of biomimetic DNA versions of natural membrane nanopores and cytoskeletons for research and nanobiotechnology.

| S-EPMC6458106 | biostudies-literature

Photoactivatable aggregation-induced emission probes for lipid droplets-specific live cell imaging.

Project description:Photoactivatable probes for lipid droplets (LDs)-specific live-cell imaging are powerful tools for investigating their biological functions through precise spatial and temporal control. Ideal photoactivatable probes for LDs imaging require high concentration accumulation of fluorophores in LDs, simple synthetic procedures, and excellent photoactivation efficiency. However, it is difficult to overcome these challenges by conventional fluorophores due to aggregation-caused quenching (ACQ). In this study, a new class of photoactivatable and LDs-specific fluorescent probes was developed based on dihydro-2-azafluorenones, which can easily undergo photooxidative dehydrogenation reaction to afford 2-azafluorenones with aggregation-induced emission (AIE) properties. Dihydro-2-azafluorenones as photoactivatable and LDs-specific probes display significant advantages of excellent photoactivation efficiency and lack of self-quenching in the aggregated state, and are expected to have broad applications in study of biological functions of LDs' through light-controlled spatiotemporal imaging.

| S-EPMC5933432 | biostudies-literature

Advanced DNA Zipper Probes for Detecting Cell Membrane Lipid Domains.

Project description:The cell membrane is a complex mixture of lipids, proteins, and other components. By forming dynamic lipid domains, different membrane molecules can selectively interact with each other to control cell signaling. Herein, we report several new types of lipid-DNA conjugates, termed as "DNA zippers", which can be used to measure cell membrane dynamic interactions and the formation of lipid domains. Dependent on the choice of lipid moieties, cholesterol- and sphingomyelin-conjugated DNA zippers specifically locate in and detect membrane lipid-ordered domains, while in contrast, a tocopherol-DNA zipper can be applied for the selective imaging of lipid-disordered phases. These versatile and programmable probes can be further engineered into membrane competition assays to simultaneously detect multiple types of membrane dynamic interactions. These DNA zipper probes can be broadly used to study the correlation between lipid domains and various cellular processes, such as the epithelial-mesenchymal transition.

| S-EPMC10368464 | biostudies-literature

Quantitative Assessment of Labeling Probes for Super-Resolution Microscopy Using Designer DNA Nanostructures.

Project description:Improving labeling probes for state-of-the-art super-resolution microscopy is becoming of major importance. However, there is currently a lack of tools to quantitatively evaluate probe performance regarding efficiency, precision, and achievable resolution in an unbiased yet modular fashion. Herein, we introduce designer DNA origami structures combined with DNA-PAINT to overcome this issue and evaluate labeling efficiency, precision, and quantification using antibodies and nanobodies as exemplary labeling probes. Whereas current assessment of binders is mostly qualitative, e. g. based on an expected staining pattern, we herein present a quantitative analysis platform of the antigen labeling efficiency and achievable resolution, allowing researchers to choose the best performing binder. The platform can furthermore be readily adapted for discovery and precise quantification of a large variety of additional labeling probes.

| S-EPMC8251534 | biostudies-literature

Quinone-Derived ?-Extended Phenazines as New Fluorogenic Probes for Live-Cell Imaging of Lipid Droplets.

Project description:We describe a new synthetic methodology for the preparation of fluorescent ?-extended phenazines from the naturally-occurring naphthoquinone lapachol. These novel structures represent the first fluorogenic probes based on the phenazine scaffold for imaging of lipid droplets in live cells. Systematic characterization and analysis of the compounds in vitro and in cells led to the identification of key structural features responsible for the fluorescent behavior of quinone-derived ?-extended phenazines. Furthermore, live-cell imaging experiments identified one compound (P1) as a marker for intracellular lipid droplets with minimal background and enhanced performance over the lipophilic tracker Nile Red.

| S-EPMC6099520 | biostudies-literature

Dynamic colloidal nanoparticle assembly triggered by aptamer-receptor interactions on live cell membranes.

Project description:Cells use dynamic systems such as enzyme cascades and signaling networks to control cellular functions. Synthetic dynamic systems that can be target-responsive have great potential to be applied for biomedical applications but the operation of such dynamic systems in complex cellular environments remains challenging. Here, we engineered an aptamer and DNA displacement reaction-based dynamic system that can transform its nanostructure in response to the epithelial cell adhesion molecule (EpCAM) on live cell membranes. The dynamic system consisted of a core nanoparticle and small satellite nanoparticles. With the modifications of different DNA hairpin strands and swing arm strands partially hybridized with an aptamer that specifically recognizes the EpCAM, the two separated particles can dynamically assemble into a core-satellite assembly by aptamer-receptor interactions on the cell membrane surface. The structural change of the system from separated particles to a core-satellite assembly generated plasmonic coupled hot spots for surface-enhanced Raman scattering (SERS) for sensitively capturing the dynamic structural change of the nanoassembly in the cellular environment. These concepts provide strategies for engineering dynamic nanotechnology systems for biological and biomedical applications in complex biological environments.

| S-EPMC6713859 | biostudies-other

Multiplexed live-cell profiling with Raman probes.

Project description:Single-cell multiparameter measurement has been increasingly recognized as a key technology toward systematic understandings of complex molecular and cellular functions in biological systems. Despite extensive efforts in analytical techniques, it is still generally challenging for existing methods to decipher a large number of phenotypes in a single living cell. Herein we devise a multiplexed Raman probe panel with sharp and mutually resolvable Raman peaks to simultaneously quantify cell surface proteins, endocytosis activities, and metabolic dynamics of an individual live cell. When coupling it to whole-cell spontaneous Raman micro-spectroscopy, we demonstrate the utility of this technique in 14-plexed live-cell profiling and phenotyping under various drug perturbations. In particular, single-cell multiparameter measurement enables powerful clustering, correlation, and network analysis with biological insights. This profiling platform is compatible with live-cell cytometry, of low instrument complexity and capable of highly multiplexed measurement in a robust and straightforward manner, thereby contributing a valuable tool for both basic single-cell biology and translation applications such as high-content cell sorting and drug discovery.

| S-EPMC8184955 | 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