Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Disperse Orange 3 as a resonance Raman probe for measuring membrane order.

ABSTRACT: Resonance Raman spectra of azobenzene derivatives were examined in the presence of lipid membranes to find a probe that can distinguish different membrane phases. The NO2 symmetric stretching band of 4-(4-nitrophenylazo)aniline, also known as Disperse Orange 3 (DO3), is downshifted by about 4 cm(-1) on the phase transition of phosphatidylcholine membranes from the liquid crystalline to the gel phase. A comparable downshift also occurs when DO3 is bound to cholesterol-containing membranes in the liquid-ordered phase. Our results demonstrate that Raman spectrum of DO3 is a unique tool for measuring the molecular order of lipids in membranes.

SUBMITTER: Numakura Y

PROVIDER: S-EPMC4637360 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Disperse Orange 3 as a resonance Raman probe for measuring membrane order.

Numakura Yuki Y Miura Takashi T

FEBS open bio 20151023

Resonance Raman spectra of azobenzene derivatives were examined in the presence of lipid membranes to find a probe that can distinguish different membrane phases. The NO2 symmetric stretching band of 4-(4-nitrophenylazo)aniline, also known as Disperse Orange 3 (DO3), is downshifted by about 4 cm(-1) on the phase transition of phosphatidylcholine membranes from the liquid crystalline to the gel phase. A comparable downshift also occurs when DO3 is bound to cholesterol-containing membranes in the ...[more]

PMID: 26636028

Similar Datasets

UV Resonance Raman Spectroscopy as a Tool to Probe Membrane Protein Structure and Dynamics.

Project description:Ultraviolet resonance Raman (UVRR) spectroscopy is a vibrational technique that reveals structures and dynamics of biological macromolecules without the use of extrinsic labels. By tuning the Raman excitation wavelength to the deep UV region (e.g., 228 nm), Raman signal from tryptophan and tyrosine residues are selectively enhanced, allowing for the study of these functionally relevant amino acids in lipid and aqueous environments. In this chapter, we present methods on the UVRR data acquisition and analysis of the tryptophan vibrational modes of a model β-barrel membrane protein, OmpA, in folded and unfolded conformations.

| S-EPMC6874512 | biostudies-literature

Cyclic Voltammetry of C.I. Disperse Orange 62 in an Aqueous Electrolyte.

Project description:Disperse dyes are an important group of colorants for dyeing polyester fibers. Approximately 30.000 tons of disperse dyes are released into the waste water annually from spent dyebaths. Therefore, methods for decolorizing such dyes are of general interest. The reductive after-treatment of disperse dyes using reducing agents, such as Na2S2O4, is a widely used process to improve rub fastness through dye reduction. Electrochemical dye reduction could be an alternative process for reductive dye treatment. In this work C.I. Disperse Orange 62 was used as a representative dye to study the direct cathodic reduction of a disperse dye with cyclic voltammetry. As anticipated for dispersed organic matter, relatively low current densities were observed, which strongly depend on the state of dispersion of the dye. The current density was increased by using dispersions prepared through dye precipitation from DMF solution and by the use of N-cetyl-N,N,N,-trimethyl-ammonium bromide as a cationic surfactant. The results demonstrate the successful cathodic reduction of a dispersed organic dye; however, the low solubility of the reaction products in the aqueous electrolyte hinders an efficient cathodic dye reduction.

| S-EPMC10647369 | biostudies-literature

Fluorescence lifetime imaging of membrane lipid order with a ratiometric fluorescent probe.

Project description:To monitor the lateral segregation of lipids into liquid-ordered (Lo) and -disordered (Ld) phases in lipid membranes, environment-sensitive dyes that partition in both phases but stain them differently have been developed. Of particular interest is the dual-color F2N12S probe, which can discriminate the two phases through the ratio of its two emission bands. These bands are associated with the normal (N(∗)) and tautomer (T(∗)) excited-state species that result from an excited-state intramolecular proton transfer. In this work, we investigated the potency of the time-resolved fluorescence parameters of F2N12S to discriminate lipid phases in model and cell membranes. Both the long and mean lifetime values of the T(∗) form of F2N12S were found to differ by twofold between Ld and Lo phases as a result of the restriction in the relative motions of the two aromatic moieties of F2N12S imposed by the highly packed Lo phase. This differed from the changes in the ratio of the two emission bands between the two phases, which mainly resulted from the decreased hydration of the N(∗) form in the Lo phase. Importantly, the strong difference in lifetimes between the two phases was preserved when cholesterol was added to the Ld phase. The two phases could be imaged with high contrast by fluorescence lifetime imaging microscopy (FLIM) on giant unilamellar vesicles. FLIM images of F2N12S-labeled live HeLa cells confirmed that the plasma membrane was mainly in the Lo-like phase. Furthermore, the two phases were found to be homogeneously distributed all over the plasma membrane, indicating that they are highly mixed at the spatiotemporal resolution of the FLIM setup. Finally, FLIM could also be used to sensitively monitor the change in lipid phase upon cholesterol depletion and apoptosis.

| S-EPMC4457243 | biostudies-literature

Rapid resonance Raman microspectroscopy to probe carbon dioxide fixation by single cells in microbial communities.

Project description:Photosynthetic microorganisms play crucial roles in aquatic ecosystems and are the major primary producers in global marine ecosystems. The discovery of new bacteria and microalgae that play key roles in CO(2) fixation is hampered by the lack of methods to identify hitherto-unculturable microorganisms. To overcome this problem we studied single microbial cells using stable-isotope probing (SIP) together with resonance Raman (RR) microspectroscopy of carotenoids, the light-absorbing pigments present in most photosynthetic microorganisms. We show that fixation of (13)CO(2) into carotenoids produces a red shift in single-cell RR (SCRR) spectra and that this SCRR-SIP technique is sufficiently sensitive to detect as little as 10% of (13)C incorporation. Mass spectrometry (MS) analysis of labelled cellular proteins verifies that the red shift in carotenoid SCRR spectra acts as a reporter of the (13)C content of single cells. Millisecond Raman imaging of cells in mixed cultures and natural seawater samples was used to identify cells actively fixing CO(2), demonstrating that the SCRR-SIP is a noninvasive method for the rapid and quantitative detection of CO(2) fixation at the single cell level in a microbial community. The SCRR-SIP technique may provide a direct method for screening environmental samples, and could help to reveal the ecophysiology of hitherto-unculturable microorganisms, linking microbial species to their ecological function in the natural environment.

| S-EPMC3309358 | biostudies-literature

Tryptophan as a probe of photosystem I electron transfer reactions: a UV resonance Raman study.

Project description:Photosystem I (PSI) is one of the two membrane-associated reaction centers involved in oxygenic photosynthesis. In photosynthesis, solar energy is converted to chemical energy in the form of a transmembrane charge separation. PSI oxidizes cytochrome c(6) or plastocyanin and reduces ferredoxin. In cyanobacterial PSI, there are 10 tryptophan residues with indole side chains located less than 10 A from the electron transfer cofactors. In this study, we apply pump-probe difference UV resonance Raman (UVRR) spectroscopy to acquire the spectrum of aromatic amino acids in cyanobacterial PSI. This UVRR technique allows the use of the tryptophan vibrational spectrum as a reporter for structural changes, which are linked to PSI electron transfer reactions. Our results show that photo-oxidation of the chlorophyll a/a' heterodimer, P(700), causes shifts in the vibrational frequencies of two or more tryptophan residues. Similar perturbations of tryptophan are observed when P(700) is chemically oxidized. The observed spectral frequencies suggest that the perturbed tryptophan side chains are only weakly or not hydrogen bonded and are located in an environment in which there is steric repulsion. The direction of the spectral shifts is consistent with an oxidation-induced increase in dielectric constant or a change in hydrogen bonding. To explain our results, the perturbation of tryptophan residues must be linked to a PSI conformational change, which is, in turn, driven by P(700) oxidation.

| S-EPMC2846372 | biostudies-literature

Forster resonance energy transfer as a probe of membrane protein folding.

Project description:The folding reaction of a β-barrel membrane protein, outer membrane protein A (OmpA), is probed with Förster resonance energy transfer (FRET) experiments. Four mutants of OmpA were generated in which the donor fluorophore, tryptophan, and acceptor molecule, a naphthalene derivative, are placed in various locations on the protein to report the evolution of distances across the bilayer and across the protein pore during a folding event. Analysis of the FRET efficiencies reveals three timescales for tertiary structure changes associated with insertion and folding into a synthetic bilayer. A narrow pore forms during the initial stage of insertion, followed by bilayer traversal. Finally, a long-time component is attributed to equilibration and relaxation, and may involve global changes such as pore expansion and strand extension. These results augment the existing models that describe concerted insertion and folding events, and highlight the ability of FRET to provide insight into the complex mechanisms of membrane protein folding. This article is part of a Special Issue entitled: Membrane protein structure and function.

| S-EPMC3253952 | biostudies-literature

Imaging Membrane Order and Dynamic Interactions in Living Cells with a DNA Zipper Probe.

Project description:The cell membrane is a dynamic and heterogeneous structure composed of distinct sub-compartments. Within these compartments, preferential interactions occur among various lipids and proteins. Currently, it is still challenging to image these short-lived membrane complexes, especially in living cells. In this work, we present a DNA-based probe, termed "DNA Zipper", which allows the membrane order and pattern of transient interactions to be imaged in living cells using standard fluorescence microscopes. By fine-tuning the length and binding affinity of DNA duplex, these probes can precisely extend the duration of membrane lipid interactions via dynamic DNA hybridization. The correlation between membrane order and the activation of T-cell receptor signaling has also been studied. These programmable DNA probes function after a brief cell incubation, which can be easily adapted to study lipid interactions and membrane order during different membrane signaling events.

| S-EPMC8792286 | biostudies-literature

Raman

Project description:Multi-excitation Raman Spectroscopy Complements Whole Genome Sequencing for Rapid Detection of Bacterial Infection and Resistance in WHO Priority Pathogens

| PRJEB59061 | ENA

Raman

Project description:Raman spectroscopy for pathogen detection and antibiotic resistance identification

| PRJEB59025 | ENA

Measuring higher order ambiguity preferences.

Project description:We report the results from an experiment designed to measure attitudes towards ambiguity beyond ambiguity aversion. In particular, we implement recently-proposed model-free preference conditions of ambiguity prudence and ambiguity temperance. Ambiguity prudence has been shown to play an important role in precautionary behavior and the mere presence of ambiguity averse agents in markets. We observe that the majority of individuals' decisions are consistent with ambiguity aversion, ambiguity prudence and ambiguity temperance. This finding confirms the prediction of many popular (specifications of) ambiguity models and has important implications for models of prevention behavior.

| S-EPMC5913386 | biostudies-other

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