Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synthesis of a dual-labeled probe of dimethyl lithospermate B with photochemical and fluorescent properties.

ABSTRACT: Dimethyl lithosermate B (DLB) is a highly potent natural antioxidant and antidiabetic polyphenol with unknown mode of action. To determine its cellular targets, a photochemical and fluorescent dimethyl lithopermate B probe was designed and efficiently synthesized. The dual-labeled chemical probe for biological application was evaluated by UV and fluorescence to determine its electrochemical absorption and emission properties. This probe could be valuable for investigating ligand-protein interactions and subcellular localization.

SUBMITTER: Lim E

PROVIDER: S-EPMC6264775 | biostudies-literature | 2011 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Synthesis of a dual-labeled probe of dimethyl lithospermate B with photochemical and fluorescent properties.

Lim Eunyoung E Ricci Jeremy J Jung Mankil M

Molecules (Basel, Switzerland) 20111128 12

Dimethyl lithosermate B (DLB) is a highly potent natural antioxidant and antidiabetic polyphenol with unknown mode of action. To determine its cellular targets, a photochemical and fluorescent dimethyl lithopermate B probe was designed and efficiently synthesized. The dual-labeled chemical probe for biological application was evaluated by UV and fluorescence to determine its electrochemical absorption and emission properties. This probe could be valuable for investigating ligand-protein interact ...[more]

PMID: 22124203

Similar Datasets

Synthesis and application of a <sup>19</sup>F-labeled fluorescent nucleoside as a dual-mode probe for i-motif DNAs.

Project description:Because of their stable orientations and their minimal interference with native DNA interactions and folding, emissive isomorphic nucleoside analogues are versatile tools for the accurate analysis of DNA structural heterogeneity. Here, we report on a bifunctional trifluoromethylphenylpyrrolocytidine derivative (FPdC) that displays an unprecedented quantum yield and highly sensitive 19F NMR signal. This is the first report of a cytosine-based dual-purpose probe for both fluorescence and 19F NMR spectroscopic DNA analysis. FPdC and FPdC-containing DNA were synthesized and characterized; our robust dual probe was successfully used to investigate the noncanonical DNA structure, i-motifs, through changes in fluorescence intensity and 19F chemical shift in response to i-motif formation. The utility of FPdC was exemplified through reversible fluorescence switching of an FPdC-containing i-motif oligonucleotide in the presence of Ag(i) and cysteine.

| S-EPMC8382138 | biostudies-literature

Dual-Function Fluorescent Probe for Detection of Hydrogen Sulfide and Water Content in Dimethyl Sulfoxide.

Project description:To detect hydrogen sulfide (H2S) and water content in dimethyl sulfoxide, the fluorescent probe (Probe 1) was used, as it not only detects H2S but also detects the water content. After H2S was added into Probe 1, the intensity of fluorescence increased and was up to 1300 times. In case the H2S concentration was in the range 0-20 μM, it was able to be detected by Probe 1, and the limit of detection was 0.851 nM. When Probe 1 and H2S underwent a reaction, the solution color had some changes. These colors changed in terms of the concentration changes of H2S, ranging from colorless to yellow. The Probe 1 test paper only needed to be exposed to hydrogen sulfide gas for 20 s for the color change to occur. Besides, Probe 1-H2S was used to detect water content in dimethyl sulfoxide which ranged from 0 to 100%. The color change of the solution was opposite to that of H2S, ranging from yellow to colorless.

| S-EPMC6648854 | biostudies-literature

Design, synthesis and photochemical properties of the first examples of iminosugar clusters based on fluorescent cores.

Project description:The synthesis and photophysical properties of the first examples of iminosugar clusters based on a BODIPY or a pyrene core are reported. The tri- and tetravalent systems designed as molecular probes and synthesized by way of Cu(I)-catalysed azide-alkyne cycloadditions are fluorescent analogues of potent pharmacological chaperones/correctors recently reported in the field of Gaucher disease and cystic fibrosis, two rare genetic diseases caused by protein misfolding.

| S-EPMC4464267 | biostudies-literature

Novel Phototransformable Fluorescent Protein SAASoti with Unique Photochemical Properties.

Project description:SAASoti is a unique fluorescent protein (FP) that combines properties of green-to-red photoconversion and reversible photoswitching (in its green state), without any amino acid substitutions in the wild type gene. In the present work, we investigated its ability to photoswitch between fluorescent red ('on') and dark ('off') states. Surprisingly, generated by 400 nm exposure, the red form of SAASoti (R1) does not exhibit any reversible photoswitching behavior under 550 nm illumination, while a combination of prior 470 nm and subsequent 400 nm irradiation led to the appearance of another-R2-form that can be partially photoswitched (550 nm) to the dark state, with a very fast recovery time. The phenomenon might be explained by chemical modification in the chromophore microenvironment during prior 470 nm exposure, and the resulting R2 SAASoti differs chemically from the R1 form. The suggestion is supported by the mass spectrometry analysis of the tryptic peptides before and after 470 nm light exposure, that revealed Met164 oxidation, as proceeds in another dual phototransformable FP, IrisFP.

| S-EPMC6678895 | biostudies-literature

Synthesis of DNA and RNA Oligonucleotides Containing a Dual-Purpose Selenium-Modified Fluorescent Nucleoside Probe.

Project description:Development of efficient tools that would enable direct correlation of nucleic acid structure and recognition in solution and in solid state at atomic resolution is highly desired. In this context, we recently developed dual-purpose nucleoside probes made of a 5-selenophene-modified uracil core, which serves both as a conformation-sensitive fluorophore and as an X-ray crystallography phasing agent. In this article, we provide a detailed synthetic procedure to synthesize the phosphoramidites of 5-selenophene-modified 2'-deoxyuridine and 5-selenophene-modified uridine analogs. We also describe their site-specific incorporation into therapeutically relevant DNA and RNA oligonucleotide motifs by an automated solid support synthesis protocol. The dual-purpose and minimally invasive nature of the probes enables efficient analysis of the conformation and ligand binding abilities of bacterial decoding site RNA (A-site) and G-quadruplex structures of the human telomeric overhang in real time by fluorescence and in 3D by X-ray crystallography. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Synthesis of 5-selenophene-2'-deoxyuridine 2 and its phosphoramidite 5 Support Protocol 1: Synthesis of 2-(tri-n-butylstannyl) selenophene Support Protocol 2: Synthesis of 5'-O-DMT-protected 5-iodo-2'-deoxyuridine 3 Basic Protocol 2: Synthesis of 5-selenophene-modified uridine 7 and its phosphoramidite 11 Basic Protocol 3: Synthesis of DNA oligonucleotides containing 5-selenophene-modified 2'-deoxyuridine 2 Basic Protocol 4: Synthesis of an RNA oligonucleotide containing 5-selenophene-modified uridine 7.

| S-EPMC7611079 | biostudies-literature

Substituted Dibenzodiazocines: Rapid Synthesis and Photochemical Properties.

Project description:11,12-Dihydrodibenzo[c,g]-1,2-diazocines have been established as a viable alternative to azobenzene for photoswitching, in particular, as they show an inverted switching behavior: the ground state is the Z isomer. In this paper, we present an improved method to obtain dibenzodiazocine and its derivatives from the respective 2-nitrotoluenes in two reaction steps, each proceeding in minutes. This fast access to a variety of derivatives permitted the study of substitution effects on the synthesis and on the photochemical properties. With biochemical applications in mind, methanol was chosen as a protic solvent system for the photochemical investigations. In contrast to the azobenzene system, none of the tested substitution patterns resulted in more efficient switching or in significantly prolonged half-lives, showing that the system is dominated by the ring strain.

| S-EPMC8296553 | biostudies-literature

Asymmetric and Reduced Xanthene Fluorophores: Synthesis, Photochemical Properties, and Application to Activatable Fluorescent Probes for Detection of Nitroreductase.

Project description:Xanthene fluorophores, including fluorescein, rhodol, and rhodamines, are representative classes of fluorescent probes that have been applied in the detection and visualization of biomolecules. "Turn on" activatable fluorescent probes, that can be turned on in response to enzymatic reactions, have been developed and prepared to reduce the high background signal of "always-on" fluorescent probes. However, the development of activity-based fluorescent probes for biological applications, using simple xanthene dyes, is hampered by their inefficient synthetic methods and the difficulty of chemical modifications. We have, thus, developed a highly efficient, versatile synthetic route to developing chemically more stable reduced xanthene fluorophores, based on fluorescein, rhodol, and rhodamine via continuous Pd-catalyzed cross-coupling. Their fluorescent nature was evaluated by monitoring fluorescence with variation in the concentration, pH, and solvent. As an application to activatable fluorescent probe, nitroreductase (NTR)-responsive fluorescent probes were also developed using the reduced xanthene fluorophores, and their fluorogenic properties were evaluated.

| S-EPMC6749439 | biostudies-literature

Micro flow photochemical synthesis of Ca-sensitive fluorescent sensor particles.

Project description:Fluorescence probes have widely been used for detecting and imaging Ca2+-enriched parts of cells but more rarely for quantitative determination of concentrations. In this study we show how this can be achieved by a novel approach using hydrogel particles. In a microfluidic co-flow arrangement spherical droplets were generated from an aqueous solution of acrylamide, N,N'-methylenebisacrylamide crosslinker and photoinitiator and subsequently photo-cured in situ yielding gel particles in a sub millimeter range. These particles were separated, dried under reduced pressure and re-swollen in water containing Rhod-5N tri potassium salt as calcium ion selective fluorescence probe. After that the particles were dried again and stored for further investigations. Upon exposure of dried particles to calcium chloride solutions they swell and take up Ca2+-ions forming a strong fluorescing complex with Rhod-5N. Thus, fluorescence intensity increases with calcium ion concentration. Up to ca. 0.50 mM the enhancement effect is strong and then becomes considerably weaker. The intensity-concentration-dependence is well described by an equation derived from the equilibrium of the formation of a 1:1 Ca2+:Rhod-5N complex. The particles allow for a fast optical determination of Ca2+-concentrations up to 0.50 mM in analyte volumes down to below 10 μL.

| S-EPMC8456324 | biostudies-literature

A Novel BODIPY Quaternary Ammonium Salt-Based Fluorescent Probe: Synthesis, Physical Properties, and Live-Cell Imaging.

Project description:The development of biological fluorescent probes is of great significance to the field of cancer bio-imaging. However, most current probes within the bulky hydrophobic group have limited application in aqueous medium and restricted imaging under physiological conditions. Herein, we proposed two efficient molecules to study their physical properties and imaging work, and the absorption and fluorescence intensity were collected with varying ions attending in aqueous medium. We enhance the water solubility through the quaternization reaction and form a balance between hydrophilic and hydrophobicity with dipyrrome-theneboron difluoride (BODIPY) fluorophore. We introduced pyridine and dimethylaminopyridine (DMAP) by quaternization and connected the BODIPY fluorophore by ethylenediamine. The final synthesized probes have achieved ideal affinity with HeLa cells (human cervical carcinoma cell line) in live-cell imaging which could be observed by Confocal Microscope. The probes also have a good affinity with subcutaneous tumor cells in mice in in vivo imaging, which may make them candidates as oncology imaging probes.

| S-EPMC7994363 | biostudies-literature

Dual wavelength asymmetric photochemical synthesis with circularly polarized light.

Project description:Asymmetric photochemical synthesis using circularly polarized (CP) light is theoretically attractive as a means of absolute asymmetric synthesis and postulated as an explanation for homochirality on Earth. Using an asymmetric photochemical synthesis of a dihydrohelicene as an example, we demonstrate the principle that two wavelengths of CP light can be used to control separate reactions. In doing so, a photostationary state (PSS) is set up in such a way that the enantiomeric induction intrinsic to each step can combine additively, significantly increasing the asymmetric induction possible in these reactions. Moreover, we show that the effects of this dual wavelength approach can be accurately determined by kinetic modelling of the PSS. Finally, by coupling a PSS to a thermal reaction to trap the photoproduct, we demonstrate that higher enantioselectivity can be achieved than that obtainable with single wavelength irradiation, without compromising the yield of the final product.

| S-EPMC5707454 | 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