Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Synthesis of Functional Fluorescent BODIPY-based Dyes through Electrophilic Aromatic Substitution: Straightforward Approach towards Customized Fluorescent Probes.

ABSTRACT: Fluorescent materials are widely used in biological and material applications as probes for imaging or sensing; however, their customization is usually complicated without the support of an organic chemistry laboratory. Here, we present a straightforward method for the customization of BODIPY cores, which are among the most commonly used fluorescent probes. The method is based on the formation of a new C-C bond through Friedel-Crafts electrophilic aromatic substitution carried out at room temperature. The method presented can be used to obtain completely customized fluorescent materials in one or two steps from commercially available compounds. Examples of the preparation of fluorescent materials for cell staining and functionalization of silica colloids are also presented.

SUBMITTER: Mirri G

PROVIDER: S-EPMC5062010 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Synthesis of Functional Fluorescent BODIPY-based Dyes through Electrophilic Aromatic Substitution: Straightforward Approach towards Customized Fluorescent Probes.

Mirri Giorgio G Schoenmakers Daniël C DC Kouwer Paul H J PH Veranič Peter P Muševič Igor I Štefane Bogdan B

ChemistryOpen 20160819 5

Fluorescent materials are widely used in biological and material applications as probes for imaging or sensing; however, their customization is usually complicated without the support of an organic chemistry laboratory. Here, we present a straightforward method for the customization of BODIPY cores, which are among the most commonly used fluorescent probes. The method is based on the formation of a new C-C bond through Friedel-Crafts electrophilic aromatic substitution carried out at room temper ...[more]

PMID: 27777837

Similar Datasets

A Straightforward Substitution Strategy to Tune BODIPY Dyes Spanning the Near-Infrared Region via Suzuki⁻Miyaura Cross-Coupling.

Project description:In this study, a series of new red and near-infrared (NIR) dyes derived from 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) were developed by introducing thiophene and its derivatives to the 3- and 5- positions of the dichloroBODIPY core. For the first time, cyclictriol boronates and N-methyliminodiacetic acid (MIDA) boronate were used as organoboron species to couple with 3,5-dichloroBODIPY via the one-step Suzuki⁻Miyaura cross-coupling. Six kinds of thieno-expended BODIPY dyes were synthesized in acceptable yields ranging from 31% to 79%. All six dyes showed different absorption and emission wavelengths spanning a wide range (c.a. 600⁻850 nm) in the red and NIR regions with relatively high quantum yields (19⁻85%). Cellular imaging of 8-(2,6-dimethylphenyl)-re3,5-di(2-thienyl)-BODIPY (dye 1) was conducted using bovine cumulus cells, and the fluorescence microscopy images indicated that the chromophore efficiently accumulated and was exclusively localized in the cytoplasm, suggesting it could be utilized as a subcellular probe. All six dyes were characterized using 1H-NMR and mass spectrometry.

| S-EPMC6117675 | biostudies-literature

Electrophilic aromatic substitution of a BN indole.

Project description:We report the first examples of a "BN-fused" indole, and we demonstrate that this new family of unnatural indole derivatives undergoes electrophilic aromatic substitution (EAS) reactions with the same regioselectivity as its organic analogue. Competition experiments reveal that N-t-Bu-BN-indole is more nucleophilic in EAS reactions than its carbonaceous counterpart. X-ray structural analysis between BN indole and classic indole highlights significant differences in bond distances, in particular for bonds associated with the boron atom.

| S-EPMC2990470 | biostudies-literature

Oligoethylene glycol-substituted aza-BODIPY dyes as red emitting ER-probes.

Project description:This study features aza-BODIPY (BF2-chelated azadipyrromethene) dyes with two aromatic substituents linked by oligoethylene glycol fragments to increase hydrophilicity of aza-BODIPY for applications in intracellular imaging. To prepare these, two chalcones were attached ?,? onto oligoethylene glycol fragments, then reacted with nitromethane anion. Conjugate addition products from this reaction were then subjected to typical conditions for synthesis of aza-BODIPY dyes (NH4OAc, (n)BuOH, 120 °C); formation of boracycles in this reaction was concomitant with creation of macrocycles containing the oligoethylene glycol fragments. Similar dyes with acyclic oligoelythene glycol substituents in the same position were used to compare the efficiencies of the intra- and inter-molecular aza-BODIPY forming reactions, and the characteristics of the products. All the fluors with oligoethylene glycol fragments, i.e. cyclic or acyclic, localized in the endoplasmic reticulum of a fibroblast cell line (WEHI-13VAR), the human pancreatic cancer cell line (PANC-1, rough ER predominates) and human liver cancer cell line (HepG2, smooth ER prevalent). These fluors are potentially useful for near IR (?max emis at 730 nm) ER staining probes.

| S-EPMC4512840 | biostudies-literature

BODIPY-Based Fluorescent Probes for Sensing Protein Surface-Hydrophobicity.

Project description:Mapping surface hydrophobic interactions in proteins is key to understanding molecular recognition, biological functions, and is central to many protein misfolding diseases. Herein, we report synthesis and application of new BODIPY-based hydrophobic sensors (HPsensors) that are stable and highly fluorescent for pH values ranging from 7.0 to 9.0. Surface hydrophobic measurements of proteins (BSA, apomyoglobin, and myoglobin) by these HPsensors display much stronger signal compared to 8-anilino-1-naphthalene sulfonic acid (ANS), a commonly used hydrophobic probe; HPsensors show a 10- to 60-fold increase in signal strength for the BSA protein with affinity in the nanomolar range. This suggests that these HPsensors can be used as a sensitive indicator of protein surface hydrophobicity. A first principle approach is used to identify the molecular level mechanism for the substantial increase in the fluorescence signal strength. Our results show that conformational change and increased molecular rigidity of the dye due to its hydrophobic interaction with protein lead to fluorescence enhancement.

| S-EPMC4683377 | biostudies-literature

Arenium ions are not obligatory intermediates in electrophilic aromatic substitution.

Project description:Our computational and experimental investigation of the reaction of anisole with Cl2 in nonpolar CCl4 solution challenges two fundamental tenets of the traditional SEAr (arenium ion) mechanism of aromatic electrophilic substitution. Instead of this direct substitution process, the alternative addition-elimination (AE) pathway is favored energetically. This AE mechanism rationalizes the preferred ortho and para substitution orientation of anisole easily. Moreover, neither the SEAr nor the AE mechanisms involve the formation of a ?-complex (Wheland-type) intermediate in the rate-controlling stage. Contrary to the conventional interpretations, the substitution (SEAr) mechanism proceeds concertedly via a single transition state. Experimental NMR investigations of the anisole chlorination reaction course at various temperatures reveal the formation of tetrachloro addition by-products and thus support the computed addition-elimination mechanism of anisole chlorination in nonpolar media. The important autocatalytic effect of the HCl reaction product was confirmed by spectroscopic (UV-visible) investigations and by HCl-augmented computational modeling.

| S-EPMC4104905 | biostudies-other

Fluorescent Chitosan Modified with Heterocyclic Aromatic Dyes.

Project description:Chitosan is a valuable, functional, and biodegradable polysaccharide that can be modified to expand its applications. This work aimed to obtain chitosan derivatives with fluorescent properties. Three heterocyclic aromatic dyes (based on benzimidazole, benzoxazole, and benzothiazole) were synthesized and used for the chemical modification of chitosan. Emission spectroscopy revealed the strong fluorescent properties of the obtained chitosan derivatives even at a low N-substitution degree of the dye. The effect of high-energy ultraviolet radiation (UV-C) on modified chitosan samples was studied in solution with UV-Vis spectroscopy and in the solid state with FTIR spectroscopy. Moreover, cytotoxicity towards three different cell types was evaluated to estimate the possibilities of biomedical applications of such fluorescent chitosan-based materials. It was found that the three new derivatives of chitosan were characterized by good resistance to UV-C, which suggests the possibility of using these materials in medicine and various industrial sectors.

| S-EPMC8585458 | biostudies-literature

Fluorinated Boron-Dipyrromethene (BODIPY) Dyes: Bright and Versatile Probes for Surface Analysis.

Project description:A family of bright boron-dipyrromethene-type fluorophores with a high number of fluorine atoms (F-BODIPYs) has been developed and characterized by X-ray crystallography and optical spectroscopy. The introduction of 3,5-bis(trifluoromethyl)phenyl and pentafluorophenyl moieties significantly enhances the photostability of such dyes, yielding for instance photostable near-infrared (NIR) fluorophores that show emission maxima>750 nm, when the BODIPY's π system is extended with two (dimethylamino)styryl and (dimethylamino)naphthastyryl moieties, or green-emitting BODIPYs with fluorescence quantum yields of unity. When equipped with a suitable group that selectively reacts for instance with amines, F-BODIPYs can be used as potent dual labels for the quantification of primary amino groups on surfaces by X-ray photoelectron spectroscopy (XPS) and fluorescence, two powerful yet complementary tools for the analysis of organic surface functional groups. The advantage of reactive F-BODIPYs is that they allow a fast and non-destructive mapping of the labelled supports with conventional fluorescence scanners and a subsequent quantification of selected areas of the same sample by the potentially traceable XPS technique. The performance is exemplarily shown here for the assessment of the amino group density on SiO2 supports, one of the most common reactive silica supports, in particular, for standard microarray applications.

| S-EPMC3594589 | biostudies-literature

Precise through-space control of an abiotic electrophilic aromatic substitution reaction.

Project description:Nature has evolved selective enzymes for the efficient biosynthesis of complex products. This exceptional ability stems from adapted enzymatic pockets, which geometrically constrain reactants and stabilize specific reactive intermediates by placing electron-donating/accepting residues nearby. Here we perform an abiotic electrophilic aromatic substitution reaction, which is directed precisely through space. Ester arms-positioned above the planes of aromatic rings-enable it to distinguish between nearly identical, neighbouring reactive positions. Quantum mechanical calculations show that, in two competing reaction pathways, both [C-H···O]-hydrogen bonding and electrophile preorganization by coordination to a carbonyl group likely play a role in controlling the reaction. These through-space-directed mechanisms are inspired by dimethylallyl tryptophan synthases, which direct biological electrophilic aromatic substitutions by preorganizing dimethylallyl cations and by stabilizing reactive intermediates with [C-H···N]-hydrogen bonding. Our results demonstrate how the third dimension above and underneath aromatic rings can be exploited to precisely control electrophilic aromatic substitutions.

| S-EPMC5382318 | biostudies-literature

A straightforward synthesis of phenyl boronic acid (PBA) containing BODIPY dyes: new functional and modular fluorescent tools for the tethering of the glycan domain of antibodies.

Project description:We report here on the efficient and straightforward synthesis of a series of modular and functional PBA-BODIPY dyes 1-4. They are an outstanding example of the efficient merge of the versatility of the 3,5-dichloro-BODIPY derivatives and the receptor-like ability of the PBA moiety. The potential bioanalytical applicability of these tools was assessed by measuring the binding to glycan chains of antibodies by a Quartz Crystal Microbalance (QCM).

| S-EPMC9072199 | biostudies-literature

Two ?-Electrons Make the Difference: From BODIPY to BODIIM Switchable Fluorescent Dyes.

Project description:(aza-)BODIPY dyes (boron dipyrromethene dyes) are well-established fluorophores due to their large quantum yields, stability, and diversity, which led to promising applications including imaging techniques, sensors, organic (opto)electronic materials, or biomedical applications. Although the control of the optical properties in (aza-)BODIPY dyes by peripheral functional groups is well studied, we herein present a novel approach to modify the 12??-electron core of the dipyrromethene scaffold. The replacement of two carbon atoms in the ?-position of a BODIPY dye by two nitrogen atoms afforded a 14??-electron system, which was termed BODIIM (boron diimidazolylmethene) in systematic analogy to the BODIPY dyes. Remarkably, the BODIIM dye was obtained with a BH2 -rigidifying entity, which is currently elusive and highly sought after for the BODIPY dye class. DFT-Calculations confirm the [12+2] ?-electron relationship between BODIPY and BODIIM and reveal a strong shape correlation between LUMO in the BODIPY and the HOMO of the BODIIM. The modification of the ?-system leads to a dramatic shift of the optical properties, of which the fluorescent emission is most noteworthy and occurs at much larger Stokes shift, that is, ?500?cm-1 in BODIPY versus >4170?cm-1 in BODIIM system in all solvents investigated. Nucleophilic reactivity was found at the meso-carbon atom in the formation of stable borane adducts with a significant shift of the fluorescent emission, and this behavior contrasts the reactivity of conventional BODIPY systems. In addition, the reverse decomplexation of the borane adducts was demonstrated in reactions with a representative N-heterocyclic carbene to retain the strongly fluorescent BODIIM compound, which suggests applications as fully reversible fluorescent switch.

| S-EPMC7027818 | 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