Browse
Submit Data
Databases
API
Help

Dataset Information

19 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

General Synthetic Method for Si-Fluoresceins and Si-Rhodamines.

ABSTRACT: The century-old fluoresceins and rhodamines persist as flexible scaffolds for fluorescent and fluorogenic compounds. Extensive exploration of these xanthene dyes has yielded general structure-activity relationships where the development of new probes is limited only by imagination and organic chemistry. In particular, replacement of the xanthene oxygen with silicon has resulted in new red-shifted Si-fluoresceins and Si-rhodamines, whose high brightness and photostability enable advanced imaging experiments. Nevertheless, efforts to tune the chemical and spectral properties of these dyes have been hindered by difficult synthetic routes. Here, we report a general strategy for the efficient preparation of Si-fluoresceins and Si-rhodamines from readily synthesized bis(2-bromophenyl)silane intermediates. These dibromides undergo metal/bromide exchange to give bis-aryllithium or bis(aryl Grignard) intermediates, which can then add to anhydride or ester electrophiles to afford a variety of Si-xanthenes. This strategy enabled efficient (3-5 step) syntheses of known and novel Si-fluoresceins, Si-rhodamines, and related dye structures. In particular, we discovered that previously inaccessible tetrafluorination of the bottom aryl ring of the Si-rhodamines resulted in dyes with improved visible absorbance in solution, and a convenient derivatization through fluoride-thiol substitution. This modular, divergent synthetic method will expand the palette of accessible xanthenoid dyes across the visible spectrum, thereby pushing further the frontiers of biological imaging.

SUBMITTER: Grimm JB

PROVIDER: S-EPMC5620978 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Synthesis of rhodamines from fluoresceins using Pd-catalyzed C-N cross-coupling.

Project description:A unified, convenient, and efficient strategy for the preparation of rhodamines and N,N'-diacylated rhodamines has been developed. Fluorescein ditriflates were found to undergo palladium-catalyzed C-N cross-coupling with amines, amides, carbamates, and other nitrogen nucleophiles to provide direct access to known and novel rhodamine derivatives, including fluorescent dyes, quenchers, and latent fluorophores.

| S-EPMC3235915 | biostudies-literature

Synthetic dimension band structures on a Si CMOS photonic platform.

Project description:Synthetic dimensions, which simulate spatial coordinates using nonspatial degrees of freedom, are drawing interest in topological science and other fields for modeling higher-dimensional phenomena on simple structures. We present the first realization of a synthetic frequency dimension on a silicon ring resonator integrated photonic device fabricated using a CMOS process. We confirm that its coupled modes correspond to a one-dimensional tight-binding model through acquisition of up to 280-GHz bandwidth optical frequency comb-like spectra and by measuring synthetic band structures. Furthermore, we realized two types of gauge potentials along the frequency dimension and probed their effects through the associated band structures. An electric field analog was produced via modulation detuning, whereas effective magnetic fields were induced using synchronized nearest- and second nearest-neighbor couplings. Creation of coupled mode lattices and two effective forces on a monolithic Si CMOS device represents a key step toward wider adoption of topological principles.

| S-EPMC8797776 | biostudies-literature

Sulfone Rhodamines for Voltage Imaging.

Project description:Fluorescent indicators that respond to changes in biological membrane potentials provide a powerful complement to existing methods for monitoring neuronal activity. Indicators that absorb and emit in the near infrared window are especially attractive, since lower energy wavelengths excite fewer biological molecules and can penetrate more deeply into biological tissues. In this work, we incorporate sulfone rhodamine chromophores into a voltage-sensitive scaffold in order to generate voltage sensitive fluorophores which absorb and emit above 700 nm. These Sulfone Rhodamine Voltage Reporters (SuRhoVRs) partition into cell membranes and display good sensitivity to membrane potential changes. The most sensitive SuRhoVR derivative also displays excellent photostability and can track membrane potential changes in dissociated rat hippocampal neurons.

| S-EPMC9772261 | biostudies-literature

General synthetic approach to functionalized dihydrooxepines.

Project description:A three-step sequence to access functionalized 4,5-dihydrooxepines from cyclohexenones has been developed. This approach features a regioselective Baeyer-Villiger oxidation and subsequent functionalization via the corresponding enol phosphate intermediate.

| S-EPMC3653422 | biostudies-literature

Selective Hg(II) detection in aqueous solution with thiol derivatized fluoresceins.

Project description:The syntheses and photophysical properties of mercury sensors 2 and 3 (MS2 and MS3), two asymmetrically derivatized fluorescein-based dyes designed for Hg(II) detection, are described. These sensors each contain a single pyridyl-amine-thiol metal-binding moiety, form 1:1 complexes with Hg(II), and exhibit selectivity for Hg(II) over other Group 12 metals, alkali and alkaline earth metals, and most divalent first-row transition metals. Both dyes display superior brightness (Phi x epsilon) and fluorescence enhancement following Hg(II) coordination in aqueous solution. At neutral pH, the fluorescence turn-on derives from greater brightness due to increased molar absorptivity. At higher pH, photoinduced electron transfer quenching of the free dye is enhanced, and the Hg(II)-induced turn-on also benefits from alleviation of this pathway. MS2 can detect ppb levels of Hg(II) in aqueous solution, demonstrating its ability to identify environmentally relevant concentrations of Hg(II).

| S-EPMC2495028 | biostudies-literature

Spiroguanidine rhodamines as fluorogenic probes for lysophosphatidic acid.

Project description:Direct determination of total lysophosphatidic acid (LPA) was accomplished using newly developed spiroguanidines derived from rhodamine B as universal fluorogenic probes. Optimum conditions for the quantitative analysis of total LPA were investigated. The linear range for the determination of total LPA is up to 5 ?M with a limit of detection of 0.512 ?M.

| S-EPMC4320994 | biostudies-literature

Synthesis of 5- and 6-carboxy-X-rhodamines.

Project description:An efficient route is reported to 5- and 6-carboxy-X-rhodamines (compounds 1 and 2) that contain multiple n-propylene or gamma,gamma-dimethylpropylene groups bridging terminal nitrogen atoms and the central xanthene core. Gram quantities of these dyes are synthesized from inexpensive starting materials. The isolated products are activated by selective transformation of the carboxylic acid group into N-hydroxysuccinimidyl esters in situ and then conjugated with an amino group of a molecule of interest.

| S-EPMC2646678 | biostudies-literature

RNA-seq data of si-Snai1, si-Snai2, si-Snai1/2 and si-Scrambled treated mouse primary myoblasts

Project description:In skeletal myogenesis, the transcription factor MyoD, activates distinct transcriptional programs in progenitors compared to terminally differentiated cells. Using ChIP-seq and gene expression analyses, we show that in primary myoblasts, Snai1/2-HDAC1/2 repressive complex bind and exclude MyoD from its targets. Notably, Snail binds E-box motifs that are G/C-rich in their central dinucleotides, and such sites are almost exclusively associated with genes expressed during differentiation. By contrast, Snai1/2 does not bind the A/T-rich E-boxes associated with MyoD targets in myoblasts. Thus, Snai1/2-HDAC1/2 prevents MyoD occupancy on differentiation-specific regulatory elements and the change from Snail1/2- to MyoD-binding often results in enhancer switching during differentiation. Furthermore, we show that a regulatory network involving Myogenic Regulatory Factors (MRFs), Snail/2, miR-30a and miR-206 acts as a molecular switch that controls entry into myogenic differentiation. Together, these results reveal a regulatory paradigm that directs distinct gene expression programs in progenitors versus terminally differentiated cells. In vivo depletion of transcription factor with siRNA followed by whole transcriptome analysis (RNA-seq) to identify target genes.

2012-07-04 | E-GEOD-38236 | biostudies-arrayexpress

Photoactivation of silicon rhodamines via a light-induced protonation.

Project description:Photoactivatable fluorophores are important for single-particle tracking and super-resolution microscopy. Here we present a photoactivatable fluorophore that forms a bright silicon rhodamine derivative through a light-dependent protonation. In contrast to other photoactivatable fluorophores, no caging groups are required, nor are there any undesired side-products released. Using this photoactivatable fluorophore, we create probes for HaloTag and actin for live-cell single-molecule localization microscopy and single-particle tracking experiments. The unusual mechanism of photoactivation and the fluorophore's outstanding spectroscopic properties make it a powerful tool for live-cell super-resolution microscopy.

| S-EPMC6783549 | biostudies-literature

General synthetic route to cell-permeable block copolymers via ROMP.

Project description:The applications of block copolymers are myriad, ranging from electronics to functionalized resins to therapeutics. The ring-opening metathesis polymerization (ROMP) is an especially valuable reaction for block copolymer assembly because each block can be generated with length control. We sought to use this polymerization to expand the repertoire of block copolymers by implementing a strategy that involves postpolymerization modification of a backbone bearing selectively reactive groups. To this end, we demonstrate that ROMP can be used to synthesize a block copolymer scaffold that possesses three types of functional groups-a succinimidyl ester, an alpha-chloroacetamide group, and a ketone-each of which can be modified independently. Thus, a single scaffold can be elaborated to afford a wide range of block copolymers. Exploiting this synthetic approach and the length control offered by ROMP, we assemble block copolymers capable of traversing the membrane and entering mammalian cells.

| S-EPMC2750816 | 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