Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ultrabright photoactivatable fluorophores created by reductive caging.

ABSTRACT: Sub-diffraction-limit imaging can be achieved by sequential localization of photoactivatable fluorophores, for which the image resolution depends on the number of photons detected per localization. We report a strategy for fluorophore caging that creates photoactivatable probes with high photon yields. Upon photoactivation, these probes can provide 10(4)-10(6) photons per localization and allow imaging of fixed samples with resolutions of several nanometers. This strategy can be applied to many fluorophores across the visible spectrum.

SUBMITTER: Vaughan JC

PROVIDER: S-EPMC3561463 | biostudies-literature | 2012 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Ultrabright photoactivatable fluorophores created by reductive caging.

Vaughan Joshua C JC Jia Shu S Zhuang Xiaowei X

Nature methods 20121028 12

Sub-diffraction-limit imaging can be achieved by sequential localization of photoactivatable fluorophores, for which the image resolution depends on the number of photons detected per localization. We report a strategy for fluorophore caging that creates photoactivatable probes with high photon yields. Upon photoactivation, these probes can provide 10(4)-10(6) photons per localization and allow imaging of fixed samples with resolutions of several nanometers. This strategy can be applied to many ...[more]

PMID: 23103881

Similar Datasets

A general design of caging-group-free photoactivatable fluorophores for live-cell nanoscopy.

Project description:The controlled switching of fluorophores between non-fluorescent and fluorescent states is central to every super-resolution fluorescence microscopy (nanoscopy) technique, and the exploration of radically new switching mechanisms remains critical to boosting the performance of established, as well as emerging super-resolution methods. Photoactivatable dyes offer substantial improvements to many of these techniques, but often rely on photolabile protecting groups that limit their applications. Here we describe a general method to transform 3,6-diaminoxanthones into caging-group-free photoactivatable fluorophores. These photoactivatable xanthones (PaX) assemble rapidly and cleanly into highly fluorescent, photo- and chemically stable pyronine dyes upon irradiation with light. The strategy is extendable to carbon- and silicon-bridged xanthone analogues, yielding a family of photoactivatable labels spanning much of the visible spectrum. Our results demonstrate the versatility and utility of PaX dyes in fixed and live-cell labelling for conventional microscopy, as well as the coordinate-stochastic and deterministic nanoscopies STED, PALM and MINFLUX.

| S-EPMC9417988 | biostudies-literature

Photoactivatable Large Stokes Shift Fluorophores for Multicolor Nanoscopy.

Project description:We designed caging-group-free photoactivatable live-cell permeant dyes with red fluorescence emission and ∼100 nm Stokes shifts based on a 1-vinyl-10-silaxanthone imine core structure. The proposed fluorophores undergo byproduct-free one- and two-photon activation, are suitable for multicolor fluorescence microscopy in fixed and living cells, and are compatible with super-resolution techniques such as STED (stimulated emission depletion) and PALM (photoactivated localization microscopy). Use of photoactivatable labels for strain-promoted tetrazine ligation and self-labeling protein tags (HaloTag, SNAP-tag), and duplexing of an imaging channel with another large Stokes shift dye have been demonstrated.

| S-EPMC9880998 | biostudies-literature

Photoactivatable Fluorescent Dyes with Hydrophilic Caging Groups and Their Use in Multicolor Nanoscopy.

Project description:We propose a series of fluorescent dyes with hydrophilic carbamate caging groups that undergo rapid photoactivation under UV (≤400 nm) irradiation but do not undergo spurious two-photon activation with high-intensity (visible or infrared) light of about twice the wavelength. The caged fluorescent dyes and labels derived therefrom display high water solubility and convert upon photoactivation into validated super-resolution and live-cell-compatible fluorophores. In combination with popular fluorescent markers, multiple (up to six)-color images can be obtained with stimulated emission depletion nanoscopy. Moreover, individual fluorophores can be localized with precision <3 nm (standard deviation) using MINSTED and MINFLUX techniques.

| S-EPMC8587603 | biostudies-literature

Fast and Durable Intraoperative Near-infrared Imaging of Ovarian Cancer Using Ultrabright Squaraine Fluorophores.

Project description:The residual tumor after surgery is the most significant prognostic factor of patients with epithelial ovarian cancer. Near-infrared (NIR) fluorescence-guided surgery is actively utilized for tumor localization and complete resection during surgery. However, currently available contrast-enhancing agents display low on-target binding, unfavorable pharmacokinetics, and toxicity, thus not ideal for clinical use. Here we report ultrabright and stable squaraine fluorophores with optimal pharmacokinetics by introducing an asymmetric molecular conformation and surface charges for rapid transporter-mediated cellular uptake. Among the tested, OCTL14 shows low serum binding and rapid distribution into cancer tissue via organic cation transporters (OCTs). Additionally, the charged squaraine fluorophores are retained in lysosomes, providing durable intraoperative imaging in a preclinical murine model of ovarian cancer up to 24 h post-injection. OCTL14 represents a significant departure from the current bioconjugation approach of using a non-targeted fluorophore and would provide surgeons with an indispensable tool to achieve optimal resection.

| S-EPMC9007913 | biostudies-literature

Superresolution imaging of targeted proteins in fixed and living cells using photoactivatable organic fluorophores.

Project description:Superresolution imaging techniques based on sequential imaging of sparse subsets of single molecules require fluorophores whose emission can be photoactivated or photoswitched. Because typical organic fluorophores can emit significantly more photons than average fluorescent proteins, organic fluorophores have a potential advantage in super-resolution imaging schemes, but targeting to specific cellular proteins must be provided. We report the design and application of HaloTag-based target-specific azido DCDHFs, a class of photoactivatable push-pull fluorogens which produce bright fluorescent labels suitable for single-molecule superresolution imaging in live bacterial and fixed mammalian cells.

| S-EPMC2972741 | biostudies-literature

Superionic Conduction in Co-Vacant P2-Nax CoO2 Created by Hydrogen Reductive Elimination.

Project description:The layered P2-Nax MO2 (M: transition metal) system has been widely recognized as electronic or mixed conductor. Here, we demonstrate that Co vacancies in P2-Nax CoO2 created by hydrogen reductive elimination lead to an ionic conductivity of 0.045 S cm(-1) at 25 °C. Using in situ synchrotron X-ray powder diffraction and Raman spectroscopy, the composition of the superionic conduction phase is evaluated to be Na0.61 (H3 O)0.18 Co0.93 O2 . Electromotive force measurements as well as molecular dynamics simulations indicate that the ion conducting species is proton rather than hydroxide ion. The fact that the Co-stoichiometric compound Nax (H3 O)y CoO2 does not exhibit any significant ionic conductivity proves that Co vacancies are essential for the occurrence of superionic conductivity.

| S-EPMC5084920 | biostudies-literature

Bathymodiolus azoricus caging experiment

Project description:Colonization of deep-sea hydrothermal vents by invertebrates was made efficient through their adaptation to a symbiotic lifestyle with chemosynthetic bacteria, the primary producers of these ecosystems. Anatomical adaptations such as the establishment of specialized cells or organs have been evidenced in numerous deep-sea invertebrates. However, very few studies detailed global inter-dependencies between host and symbionts in these ecosystems. In this study, we proposed to describe, using a proteo-transcriptomic approach, the effects of symbionts on the deep-sea mussel Bathymodiolus azoricus’ molecular biology. We induced an in situ depletion of symbionts and compared the proteo-transcriptome of the gills of mussels in three conditions: symbiotic mussels (natural population), symbiont-depleted mussels and aposymbiotic mussels

2019-02-13 | GSE124699 | GEO

Ultrabright fluorescent nanothermometers.

Project description:Here we report on the first ultrabright fluorescent nanothermometers, ∼50 nm-size particles, capable of measuring temperature in 3D and down to the nanoscale. The temperature is measured through the recording of the ratio of fluorescence intensities of fluorescent dyes encapsulated inside the nanochannels of the silica matrix of each nanothermometer. The brightness of each particle excited at 488 nm is equivalent to the fluorescence coming from 150 molecules of rhodamine 6G and 1700 molecules of rhodamine B dyes. The fluorescence of both dyes is excited with a single wavelength due to the Förster resonance energy transfer (FRET). We demonstrate repeatable measurements of temperature with the uncertainty down to 0.4 K and a constant sensitivity of ∼1%/K in the range of 20-50 °C, which is of particular interest for biomedical applications. Due to the high fluorescence brightness, we demonstrate the possibility of measurement of accurate 3D temperature distributions in a hydrogel. The accuracy of the measurements is confirmed by numerical simulations. We further demonstrate the use of single nanothermometers to measure temperature. As an example, 5-8 nanothermometers are sufficient to measure temperature with an error of 2 K (with the measurement time of >0.7 s).

| S-EPMC9418727 | biostudies-literature

Bathymodiolus azoricus caging experiment

Project description:Bathymodiolus azoricus caging experiment

| PRJNA513131 | ENA

Chemotactic self-caging in active emulsions.

Project description:A common feature of biological self-organization is how active agents communicate with each other or their environment via chemical signaling. Such communications, mediated by self-generated chemical gradients, have consequences for both individual motility strategies and collective migration patterns. Here, in a purely physicochemical system, we use self-propelling droplets as a model for chemically active particles that modify their environment by leaving chemical footprints, which act as chemorepulsive signals to other droplets. We analyze this communication mechanism quantitatively both on the scale of individual agent-trail collisions as well as on the collective scale where droplets actively remodel their environment while adapting their dynamics to that evolving chemical landscape. We show in experiment and simulation how these interactions cause a transient dynamical arrest in active emulsions where swimmers are caged between each other's trails of secreted chemicals. Our findings provide insight into the collective dynamics of chemically active particles and yield principles for predicting how negative autochemotaxis shapes their navigation strategy.

| S-EPMC9214524 | 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