Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

BENA435, a new cell-permeant photoactivated green fluorescent DNA probe.

ABSTRACT: N'-(2,8-Dimethoxy-12-methyl-dibenzo [c,h] [1,5] naphthyridin-6-yl)-N,N-dimethyl-propane-1,3-diamine (BENA435) is a new cell-membrane permeant DNA dye with absorption/emission maxima in complex with DNA at 435 and 484 nm. This new reagent is unrelated to known DNA dyes, and shows a distinct preference to bind double-stranded DNA over RNA. Hydrodynamic studies suggest that BENA435 intercalates between the opposite DNA strands. BENA435 fluoresces much stronger when bound to dA/dT rather than dG/dC homopolymers. We evaluated 14 related dibenzonaphthyridine derivatives and found BENA435 to be superior in its in vivo DNA-binding properties. Molecular modelling was used to develop a model of BENA435 intercalation between base pairs of a DNA helix. BENA435 fluorescence in the nuclei of cells increases upon illumination, suggesting photoactivation. BENA435 represents thus the first known cell-permeant photoactivated DNA-binding dye.

SUBMITTER: Erve A

PROVIDER: S-EPMC1409678 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

A nitroreductase responsive and photoactivated fluorescent probe for dual-controlled tumor hypoxia imaging.

Project description:Tumor hypoxia has great importance in tumor progression and resistance to antitumor therapies. To precisely monitor tumor hypoxia, a controllable hypoxia imaging method is meaningful but still lacking. Herein, we develop a dual-controlled tumor hypoxia probe (TNB) by introducing a nitrophenol group and methyltetrazine group to the boron-dipyrromethene (BODIPY) dye. The fluorescence-quenching group nitrophenol is reduced to aminophenol by upregulated nitroreductase in hypoxic tumors, and the photocage methyltetrazine is cleaved by light irradiation. Hence the fluorescence of TNB is dual-controlled by hypoxia and photoactivation. We first evaluated TNB's potential for controllable hypoxia imaging in solution and tumor cells. The fluorescence of TNB under nitroreductase incubation and photoactivation increased more than 60 fold over that which was untreated or only treated with nitroreductase. Furthermore, results validate that TNB possesses photo-controllable activation features in tumor sections. We believe that the probe design based on enzyme and photoactivation responsiveness provides potential for spatiotemporal detection of other biomarkers.

| S-EPMC9396718 | biostudies-literature

Highly Fluorescent Green Carbon Dots as a Fluorescent Probe for Detecting Mineral Water pH.

Project description:In this report, high-brightness green carbon dots were successfully prepared using 3,5-diaminobenzoic acid as the sole precursor and synthesized in one step using a solvothermal strategy. Under the excitation of 365 nm ultraviolet light, the quantum yield of carbon dots is as high as 53.8%. Experiments revealed that the carbon dots are highly carbonized and the surface is rich in amino and carboxyl groups. The synthesized carbon dots have good water solubility, and are resistant to ions and temperature. The fluorescence intensity of CDs is sensitive to pH changes and is linearly correlated with the pH in the near-neutral range (pH = 6.0 to 9.0). Our experiments showed that carbon dots were sensitive and accurate fluorescent probes for measuring the pH value of drinking water, which could provide an effective method for measuring the pH value of water in the future.

| S-EPMC6749429 | biostudies-literature

Quantifying tensile forces at cell-cell junctions with a DNA-based fluorescent probe.

Project description:Cells are physically contacting with each other. Direct and precise quantification of forces at cell-cell junctions is still challenging. Herein, we have developed a DNA-based ratiometric fluorescent probe, termed DNAMeter, to quantify intercellular tensile forces. These lipid-modified DNAMeters can spontaneously anchor onto live cell membranes. The DNAMeter consists of two self-assembled DNA hairpins of different force tolerance. Once the intercellular tension exceeds the force tolerance to unfold a DNA hairpin, a specific fluorescence signal will be activated, which enables the real-time imaging and quantification of tensile forces. Using E-cadherin-modified DNAMeter as an example, we have demonstrated an approach to quantify, at the molecular level, the magnitude and distribution of E-cadherin tension among epithelial cells. Compatible with readily accessible fluorescence microscopes, these easy-to-use DNA tension probes can be broadly used to quantify mechanotransduction in collective cell behaviors.

| S-EPMC8163409 | biostudies-literature

Detection of cell carcinogenic transformation by a quadruplex DNA binding fluorescent probe.

Project description:Cancer can be easily treated when found early. A probe capable of detecting cell transformation may increase the success rate of early diagnosis of cancer. In this report we have tested the ability of a fluorescent, quadruplex DNA binding probe, 3,6-bis(1-methyl-4- vinylpyridinium) carbazole diiodide (BMVC), to detect cell transformation in vitro. BMVC was applied to living cells in several different models of cell transformation, and the fluorescence signals of BMVC were measured. The degrees of cell transformation in these models were characterized by alterations in cellular morphological phenotype and subcellular organization. When BMVC probes were applied, the number of BMVC-positive cells increased in accordance with the degree of transformation. BMVC was capable of significantly detecting formation of foci, increased cellular motility, cell proliferation, cell apoptosis, anchorage-independent growth, and increased invasiveness of transformed cells. These results demonstrate the ability of BMVC probes to detect cell transformation and indicate that BMVC is of promise for use as a probe in early cancer detection.

| S-EPMC3904876 | biostudies-literature

What Makes Thienoguanosine an Outstanding Fluorescent DNA Probe?

Project description:Thienoguanosine (thG) is an isomorphic guanosine (G) surrogate that almost perfectly mimics G in nucleic acids. To exploit its full potential and lay the foundation for future applications, 20 DNA duplexes, where the bases facing and neighboring thG were systematically varied, were thoroughly studied using fluorescence spectroscopy, molecular dynamics simulations, and mixed quantum mechanical/molecular mechanics calculations, yielding a comprehensive understanding of its photophysics in DNA. In matched duplexes, thG's hypochromism was larger for flanking G/C residues but its fluorescence quantum yield (QY) and lifetime values were almost independent of the flanking bases. This was attributed to high duplex stability, which maintains a steady orientation and distance between nucleobases, so that a similar charge transfer (CT) mechanism governs the photophysics of thG independently of its flanking nucleobases. thG can therefore replace any G residue in matched duplexes, while always maintaining similar photophysical features. In contrast, the local destabilization induced by a mismatch or an abasic site restores a strong dependence of thG's QY and lifetime values on its environmental context, depending on the CT route efficiency and solvent exposure of thG. Due to this exquisite sensitivity, thG appears ideal for monitoring local structural changes and single nucleotide polymorphism. Moreover, thG's dominant fluorescence lifetime in DNA is unusually long (9-29 ns), facilitating its selective measurement in complex media using a lifetime-based or a time-gated detection scheme. Taken together, our data highlight thG as an outstanding emissive substitute for G with good QY, long fluorescence lifetimes, and exquisite sensitivity to local structural changes.

| S-EPMC7544670 | biostudies-literature

Blue‐shifting green fluorescent proteins using REPLACE

Project description:In the directed evolution experiments of EGFP or StayGold, the objective was to blue-shift the excitation light spectrum of GFP towards shorter wavelengths, resulting in an enhancement of fluorescence intensity upon 405 nm laser excitation. This facilitates the advancement of novel fluorescent proteins. These experiments represent a category of experiments that utilize REPLACE to achieve discontinuous directed evolution through FACS sorting (screening).

2024-09-30 | GSE271876 | GEO

Development of Photoactivated Fluorescent N-Hydroxyoxindoles and Their Application for Cell-Selective Imaging.

Project description:Photoactivatable fluorophores are essential tools for studying the dynamic molecular interactions within important biological systems with high spatiotemporal resolution. However, currently developed photoactivatable fluorophores based on conventional dyes have several limitations including reduced photoactivation efficiency, cytotoxicity, large molecular size, and complicated organic synthesis. To overcome these challenges, we herein report a class of photoactivatable fluorescent N-hydroxyoxindoles formed through the intramolecular photocyclization of substituted o-nitrophenyl ethanol (ONPE). These oxindole fluorophores afford excellent photoactivation efficiency with ultra-high fluorescence enhancement (up to 800-fold) and are small in size. Furthermore, the oxindole derivatives show exceptional biocompatibility by generating water as the only photolytic side product. Moreover, structure-activity relationship analysis clearly revealed the strong correlation between the fluorescent properties and the substituent groups, which can serve as a guideline for the further development of ONPE-based fluorescent probes with desired photophysical and biological properties. As a proof-of-concept, we demonstrated the capability of a new substituted ONPE that has an uncaging wavelength of 365-405?nm and an excitation/emission at 515 and 620?nm, for the selective imaging of a cancer cell line (Hela cells) and a human neural stem cell line (hNSCs).

| S-EPMC5808866 | biostudies-literature

Photoactivated Refractive Index Anisotropy in Fluorescent Thiophene Derivatives.

Project description:The optical control of anisotropy in materials is highly advantageous for many technological applications, including the real-time modulation of another light signal in photonic switches and sensors. Here, we introduce three thiophene derivatives with a donor-acceptor structure, which feature different positions of an electron-acceptor nitrile group, and both photoalignment and luminescence properties. Quantum chemical calculations highlight the presence of trans-forms stable at room temperature and metastable cis-isomers. Besides photoluminescence peaked at 440-460 nm and 0.4 ns lifetime, the three nonlinear optical chromophores exhibit photoinduced anisotropy of the refractive index closely depending on the specific molecular structure, with higher values of birefringence at lower driving signal being obtained for ortho substitution of the nitrile group. All-optical modulation of an external light beam at rates of hundreds of hertz is demonstrated in the fluorescent systems. This finding opens an interesting route to multispectral photonic switches embedded in the active layers of light-emitting devices.

| S-EPMC7706105 | biostudies-literature

A new strategy to photoactivate green fluorescent protein.

Project description: Not available

| S-EPMC2953579 | biostudies-literature

Singlet oxygen imaging using fluorescent probe Singlet Oxygen Sensor Green in photosynthetic organisms.

Project description:Formation of singlet oxygen (1O2) was reported to accompany light stress in plants, contributing to cell signaling or oxidative damage. So far, Singlet Oxygen Sensor Green (SOSG) has been the only commercialized fluorescent probe for 1O2 imaging though it suffers from several limitations (unequal penetration and photosensitization) that need to be carefully considered to avoid misinterpretation of the analysed data. Herein, we present results of a comprehensive study focused on the appropriateness of SOSG for 1O2 imaging in three model photosynthetic organisms, unicellular cyanobacteria Synechocystis sp. PCC 6803, unicellular green alga Chlamydomonas reinhardtii and higher plant Arabidopsis thaliana. Penetration of SOSG differs in both unicellular organisms; while it is rather convenient for Chlamydomonas it is restricted by the presence of mucoid sheath of Synechocystis, which penetrability might be improved by mild heating. In Arabidopsis, SOSG penetration is limited due to tissue complexity which can be increased by pressure infiltration using a shut syringe. Photosensitization of SOSG and SOSG endoperoxide formed by its interaction with 1O2 might be prevented by illumination of samples by a red light. When measured under controlled conditions given above, SOSG might serve as specific probe for detection of intracellular 1O2 formation in photosynthetic organisms.

| S-EPMC6135792 | 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