Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ncm, a Photolabile Group for Preparation of Caged Molecules: Synthesis and Biological Application.

ABSTRACT: Ncm, 6-nitrocoumarin-7-ylmethyl, is a photolabile protective group useful for making "caged" molecules. Ncm marries the reliable photochemistry of 2-nitrobenzyl systems with the excellent stability and spectroscopic properties of the coumarin chromophore. From simple, commercially available starting materials, preparation of Ncm and its caged derivatives is both quick and easy. Photorelease of Ncm-caged molecules occurs on the microsecond time scale, with quantum efficiencies of 0.05-0.08. We report the synthesis and physical properties of Ncm and its caged derivatives. The utility of Ncm-caged glutamate for neuronal photostimulation is demonstrated in cultured hippocampal neurons and in brain slice preparations.

SUBMITTER: Muralidharan S

PROVIDER: S-EPMC5047466 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Ncm, a Photolabile Group for Preparation of Caged Molecules: Synthesis and Biological Application.

Muralidharan Sukumaran S Dirda Nathaniel D A ND Katz Elizabeth J EJ Tang Cha-Min CM Bandyopadhyay Sharba S Kanold Patrick O PO Kao Joseph P Y JP

PloS one 20161003 10

Ncm, 6-nitrocoumarin-7-ylmethyl, is a photolabile protective group useful for making "caged" molecules. Ncm marries the reliable photochemistry of 2-nitrobenzyl systems with the excellent stability and spectroscopic properties of the coumarin chromophore. From simple, commercially available starting materials, preparation of Ncm and its caged derivatives is both quick and easy. Photorelease of Ncm-caged molecules occurs on the microsecond time scale, with quantum efficiencies of 0.05-0.08. We re ...[more]

PMID: 27695074

Similar Datasets

A Photolabile Carboxyl Protecting Group for Solid Phase Peptide Synthesis.

Project description:A new kind of photolabile protecting group (PLPG) for carboxyl moieties was designed and synthesized as the linker between resin and peptide. This group can be used for the protection of amino acid carboxyl groups. The peptide was synthesized on Nph (2-hydroxy-3-(2-nitrophenyl)-heptanoic acid)-derivatized resins and could be cleaved under UV exposure, thus avoiding the necessity for harsh acid-mediated resin cleavage. The PLPG has been successfully used for solid-phase synthesis of peptides.

| S-EPMC8080293 | biostudies-literature

Synthesis of Cyclic Peptides in SPPS with Npb-OH Photolabile Protecting Group.

Project description:Significant efforts have been made in recent years to identify more environmentally benign and safe alternatives to side-chain protection and deprotection in solid-phase peptide synthesis (SPPS). Several protecting groups have been endorsed as suitable candidates, but finding a greener protecting group in SPPS has been challenging. Here, based on the 2-(o-nitrophenyl) propan-1-ol (Npp-OH) photolabile protecting group, a structural modification was carried out to synthesize a series of derivatives. Through experimental verification, we found that 3-(o-Nitrophenyl) butan-2-ol (Npb-OH) had a high photo-release rate, high tolerance to the key conditions of Fmoc-SPPS (20% piperidine DMF alkaline solution, and pure TFA acidic solution), and applicability as a carboxyl-protective group in aliphatic and aromatic carboxyl groups. Finally, Npb-OH was successfully applied to the synthesis of head-tail cyclic peptides and side-chain-tail cyclic peptides. Moreover, we found that Npb-OH could effectively resist diketopiperazines (DKP). The α-H of Npb-OH was found to be necessary for its photosensitivity in comparison to 3-(o-Nitrophenyl)but-3-en-2-ol (Npbe-OH) during photolysis-rate verification.

| S-EPMC9000773 | biostudies-literature

Improved Synthesis of Caged Glutamate and Caging Each Functional Group.

Project description:Glutamate is an excitatory neurotransmitter that controls numerous pathways in the brain. Neuroscientists make use of photoremovable protecting groups, also known as cages, to release glutamate with precise spatial and temporal control. Various cage designs have been developed and among the most effective has been the nitroindolinyl caging of glutamate. We, hereby, report an improved synthesis of one of the current leading molecules of caged glutamate, 4-carboxymethoxy-5,7-dinitroindolinyl glutamate (CDNI-Glu), which possesses efficiencies with the highest reported quantum yield of at least 0.5. We present the shortest route, to date, for the synthesis of CDNI-Glu in 4 steps, with a total reaction time of 40 h and an overall yield of 20%. We also caged glutamate at the other two functional groups, thereby, introducing two new cage designs: ?-CDNI-Glu and N-CDNI-Glu. We included a study of their photocleavage properties using UV-vis, NMR, as well as a physiology experiment of a two-photon uncaging of CDNI-Glu in acute hippocampal brain slices. The newly introduced cage designs may have the potential to minimize the interference that CDNI-Glu has with the GABAA receptor. We are broadly disseminating this to enable neuroscientists to use these photoactivatable tools.

| S-EPMC6294478 | biostudies-literature

Chemo-enzymatic synthesis and biological evaluation of photolabile nicotinic acid adenine dinuclotide phosphate (NAADP+).

Project description:A chemo-enzymatic synthesis of novel caged NAADP+ without the formation of multiple cage compounds has been achieved. The biological activity of the caged NAADP+ was demonstrated by its fast uncaging in intact sea-urchin eggs.

| S-EPMC2518626 | biostudies-literature

Improved synthesis of the two-photon caging group 3-nitro-2-ethyldibenzofuran and its application to a caged thymidine phosphoramidite.

Project description:A new and efficient route to the recently reported 3-nitro-2-ethyldibenzofuran caging group was developed. Furthermore, its installation on a thymidine phosphoramidite is described. This caging group is efficiently removed through light-irradiation at 365 nm.

| S-EPMC2830370 | biostudies-literature

Resolution of ntla-dependent transcriptome using caged molecules

Project description:This SuperSeries is composed of the SubSeries listed below.

2012-03-01 | GSE31882 | GEO

Preparation of Electrospun Active Molecules Membrane Application to Atmospheric Free Radicals.

Project description:Atmospheric reactive oxygen species (ROS) play a key role in the process of air pollution and oxidative damage to organisms. The analysis of ROS was carried out by the capture-derivative method. Therefore, it is necessary to prepare an effective molecular membrane to trap and detect ROS. Electrospinning membranes were prepared by combining the electrospinning technique with chrysin, baicalein, scutellarin, genistein, quercetin, and baicalin. By comparing the structures of the membranes before and after the reaction, the fluorescence enhancement characteristics of the reactive molecular membranes and the atmospheric radicals were studied. The ability of the active molecular membranes to trap atmospheric radicals was also studied. It was found that the genistein active molecular membrane had good trapping ability in four environments. The fluorescence enhancement rates in ROS, OH radical and O3 simulated environments were 39.32%, 7.99% and 11.92%, respectively. The fluorescence enhancement rate in atmospheric environment was 16.16%. Indeed, the sites where the atmospheric radicals react with the active molecular membranes are discussed. It is found that it is mainly related to the 5,7 phenolic hydroxyl of ring A, catechol structure and the coexistence structure of 4' phenolic hydroxyl of ring B and 7 phenolic hydroxyl of ring A. Therefore, the genistein molecular membrane has shown great potential in its trapping ability and it is also environmentally friendly.

| S-EPMC9143268 | biostudies-literature

Computational Design, Synthesis, and Photochemistry of Cy7-PPG, an Efficient NIR-Activated Photolabile Protecting Group for Therapeutic Applications.

Project description:Photolabile Protecting Groups (PPGs) are molecular tools used, for example, in photopharmacology for the activation of drugs with light, enabling spatiotemporal control over their potency. Yet, red-shifting of PPG activation wavelengths into the NIR range, which penetrates the deepest in tissue, has often yielded inefficient or insoluble molecules, hindering the use of PPGs in the clinic. To solve this problem, we report herein a novel concept in PPG design, by transforming clinically-applied NIR-dyes with suitable molecular orbital configurations into new NIR-PPGs using computational approaches. Using this method, we demonstrate how Cy7, a class of NIR dyes possessing ideal properties (NIR-absorption, high molecular absorptivity, excellent aqueous solubility) can be successfully converted into Cy7-PPG. We report a facile synthesis towards Cy7-PPG from accessible precursors and confirm its excellent properties as the most redshifted oxygen-independent NIR-PPG to date (λmax =746 nm).

| S-EPMC9311213 | biostudies-literature

Resolution of ntla-dependent transcriptome using caged molecules

Project description:This SuperSeries is composed of the following subset Series: GSE31880: Resolution of ntla-dependent transcriptome at 9 hpf using caged molecules GSE31881: Resolution of ntla-dependent transcriptome at 16 hpf using caged molecules Refer to individual Series

2012-03-01 | E-GEOD-31882 | biostudies-arrayexpress

Resolution of ntla-dependent transcriptome at 16 hpf using caged molecules

Project description:Transcription factors play diverse roles during embryonic development, combinatorially controlling multiple cellular states in a spatially and temporally defined manner. Resolving the dynamic transcriptional profiles that underlie these patterning processes is essential for understanding embryogenesis at the molecular level. Here we show how temporal, tissue-specific changes in embryonic transcription factor function can be discerned by integrating caged morpholinos (cMOs) with photoactivatable fluorophores, fluorescence-activated cell sorting (FACS), and microarray technologies. As a proof of principle, we have dynamically profiled No tail-a (Ntla)-dependent genes at different stages of axial mesoderm development in zebrafish, discovering and characterizing discrete sets of transcripts that are coincident with either notochord cell fate commitment or differentiation. Our studies demonstrate how optically controlled chemical tools can be use to probe developmental processes with spatiotemporal precision and reveal the sequential activation of distinct transcriptomes within a cell lineage by a single transcriptional factor. Zebrafish zygotes were injected with a mixture of ntla caged morpholino (cMO) and caged fluorescein dextran (cFD), and a 100 µm-diameter region of the posterior chordamesoderm 125 μm anterior to the center of Kupffer’s vesicle was UV-irradiated at 12 hours post fertilization (hpf). The UV irradiation generated an active morpholino targeting the ntla 5'UTR and simultaneously labeled the cells with green fluorescence. By 36 hpf, the irradiated, green-fluorescent cells contributed to both notochord and floor plate, but the notochord cells were partially vacuolated and disorganized. Combining these caged reagents with microarray analysis identified transcriptional changes coincident with loss of ntla at 16 hpf and subsequent notochord differentiation.

2012-03-01 | GSE31881 | GEO

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