Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantification of azide groups on a material surface and a biomolecule using a clickable and cleavable fluorescent compound.

ABSTRACT: Here, we propose a novel method for quantifying azide groups on a solid surface and a protein using a clickable and cleavable fluorescent compound. The clickable and cleavable fluorescent compound conjugates with the azide groups on the material surface and the fluorophore is then liberated into the solvent via a cleavage reaction, which can be simply quantified with a conventional fluorometer.

SUBMITTER: Sakai R

PROVIDER: S-EPMC9060625 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Quantification of azide groups on a material surface and a biomolecule using a clickable and cleavable fluorescent compound.

Sakai Rika R Iguchi Hiroki H Maruyama Tatsuo T

RSC advances 20190101 8

Here, we propose a novel method for quantifying azide groups on a solid surface and a protein using a clickable and cleavable fluorescent compound. The clickable and cleavable fluorescent compound conjugates with the azide groups on the material surface and the fluorophore is then liberated into the solvent <i>via</i> a cleavage reaction, which can be simply quantified with a conventional fluorometer. ...[more]

PMID: 35520182

Similar Datasets

A "Clickable" Photoconvertible Small Fluorescent Molecule as a Minimalist Probe for Tracking Individual Biomolecule Complexes.

Project description:Photoconvertible fluorophores can enable the visualization and tracking of a specific biomolecules, complexes, and cellular compartments with precise spatiotemporal control. The field of photoconvertible probes is dominated by fluorescent protein variants, which can introduce perturbations to the target biomolecules due to their large size. Here, we present a photoconvertible small molecule, termed CPX, that can be conjugated to any target through azide-alkyne cycloaddition ("click" reaction). To demonstrate its utility, we have applied CPX to study (1) trafficking of biologically relevant synthetic vesicles and (2) intracellular processes involved in transmission of α-synuclein (αS) pathology. Our results demonstrate that CPX can serve as a minimally perturbing probe for tracking the dynamics of biomolecules.

| S-EPMC6732186 | biostudies-literature

Clickable azide-functionalized bromoarylaldehydes - synthesis and photophysical characterization.

Project description:Herein, we present a facile synthesis of three azide-functionalized fluorophores and their covalent attachment as triazoles in Huisgen-type cycloadditions with model alkynes. Besides two ortho- and para-bromo-substituted benzaldehydes, the azide functionalization of a fluorene-based structure will be presented. The copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) of the so-synthesized azide-functionalized bromocarbaldehydes with terminal alkynes, exhibiting different degrees of steric demand, was performed in high efficiency. Finally, we investigated the photophysical properties of the azide-functionalized arenes and their covalently linked triazole derivatives to gain deeper insight towards the effect of these covalent linkers on the emission behavior.

| S-EPMC7372231 | biostudies-literature

Ultrasensitive and multiplexed protein imaging with clickable and cleavable fluorophores.

Project description:Single-cell spatial proteomic analysis holds great promise to advance our understanding of the composition, organization, interaction and function of the various cell types in complex biological systems. However, the current multiplexed protein imaging technologies suffer from low detection sensitivity, limited multiplexing capacity or technically demanding. To tackle these issues, here we report the development of a highly sensitive and multiplexed in situ protein profiling method using off-the-shelf antibodies. In this approach, the protein targets are stained with horseradish peroxidase (HRP) conjugated antibodies and cleavable fluorophores via click chemistry. Through reiterative cycles of target staining, fluorescence imaging, and fluoropohore cleavage, many proteins can be profiled in single cells in situ. Applying this approach, we successfully quantified 28 different proteins in a human formalin-fixed paraffin-embedded (FFPE) tonsil tissue, which represents the highest multiplexing capacity among the tyramide signal amplification (TSA) methods. Based on their unique protein expression patterns and their microenvironment, ~820,000 cells in the tissue are classified into distinct cell clusters. We also explored the cell-cell interactions between these varied cell clusters and observed different subregions of the tissue are composed of cells from specific clusters.

| S-EPMC10634699 | biostudies-literature

Cleavable biotin probes for labeling of biomolecules via azide-alkyne cycloaddition.

Project description:The azide-alkyne cycloaddition provides a powerful tool for bio-orthogonal labeling of proteins, nucleic acids, glycans, and lipids. In some labeling experiments, e.g., in proteomic studies involving affinity purification and mass spectrometry, it is convenient to use cleavable probes that allow release of labeled biomolecules under mild conditions. Five cleavable biotin probes are described for use in labeling of proteins and other biomolecules via azide-alkyne cycloaddition. Subsequent to conjugation with metabolically labeled protein, these probes are subject to cleavage with either 50 mM Na(2)S(2)O(4), 2% HOCH(2)CH(2)SH, 10% HCO(2)H, 95% CF(3)CO(2)H, or irradiation at 365 nm. Most strikingly, a probe constructed around a dialkoxydiphenylsilane (DADPS) linker was found to be cleaved efficiently when treated with 10% HCO(2)H for 0.5 h. A model green fluorescent protein was used to demonstrate that the DADPS probe undergoes highly selective conjugation and leaves a small (143 Da) mass tag on the labeled protein after cleavage. These features make the DADPS probe especially attractive for use in biomolecular labeling and proteomic studies.

| S-EPMC3016050 | biostudies-literature

A biomolecule-compatible visible-light-induced azide reduction from a DNA-encoded reaction-discovery system.

Project description:Using a system that accelerates the serendipitous discovery of new reactions by evaluating hundreds of DNA-encoded substrate combinations in a single experiment, we explored a broad range of reaction conditions for new bond-forming reactions. We discovered reactivity that led to a biomolecule-compatible, Ru(II)-catalysed azide-reduction reaction induced by visible light. In contrast to current azide-reduction methods, this reaction is highly chemoselective and is compatible with alcohols, phenols, acids, alkenes, alkynes, aldehydes, alkyl halides, alkyl mesylates and disulfides. The remarkable functional group compatibility and mild conditions of the reaction enabled the azide reduction of nucleic acid and oligosaccharide substrates, with no detectable occurrence of side reactions. The reaction was also performed in the presence of a protein enzyme without the loss of enzymatic activity, in contrast to two commonly used azide-reduction methods. The visible-light dependence of this reaction provides a means of photouncaging functional groups, such as amines and carboxylates, on biological macromolecules without using ultraviolet irradiation.

| S-EPMC3078041 | biostudies-literature

Nitric oxide-generating compound and bio-clickable peptide mimic for synergistically tailoring surface anti-thrombogenic and anti-microbial dual-functions.

Project description:Application of extracorporeal circuits and indwelling medical devices has saved many lives. However, it is accompanied with two major complications: thrombosis and infection. To address this issue, we apply therapeutic nitric oxide gas (NO) and antibacterial peptide for synergistically tailoring such devices for surface anti-thrombogenic and antifouling dual functions. Such functional surface is realized by stepwise conjugation of NO-generating compound of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelated copper ions (Cu-DOTA) and dibenzylcyclooctyne- (DBCO-) modified antimicrobial peptide based on carbodiimide and click chemistry respectively. The integration of peptide and Cu-DOTA grants the modified surface the ability to not only efficiently inhibit bacterial growth, but also catalytically generate NO from endogenous s-nitrosothiols (RSNO) to reduce adhesion and activation of platelets, preventing the formation of thrombus. We envision that the stepwise synergistic modification strategy by using anticoagulant NO and antibacterial peptide would facilitate the surface multifunctional engineering of extracorporeal circuits and indwelling medical devices, with reduced clinical complications associated with thrombosis and infection.

| S-EPMC7695912 | biostudies-literature

AptaFluorescence: An aptamer-based fluorescent imaging protocol for biomolecule visualization.

Project description:Immunofluorescence is highly dependent on antibody-antigen interactions for accurate visualization of proteins and other biomolecules within cells. However, obtaining antibodies with high specificity and affinity for their target proteins can be challenging, especially for targets that are complex or naturally present at low levels. Therefore, we developed AptaFluorescence, a protocol that utilizes fluorescently labeled aptamers for in vitro biomolecule visualization. Aptamers are single-stranded nucleic acid molecules that fold into three-dimensional structures to bind biomolecules with high specificity. AptaFluorescence targeting the c-MYC protein was evaluated in doxycycline-inducible c-MYC U2OS cells. AptaFluorescence signals were more distinct compared to the diffuse immunofluorescence signals. AptaFluorescence also reliably differentiated doxycycline-treated cells from untreated cells. In conclusion, AptaFluorescence is a novel, easy to perform, aptamer-based protocol that will have broad applicability across various biological endeavours for visualizing biomolecules, especially in cases where antibodies with high affinity and specificity for their target proteins are lacking.

| S-EPMC11676843 | biostudies-literature

Core-clickable PEG-branch-azide bivalent-bottle-brush polymers by ROMP: grafting-through and clicking-to.

Project description:The combination of highly efficient polymerizations with modular "click" coupling reactions has enabled the synthesis of a wide variety of novel nanoscopic structures. Here we demonstrate the facile synthesis of a new class of clickable, branched nanostructures, polyethylene glycol (PEG)-branch-azide bivalent-brush polymers, facilitated by "graft-through" ring-opening metathesis polymerization of a branched norbornene-PEG-chloride macromonomer followed by halide-azide exchange. The resulting bivalent-brush polymers possess azide groups at the core near a polynorbornene backbone with PEG chains extended into solution; the structure resembles a unimolecular micelle. We demonstrate copper-catalyzed azide-alkyne cycloaddition (CuAAC) "click-to" coupling of a photocleavable doxorubicin (DOX)-alkyne derivative to the azide core. The CuAAC coupling was quantitative across a wide range of nanoscopic sizes (∼6-∼50 nm); UV photolysis of the resulting DOX-loaded materials yielded free DOX that was therapeutically effective against human cancer cells.

| S-EPMC3077470 | biostudies-literature

Cell surface display yields evolvable, clickable antibody fragments.

Project description:Non-canonical amino acids (ncAAs) provide powerful tools for engineering the chemical and physical properties of proteins. However, introducing ncAAs into proteins can affect protein properties in unpredictable ways, thus necessitating screening efforts to identify mutants with desirable properties. In this work, we describe an Escherichia coli cell surface display platform for the directed evolution of clickable antibody fragments. This platform enabled isolation of antibody fragments with improved digoxigenin binding and modest affinity maturation in several different ncAA contexts. Azide-functionalized fragments exhibited improved binding kinetics relative to their methionine counterparts, facile chemical modification through azide-alkyne cycloaddition, and retention of binding properties after modification. The results described here suggest new possibilities for protein engineering, including modulation of molecular recognition events by ncAAs and direct screening of libraries of chemically modified proteins.

| S-EPMC4199383 | biostudies-literature

"Clickable" polymer nanoparticles: a modular scaffold for surface functionalization.

Project description:The versatility of copper-catalyzed alkyne-azide coupling (CuAAC) in functionalizing drug-loaded polymer nanoparticles is demonstrated via the modification of surfaces of acetylene-functionalized PNPs with folate, biotin, and gold nanoparticles.

| S-EPMC3861897 | 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