Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Click Chemistry in Ultra-high Vacuum - Tetrazine Coupling with Methyl Enol Ether Covalently Linked to Si(001).

ABSTRACT: The additive-free tetrazine/enol ether click reaction was performed in ultra-high vacuum (UHV) with an enol ether group covalently linked to a silicon surface: Dimethyl 1,2,4,5-tetrazine-3,6-dicarboxylate molecules were coupled to the enol ether group of a functionalized cyclooctyne which was adsorbed on the silicon (001) surface via the strained triple bond of cyclooctyne. The reaction was observed at a substrate temperature of 380 K by means of X-ray photoelectron spectroscopy (XPS). A moderate energy barrier was deduced for this click reaction in vacuum by means of density functional theory based calculations, in good agreement with the experimental results. This UHV-compatible click reaction thus opens a new, flexible route for synthesizing covalently bound organic architectures.

SUBMITTER: Glaser T

PROVIDER: S-EPMC8252806 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Metabolic glycan imaging by isonitrile-tetrazine click chemistry.

Project description:Seeing the sugar coating: N-Acetyl-glucosamine and mannosamine derivatives tagged with an isonitrile group are metabolically incorporated into cell-surface glycans and can be detected with a fluorescent tetrazine. This bioorthogonal isonitrile-tetrazine ligation is also orthogonal to the commonly used azide-cyclooctyne ligation, and so will allow simultaneous detection of the incorporation of two different sugars.

| S-EPMC3743162 | biostudies-literature

Selective Vacuum Evaporation by the Control of the Chemistry of Gas Phase in Vacuum Refining of Si.

Project description:The evaporation of P from liquid Si under vacuum and reduced pressures of H2, He, and Ar was studied to evaluate the feasibility of effective P removal with insignificant Si loss. It was found that the introduction of Ar and He inert gases at low pressures reduces the rate of P removal, and their pressure decrease will increase the process rate. Moreover, the kinetics of P removal was higher in He than in Ar, with simultaneous lower Si loss. Under reduced pressures of H2 gas, however, the P removal rate was higher than that under vacuum conditions with the lowest Si loss. Quantum chemistry and dynamics simulations were applied, and the results indicated that P can maintain its momentum for longer distances in H2 once it is evaporated from the melt surface and then can travel far away from the surface, while Si atoms lose their momentum in closer distances, yielding less net Si flux to the gas phase. Moreover, this distance is significantly increased with decreasing pressure for H2, He, and Ar gases; however, it is the largest for H2 and the lowest for Ar for a given pressure, while the temperature effect is insignificant. The rate of P evaporation was accelerated by applying an additional vacuum tube close to the melt surface for taking out the hot gas particles before they lose their temperature and velocity. It was shown that this technique contributes to the rate of process by preventing condensing gas stream back to the melt surface.

| S-EPMC8280733 | biostudies-literature

Synthetically tractable click hydrogels for three-dimensional cell culture formed using tetrazine-norbornene chemistry.

Project description:The implementation of bio-orthogonal click chemistries is a topic of growing importance in the field of biomaterials, as it is enabling the development of increasingly complex hydrogel materials capable of providing dynamic, cell-instructive microenvironments. Here, we introduce the tetrazine-norbornene inverse electron demand Diels-Alder reaction as a new cross-linking chemistry for the formation of cell laden hydrogels. The fast reaction rate and irreversible nature of this click reaction allowed for hydrogel formation within minutes when a multifunctional PEG-tetrazine macromer was reacted with a dinorbornene peptide. In addition, the cytocompatibility of the polymerization led to high postencapsulation viability of human mesenchymal stem cells, and the specificity of the tetrazine-norbornene reaction was exploited for sequential modification of the network via thiol-ene photochemistry. These advantages, combined with the synthetic accessibility of the tetrazine molecule compared to other bio-orthogonal click reagents, make this cross-linking chemistry an interesting and powerful new tool for the development of cell-instructive hydrogels for tissue engineering applications.

| S-EPMC3623454 | biostudies-literature

Broadening the Utility of Farnesyltransferase-Catalyzed Protein Labeling Using Norbornene–Tetrazine Click Chemistry

Project description:Bio-orthogonal chemistry has gained widespread use in the study of many biological systems of interest, including protein prenylation. Prenylation is a post-translational modification in which a 15 or 20 carbon isoprenoid chain is transferred onto a cysteine near the C-terminus of a target protein. The three enzymes, protein farnesyltransferase (FTase), geranylgeranyl transferase I (GGTase I), and geranylgeranyl transferase II (GGTase II), that catalyze this process have been shown to exhibit some variability in substrate selection. This trait has been utilized in the past to transfer an array of farnesyl diphosphate analogues with a range of functionality, like an alkyne- containing analogue for copper-catalyzed bioconjugation reactions for example. Reported here is the synthesis of an analogue of the isoprenoid substrate embedded with norbornene functionality (C10NorOPP) for the study of prenylation and development of multifaceted protein-polymer-label conjugates. This analogue undergoes the inverse electron demand Diels Alder reaction with a tetrazine containing tags, allowing for copper-free labeling of proteins in the prenylome. This probe was synthesized in 7 steps with an overall yield of 7%. The use of C10NorOPP for the study of prenylation was explored in metabolic labeling of prenylated proteins in HeLa, COS-7, and astrocyte cells. Furthermore, in HeLa cells, these modified prenylated proteins were identified and quantified using LFQ proteomics, finding 24 enriched prenylated proteins. Additionally, here we utilize the unique chemistry of C10NorOPP in the construction of a multi- protein-polymer conjugate for the targeted labeling of cancer cells. This combines the specificity of the norbornene-tetrazine conjugation with traditional azide-alkyne cycloaddition for the construction of a polymer linked fluorescent trimer increasing cell binding.

2024-05-21 | PXD045277 | Pride

Syntheses of hemoprotein models that can be covalently attached onto electrode surfaces by click chemistry.

Project description:Five alkyne-containing hemoprotein models have been synthesized in a convergent manner. Sonogashira coupling was used to introduce the alkyne functional group on the proximal imidazole before or after being attached on the porphyrin. One model was immobilized onto a gold electrode surface via copper(I)-catalyzed azide-alkyne cycloaddition (Sharpless click chemistry).

| S-EPMC2532528 | biostudies-literature

Facile and efficient Lewis acid catalyzed synthesis of an asymmetric tetrazine useful for bio-orthogonal click chemistry applications.

Project description:Bio-orthogonal tetrazine click reactions have recently attracted significant interest for applications spanning biological imaging, cancer targeting, and biomaterials science. Here, we report a simple and efficient two-step scheme for the synthesis of an asymmetric tetrazine molecule containing a carboxylic acid handle for subsequent macromolecular conjugation. Yields as high as 75% were achieved using as little as 0.005 equivalents of nickel triflate catalyst, which is a significant improvement over previous methodologies.

| S-EPMC3834559 | biostudies-literature

Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [Click-Seq 2]

Project description:The success of targeted therapies hinges on our ability to understand the molecular and cellular mechanism of action of these agents. Here we modify various BET bromodomain inhibitors, an exemplar novel targeted therapy, to create functionally conserved compounds that are amenable to click-chemistry and can be used as molecular probes in vitro and in vivo. Using click-proteomics and click-sequencing we provide new mechanistic insights to explain the gene regulatory function of BRD4 and the transcriptional changes invoked by BET inhibitors. In mouse models of acute leukaemia, we use high resolution microscopy and flow cytometry to highlight the underappreciated heterogeneity of drug activity within tumour cells located in different tissue compartments. We also demonstrate the differential distribution and effects of the drug in normal and malignant cells in vivo. These data provide critical insights that reveal the cellular and molecular details for the efficacy and limitations of these agents. This study provides a framework for the pre-clinical assessment of other conventional and targeted therapies.

2017-07-13 | GSE88749 | GEO

Click chemistry enables comprehensive preclinical evaluation of targeted epigenetic therapies [Click-Seq 1]

2017-07-13 | GSE88748 | GEO

Solid phase chemistry to covalently and reversibly capture thiolated RNA

Project description:Here, we describe an approach to enrich newly transcribed RNAs from primary mouse neurons using 4-thiouridine (s4U) metabolic labeling and solid phase chemistry. This one-step enrichment procedure captures s4U-RNA by using highly efficient methane thiosulfonate (MTS) chemistry in an immobilized format. Like solution-based methods, this solid-phase enrichment can distinguish mature RNAs (mRNA) with differential stability, and can be used to reveal transient RNAs such as enhancer RNAs (eRNAs) and primary microRNAs (pri-miRNAs) from short metabolic labeling. Most importantly, the efficiency of this solid-phase chemistry made possible the first large scale measurements of RNA polymerase II (RNAPII) elongation rates in mouse cortical neurons. Thus, our approach provides the means to study regulation of RNA metabolism in specific tissue contexts as a means to better understand gene expression in vivo.

2018-07-19 | GSE110951 | GEO

Mechanochemical generation of acid-degradable poly(enol ether)s.

Project description:In an effort to develop polymers that can undergo extensive backbone degradation in response to mechanical stress, we report a polymer system that is hydrolytically stable but unmasks easily hydrolysable enol ether backbone linkages when force is applied. These polymers were synthesized by ring-opening metathesis polymerization (ROMP) of a novel mechanophore monomer consisting of cyclic ether fused bicyclohexene. Hydrogenation of the resulting polymers led to significantly enhanced thermal stability (T d > 400 °C) and excellent resistance toward acidic or basic conditions. Solution ultrasonication of the polymers resulted in up to 65% activation of the mechanophore units and conversion to backbone enol ether linkages, which then allowed facile degradation of the polymers to generate small molecule or oligomeric species under mildly acidic conditions. We also achieved solid-state mechano-activation and polymer degradation via grinding the solid polymer. Force-induced hydrolytic polymer degradability can enable materials that are stable under force-free conditions but readily degrade under stress. Facile degradation of mechanically activated polymechanophores also facilitates the analysis of mechanochemical products.

| S-EPMC8179558 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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