Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Programmable site-selective labeling of oligonucleotides based on carbene catalysis.

ABSTRACT: Site-selective modification of oligonucleotides serves as an indispensable tool in many fields of research including research of fundamental biological processes, biotechnology, and nanotechnology. Here we report chemo- and regioselective modification of oligonucleotides based on rhodium(I)-carbene catalysis in a programmable fashion. Extensive screening identifies a rhodium(I)-catalyst that displays robust chemoselectivity toward base-unpaired guanosines in single and double-strand oligonucleotides with structurally complex secondary structures. Moreover, high regioselectivity among multiple guanosines in a substrate is achieved by introducing guanosine-bulge loops in a duplex. This approach allows the introduction of multiple unique functional handles in an iterative fashion, the utility of which is exemplified in DNA-protein cross-linking in cell lysates.

SUBMITTER: Lee YH

PROVIDER: S-EPMC7966772 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Site-selective 13C labeling of proteins using erythrose.

Project description:NMR-spectroscopy enables unique experimental studies on protein dynamics at atomic resolution. In order to obtain a full atom view on protein dynamics, and to study specific local processes like ring-flips, proton-transfer, or tautomerization, one has to perform studies on amino-acid side chains. A key requirement for these studies is site-selective labeling with 13C and/or 1H, which is achieved in the most general way by using site-selectively 13C-enriched glucose (1- and 2-13C) as the carbon source in bacterial expression systems. Using this strategy, multiple sites in side chains, including aromatics, become site-selectively labeled and suitable for relaxation studies. Here we systematically investigate the use of site-selectively 13C-enriched erythrose (1-, 2-, 3- and 4-13C) as a suitable precursor for 13C labeled aromatic side chains. We quantify 13C incorporation in nearly all sites in all 20 amino acids and compare the results to glucose based labeling. In general the erythrose approach results in more selective labeling. While there is only a minor gain for phenylalanine and tyrosine side-chains, the 13C incorporation level for tryptophan is at least doubled. Additionally, the Phe ? and Trp ?2 positions become labeled. In the aliphatic side chains, labeling using erythrose yields isolated 13C labels for certain positions, like Ile ? and His ?, making these sites suitable for dynamics studies. Using erythrose instead of glucose as a source for site-selective 13C labeling enables unique or superior labeling for certain positions and is thereby expanding the toolbox for customized isotope labeling of amino-acid side-chains.

| S-EPMC5388708 | biostudies-literature

Site-Selective Orbital Interactions in an Ultrathin Iron-Carbene Photosensitizer Film.

Project description:We present the first experimental study of the frontier orbitals in an ultrathin film of the novel hexa-carbene photosensitizer [Fe(btz)3]3+, where btz is 3,3'-dimethyl-1,1'-bis(p-tolyl)-4,4'-bis(1,2,3-triazol-5-ylidene). Resonant photoelectron spectroscopy (RPES) was used to probe the electronic structure of films where the molecular and oxidative integrities had been confirmed with optical and X-ray spectroscopies. In combination with density functional theory calculations, RPES measurements provided direct and site-selective information about localization and interactions of occupied and unoccupied molecular orbitals. Fe 2p, N 1s, and C 1s measurements selectively probed the metal, carbene, and side-group contributions revealing strong metal-ligand orbital mixing of the frontier orbitals. This helps explain the remarkable photophysical properties of iron-carbenes in terms of unconventional electronic structure properties and favorable metal-ligand bonding interactions-important for the continued development of these type of complexes toward light-harvesting and light-emitting applications.

| S-EPMC7307919 | biostudies-literature

Site-Selective Functionalization of Methionine Residues via Photoredox Catalysis.

Project description:Bioconjugation technologies have revolutionized the practice of biology and medicine by allowing access to novel biomolecular scaffolds. New methods for residue-selective bioconjugation are highly sought to expand the toolbox for a variety of bioconjugation applications. Herein we report a site-selective methionine bioconjugation protocol that uses photoexcited lumiflavin to generate open-shell intermediates. This reduction-potential-gated strategy enables access to residues unavailable with traditional nucleophilicity-based conjugation methods. To demonstrate the versatility and robustness of this new protocol, we have modified various proteins and further utilized this functional handle to append diverse biological payloads.

| S-EPMC8647115 | biostudies-literature

Site-selective catalysis: toward a regiodivergent resolution of 1,2-diols.

Project description:This paper demonstrates that the secondary hydroxyl can be functionalized in preference to the primary hydroxyl of a 1,2-diol. The site selectivity is achieved by using an enantioselective organic catalyst that is able to bond to the diol reversibly and covalently. The reaction has been parlayed into a divergent kinetic resolution on a racemic mixture, providing access to highly enantioenriched secondary-protected 1,2-diols in a single synthetic step.

| S-EPMC3342470 | biostudies-literature

Aryl radical-mediated N-heterocyclic carbene catalysis.

Project description:There have been significant advancements in radical reactions using organocatalysts in modern organic synthesis. Recently, NHC-catalyzed radical reactions initiated by single electron transfer processes have been actively studied. However, the reported examples have been limited to catalysis mediated by alkyl radicals. In this article, the NHC organocatalysis mediated by aryl radicals has been achieved. The enolate form of the Breslow intermediate derived from an aldehyde and thiazolium-type NHC in the presence of a base undergoes single electron transfer to an aryl iodide, providing an aryl radical. The catalytically generated aryl radical could be exploited as an arylating reagent for radical relay-type arylacylation of styrenes and as a hydrogen atom abstraction reagent for α-amino C(sp3)-H acylation of secondary amides.

| S-EPMC8219674 | biostudies-literature

Asymmetric catalysis at a distance: catalytic, site-selective phosphorylation of teicoplanin.

Project description:We report three distinct, peptide-based catalysts that enable site-selective phosphorylation of three distinct hydroxyl groups within the complex glycopeptide antibiotic teicoplanin A2-2. Two of the catalysts are based on a design that capitalizes on a catalyst-substrate interaction that mimics the biological mechanism of action for teicoplanin. These catalysts are based on a DXaa-DXaa peptide motif that is known to target the teicoplanin structure in a specific manner. The third was identified through evaluation of a set of catalysts that had been developed for historically distinct projects. Each catalyst contains additional functionality designed to dispose a catalytic moiety (a nucleophilic alkylimidazole) at a different region of the glycopeptide structure. A combination of mass spectrometry and 2D-NMR spectroscopy allowed structural assignment of the distinct phosphorylated teicoplanin derivatives. Mechanistic studies are also reported that support the hypotheses that led to the discovery of the catalysts. In this manner, small molecule catalysts have been achieved that allow rational, catalytic control over reactions at sites that are separated by 11.6, 16.5, and nearly 17.7 Å, based on the X-ray crystal structure of teicoplanin A2-2. Finally, we report the biological activity of the new phosphorylated teicoplanin analogs and compare the results to the natural product itself.

| S-EPMC3790668 | biostudies-literature

Site-Selective Aerobic C-H Monoacylation of Carbazoles Using Palladium Catalysis.

Project description:This manuscript describes the development of a remarkably general palladium-catalyzed monoacylation of carbazoles using toluene derivatives playing the dual role of acyl source and organic solvent. The method uses NHPI as the cocatalyst and oxygen as the sole oxidant. Interestingly, the acylation of monosubstituted N-pyridylcarbazoles takes place regioselectively at the C-8 position. The scope of the method is explored using aldehyde as the acyl source. This highly site-selective acylation proceeds through a radical process.

| S-EPMC7613175 | biostudies-literature

Site-Selective Alkoxylation of Benzylic C-H Bonds by Photoredox Catalysis.

Project description:Methods that enable the direct C-H alkoxylation of complex organic molecules are significantly underdeveloped, particularly in comparison to analogous strategies for C-N and C-C bond formation. In particular, almost all methods for the incorporation of alcohols by C-H oxidation require the use of the alcohol component as a solvent or co-solvent. This condition limits the practical scope of these reactions to simple, inexpensive alcohols. Reported here is a photocatalytic protocol for the functionalization of benzylic C-H bonds with a wide range of oxygen nucleophiles. This strategy merges the photoredox activation of arenes with copper(II)-mediated oxidation of the resulting benzylic radicals, which enables the introduction of benzylic C-O bonds with high site selectivity, chemoselectivity, and functional-group tolerance using only two equivalents of the alcohol coupling partner. This method enables the late-stage introduction of complex alkoxy groups into bioactive molecules, providing a practical new tool with potential applications in synthesis and medicinal chemistry.

| S-EPMC6923605 | biostudies-literature

Ru-Based Z-Selective Metathesis Catalysts with Modified Cyclometalated Carbene Ligands.

Project description:A series of cyclometalated Z-selective ruthenium olefin metathesis catalysts with alterations to the N-heterocyclic carbene (NHC) ligand were prepared. X-Ray crystal structures of several new catalysts were obtained, elucidating the structural features of this class of cyclometalated complexes. The metathesis activity of each stable complex was evaluated, and one catalyst, bearing geminal dimethyl backbone substitution, was found to be comparable to our best Z-selective metathesis catalyst to date.

| S-EPMC4204212 | biostudies-literature

A Cooperative N-Heterocyclic Carbene/Palladium Catalysis System.

Project description:N-heterocyclic carbenes (NHC) have been extensively studied as organocatalysts and ligands for transition metals, but the successful integration of NHCs and late transition metals in cooperative catalysis remains an underexplored area. We have developed a cooperative palladium-catalyzed allylation of NHC-activated aldehydes to access a variety of 3-allyl dihydrocoumarin derivatives. Kinetic experiments support a cooperative pathway for this transformation.

| S-EPMC4212655 | 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