Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection.

ABSTRACT: Solid-phase synthesis of electrophilic oligodeoxynucleotides (ODNs) was achieved using dimethyl-Dmoc (dM-Dmoc) as amino protecting group. Due to the high steric hindrance of the 2-(propan-2-ylidene)-1,3-dithiane side product from deprotection, the use of excess nucleophilic scavengers such as aniline to prevent Michael addition of the side product to the deprotected ODN during ODN cleavage and deprotection was no longer needed. The improved technology was demonstrated by the synthesis and characterization of five ODNs including three modified ones. The modified ODNs contained the electrophilic groups ethyl ester, ?-chloroamide, and thioester. Using the technology, the sensitive groups can be installed at any location within the ODN sequences without using any sequence- or functionality-specific conditions and procedures.

SUBMITTER: Shahsavari S

PROVIDER: S-EPMC6541367 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection.

Shahsavari Shahien S Eriyagama Dhananjani N A M DNAM Halami Bhaskar B Begoyan Vagarshak V Tanasova Marina M Chen Jinsen J Fang Shiyue S

Beilstein journal of organic chemistry 20190520

Solid-phase synthesis of electrophilic oligodeoxynucleotides (ODNs) was achieved using dimethyl-Dmoc (dM-Dmoc) as amino protecting group. Due to the high steric hindrance of the 2-(propan-2-ylidene)-1,3-dithiane side product from deprotection, the use of excess nucleophilic scavengers such as aniline to prevent Michael addition of the side product to the deprotected ODN during ODN cleavage and deprotection was no longer needed. The improved technology was demonstrated by the synthesis and charac ...[more]

PMID: 31164948

Similar Datasets

Sensitive Oligodeoxynucleotide Synthesis Using Dim and Dmoc as Protecting Groups.

Project description:In traditional oligodeoxynucleotide (ODN) synthesis, phosphate groups are protected with the 2-cyanoethyl group, and amino groups are protected with acyl groups. At the end of ODN synthesis, deprotection is achieved with strong bases and nucleophiles. Therefore, traditional technologies are not suitable for the synthesis of ODNs containing sensitive functionalities. To address the problem, we report the use of Dim and Dmoc groups, which are based on the 1,3-dithian-2-yl-methyl function, for phosphate and amine protection for the solid phase ODN synthesis. Using the new Dim-Dmoc protection, deprotection was achieved under mild oxidative conditions without using any strong bases and nucleophiles. As a result, the new technology is suitable for the synthesis of ODNs containing sensitive functions. To demonstrate feasibility, seven 20-mer ODNs including four that contain sensitive ester and alkyl chloride groups were synthesized, purified with RP HPLC, and characterized with MALDI-TOF MS and enzyme digestion essays. High purity ODNs were obtained.

| S-EPMC6825528 | biostudies-literature

dM-Dim for Carboxylic Acid Protection.

Project description:The 1,3-dithian-2-yl-methyl (Dim) and its analogous groups including dimethyl-Dim (dM-Dim) can provide a new dimension of orthogonality for carboxylic acid protection. They can be deprotected under nearly neutral oxidative conditions. In this paper, the protection of carboxylic acid with dM-Dim, deprotection of dM-Dim ester with sodium periodate, stability of dM-Dim protected carboxylic acid under acidic and basic conditions, and selective deprotection of dM-Dim protected carboxylic acids in the presence of tertiary butyl and methyl esters are presented.

| S-EPMC6161831 | biostudies-literature

Synthesis of Oligodeoxynucleotides Containing Electrophilic Groups.

Project description:By use of 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) as a protecting group and linker for oligodeoxynucleotide (ODN) synthesis, deprotection and cleavage are achieved under non-nucleophilic oxidative conditions. The nucleophile-sensitive thioester and α-chloroacetyl groups are conveniently incorporated into ODN sequences. The technology could be universally useful for electrophilic ODN synthesis.

| S-EPMC4975647 | biostudies-literature

The Potassium Efflux System Kef: Bacterial Protection against Toxic Electrophilic Compounds.

Project description:Kef couples the potassium efflux with proton influx in gram-negative bacteria. The resulting acidification of the cytosol efficiently prevents the killing of the bacteria by reactive electrophilic compounds. While other degradation pathways for electrophiles exist, Kef is a short-term response that is crucial for survival. It requires tight regulation since its activation comes with the burden of disturbed homeostasis. Electrophiles, entering the cell, react spontaneously or catalytically with glutathione, which is present at high concentrations in the cytosol. The resulting glutathione conjugates bind to the cytosolic regulatory domain of Kef and trigger activation while the binding of glutathione keeps the system closed. Furthermore, nucleotides can bind to this domain for stabilization or inhibition. The binding of an additional ancillary subunit, called KefF or KefG, to the cytosolic domain is required for full activation. The regulatory domain is termed K+ transport-nucleotide binding (KTN) or regulator of potassium conductance (RCK) domain, and it is also found in potassium uptake systems or channels in other oligomeric arrangements. Bacterial RosB-like transporters and K+ efflux antiporters (KEA) of plants are homologs of Kef but fulfill different functions. In summary, Kef provides an interesting and well-studied example of a highly regulated bacterial transport system.

| S-EPMC10224563 | biostudies-literature

Electrical DNA Sequence Mapping Using Oligodeoxynucleotide Labels and Nanopores.

Project description:Identifying DNA species is crucial for diagnostics. For DNA identification, single-molecule DNA sequence mapping is an alternative to DNA sequencing toward fast point-of-care testing, which traditionally relies on targeting and labeling DNA sequences with fluorescent labels and readout using optical imaging methods. A nanopore is a promising sensor as a complement to optical mapping with advantages of electric measurement suitable for portable devices and potential for high resolution. Here, we demonstrate a high-resolution nanopore-based DNA sequence mapping by labeling specific short sequence motifs with oligodeoxynucleotides (ODNs) using DNA methyltransferase (MTase) and detecting them using nanopores. We successfully detected ODNs down to the size of 11 nucleotides without introducing extra reporters and resolved neighboring sites with a distance of 141 bp (∼48 nm) on a single DNA molecule. To accurately locate the sequence motif positions on DNA, a nanopore data analysis method is proposed by considering DNA velocity change through nanopores and using ensemble statistics to translate the time-dependent signals to the location information. Our platform enables high-resolution detection of small labels on DNA and high-accuracy localization of them for DNA species identification in an all-electrical format. The method presents an alternative to optical techniques relying on fluorescent labels and is promising for miniature-scale integration for diagnostic applications.

| S-EPMC7905879 | biostudies-literature

Prediction of the Synthesis of Spiro Derivatives by Double Intramolecular Aromatic Electrophilic Substitution Using Reactivity Indices.

Project description:The synthesis of heterocyclic spirobifluorene (SBF) analogs generally requires long and complicated synthetic pathways. Despite this synthetic effort, such structural modification allows the (opto)electronic properties of this remarkable three-dimensional node to be tuned especially for molecular electronic applications. For this reason, the development of a simple, robust, and efficient synthetic methodology to introduce various heterocycles in place of classical phenyl rings in the spirofluorene motif is highly and timely desirable. In this context, we describe herein our efforts to develop a straightforward and efficient synthesis leading to replacement of 2 phenyl rings by various heterocycles in spiro compounds from 2,2'-dibromobenzophenone. As the same procedure to form fully heterocyclic compounds failed, an original theoretical approach based mainly on the uncommon Fukui dual function was developed in order to determine clearly the limitation of this strategy and provide an efficient predictive tool. Indeed, such calculation allows prediction of the thermodynamic and kinetic aspects of the synthesis of spiro derivatives using a double aromatic electrophilic substitution. If this procedure reproduces well our experimental results focused on (heterocyclic) SBF compounds, it can be certainly adapted and generalized to other intramolecular substitutions.

| S-EPMC6647987 | biostudies-literature

Transfer of Electrophilic NH Using Convenient Sources of Ammonia: Direct Synthesis of NH Sulfoximines from Sulfoxides.

Project description:A new system for NH transfer is developed for the preparation of sulfoximines, which are emerging as valuable motifs for drug discovery. The protocol employs readily available sources of nitrogen without the requirement for either preactivation or for metal catalysts. Mixing ammonium salts with diacetoxyiodobenzene directly converts sulfoxides into sulfoximines. This report describes the first example of using of ammonia sources with diacetoxyiodobenzene to generate an electrophilic nitrogen center. Control and mechanistic studies suggest a short-lived electrophilic intermediate, which is likely to be PhINH or PhIN(+) .

| S-EPMC5074267 | biostudies-literature

Copper-Catalyzed Electrophilic Chlorocyclization Reaction Using Sodium Chloride as the Source of Electrophilic Chlorine.

Project description:The synthesis of 2,3-disubstituted benzo[b]thiophenes with selective placement of a chlorine moiety at the 3 position while maintaining diversity at the 2 position has only been accomplished by a handful of conditions in the past. The development of a greener, less expensive, and simpler method is paramount for the exploration of innovative compounds for application in medicinal and materials chemistry. Herein, the first reported copper-catalyzed electrophilic chlorocyclization method was developed and employed across diverse substrates to generate highly functionalized 2,3-disubstituted benzo[b]thiophenes and 2,3,5-trisubstituted thiophenes in very high yields. This method was optimized in both ethanol and acetonitrile in a comparative solvent study. The utility of this method was further expanded beyond chlorocyclization by changing the sodium halide to generate bromo- and iodocyclization products in excellent yields.

| S-EPMC6648761 | biostudies-literature

Direct Synthesis of Enamides via Electrophilic Activation of Amides.

Project description:A novel, one-step N-dehydrogenation of amides to enamides is reported. This reaction employs the unlikely combination of LiHMDS and triflic anhydride, which serves as both the electrophilic activator and the oxidant, and is characterized by its simple setup and broad substrate scope. The synthetic utility of the formed enamides was readily demonstrated in a range of downstream transformations.

| S-EPMC8299460 | biostudies-literature

Divergent Strain-Release Amino-Functionalization of [1.1.1]Propellane with Electrophilic Nitrogen-Radicals.

Project description:Herein we report the development of a photocatalytic strategy for the divergent preparation of functionalized bicyclo[1.1.1]pentylamines. This approach exploits, for the first time, the ability of nitrogen-radicals to undergo strain-release reaction with [1.1.1]propellane. This reactivity is facilitated by the electrophilic nature of these open-shell intermediates and the presence of strong polar effects in the transition-state for C-N bond formation/ring-opening. With the aid of a simple reductive quenching photoredox cycle, we have successfully harnessed this novel radical strain-release amination as part of a multicomponent cascade compatible with several external trapping agents. Overall, this radical strategy enables the rapid construction of novel amino-functionalized building blocks with potential application in medicinal chemistry programs as p-substituted aniline bioisosteres.

| S-EPMC7318212 | 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