Browse
Submit Data
Databases
API
Help

Dataset Information

26 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Solid-phase synthesis of oligodeoxynucleotides containing N4-[2-(t-butyldisulfanyl)ethyl]-5-methylcytosine moieties.

ABSTRACT: An efficient route for the synthesis of the phosphoramidite derivative of 5-methylcytosine bearing a tert-butylsulfanyl group protected thiol is described. This building block is used for the preparation of oligonucleotides carrying a thiol group at the nucleobase at the internal position of a DNA sequence. The resulting thiolated oligonucleotides are useful intermediates to generate oligonucleotide conjugates carrying molecules of interest at internal positions of a DNA sequence.

SUBMITTER: Perez-Rentero S

PROVIDER: S-EPMC6257692 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Solid-phase synthesis of oligodeoxynucleotides containing N4-[2-(t-butyldisulfanyl)ethyl]-5-methylcytosine moieties.

Pérez-Rentero Sónia S Garibotti Alejandra V AV Eritja Ramón R

Molecules (Basel, Switzerland) 20100818 8

An efficient route for the synthesis of the phosphoramidite derivative of 5-methylcytosine bearing a tert-butylsulfanyl group protected thiol is described. This building block is used for the preparation of oligonucleotides carrying a thiol group at the nucleobase at the internal position of a DNA sequence. The resulting thiolated oligonucleotides are useful intermediates to generate oligonucleotide conjugates carrying molecules of interest at internal positions of a DNA sequence. ...[more]

PMID: 20720521

Similar Datasets

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

Incorporation of Sensitive Ester and Chloropurine Groups into Oligodeoxynucleotides through Solid Phase Synthesis.

Project description:Nucleosides containing ester groups that are sensitive to nucleophiles were incorporated into oligodeoxynucleotides (ODNs) through solid phase chemical synthesis. The sensitive esters are located on a purine nucleobase. They are the esters of ethyl, 2-methoxyethyl, 4-methoxyphenyl and phenyl groups, and a thioester. These esters cannot survive the deprotection and cleavage conditions used in known ODN synthesis technologies, which involve strong nucleophiles such as ammonium hydroxide and potassium methoxide (potassium carbonate in anhydrous methanol). To incorporate these sensitive groups into ODNs, the Dmoc phosphoramidites and linker were used for solid phase synthesis, which allowed ODN deprotection and cleavage to be carried out under non-nucleophilic oxidative conditions. Sixteen ODN sequences containing these groups were synthesized and characterized with MALDI MS. In addition, the synthesis and characterization of three ODNs containing a nucleophile sensitive 6-chloropurine using the same strategy are described.

| S-EPMC6420219 | biostudies-literature

Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows

Project description:Macrocyclic peptides are attractive for chemoproteomic applications due to their modular synthesis and potential for high target selectivity. We describe a solid phase synthesis method for the efficient generation of libraries of small macrocycles that contain an electrophile and alkyne handle. The modular synthesis produces libraries that can be directly screened using simple SDS-PAGE readouts and then optimal lead molecules applied to proteomic analysis. We generated a library of 480 macrocyclic peptides containing the weakly reactive fluorosulfate (OSF) electrophile. Initial screening of a subset of the library containing each of the various diversity elements identified initial molecules of interest. The corresponding positional and confirmational isomers were then screened to select molecules that showed specific protein labeling patterns that were dependent on the probe structure. The most promising hits were applied to standard chemoproteomic workflows to identify protein targets. Our results demonstrate the feasibility of rapid, on-resin synthesis of diverse macrocyclic electrophiles to generate new classes of covalent ligands.

2023-03-02 | PXD039931 | Pride

Automated solid-phase synthesis of oligosaccharides containing sialic acids.

Project description:A sialic acid glycosyl phosphate building block was designed and synthesized. This building block was used to prepare ?-sialylated oligosaccharides by automated solid-phase synthesis selectively.

| S-EPMC4464161 | biostudies-literature

Chemical synthesis and thermodynamic characterization of oxanine-containing oligodeoxynucleotides.

Project description:Oxanine (Oxa, O), one of the major damaged bases from guanine generated by NO- or HNO2-induced nitrosative deamination, has been considered as a mutagen-potent lesion. For exploring more detailed properties of Oxa, large-scale preparation of Oxa-containing oligodeoxynucleotide (Oxa-ODN) with the desired base sequence is a prerequisite. In the present study, we have developed a chemical synthesis procedure of Oxa-ODNs and characterized thermodynamic properties of Oxa in DNA strands. First, 2'-deoxynucleoside of Oxa (dOxo) obtained from 2'-deoxyguanosine by HNO2-nitrosation was subjected to 5'-O-selective tritylation to give 5'-O-(4,4'-dimethoxytrityl)-dOxo (DMT-dOxo) with a maximum yield of 70%. Subsequently, DMT-dOxo was treated with conventional phosphoramidation, which resulted in DMT-dOxo-amidite monomer with a maximum yield of 72.5%. The amidite obtained was used for synthesizing Oxa-ODNs: the coupling yields for Oxa incorporation were over 93%. The prepared Oxa-ODNs were employed for analyzing the thermodynamic properties of DNA duplexes containing base-matches of O:N [N; C (cytosine), T (thymine), G (guanine) or A (adenine)]. Melting temperatures (Tm) and thermodynamic stability (DeltaG37(0)) were found to be lower by 6.83 approximately 13.41 degrees C and 2.643 approximately 6.047 kcal mol(-1), respectively, compared with those of oligodeoxynucleotides, which had the same base sequence except that O:N was replaced by G:C (wild type). It has also been found that Oxa-pairing with cytosine shows relatively high stability in DNA duplex compared with other base combinations. The orders of DeltaDeltaG37(0) were O:C > O:T > O:A > O:G. The chemical synthesis procedure and thermodynamic characteristics of Oxa-ODNs established here will be helpful for elucidating the biological significance of Oxa in relation to genotoxic and repair mechanisms.

| S-EPMC1255731 | biostudies-literature

Synthesis and Biological Activities of Ethyl 2-(2-pyridylacetate) Derivatives Containing Thiourea, 1,2,4-triazole, Thiadiazole and Oxadiazole Moieties.

Project description:Thirty six novel heterocyclic derivatives of ethyl 2-(2-pyridylacetate) were efficiently synthesized. The new compounds involve the linkage of a 2-pyridyl ring with thiosemicarbazide (compounds 1-7), 1,2,4-triazole (compounds 1a-7a), 1,3,4-thiadiazole (compounds 1b-7b), and 1,3,4-oxadiazole (compounds 1f-7f) moieties. The last group of compounds 1e-7e involves the connection of a 2-pyridyl ring with 1,2,4-triazole and thiourea. ¹H-NMR, 13C-NMR and MS methods were used to confirm the structures of the obtained derivatives. The molecular structures of 3, 3b, 7a and 7f were further confirmed by X-ray crystallography. All obtained compounds were tested in vitro against a number of microorganisms, including Gram-positive cocci, Gram-negative rods and Candida albicans. In addition, the obtained compounds were tested for cytotoxicity and antiviral activity against HIV-1.

| S-EPMC6155191 | biostudies-literature

Solid-State Luminescent Materials Containing Both Indole and Pyrimidine Moieties: Design, Synthesis, and Density Functional Theory Calculations.

Project description:Heterocyclic compounds with effective solid-state luminescence offer a wide range of uses. It has been observed that combining pyrimidine and indole moieties in a single molecule can enhance material behavior dramatically. Here, different heterocyclic compounds with indole and pyrimidine moieties have been synthesized effectively, and their structures have been validated using NMR, IR, and mass spectroscopy. The photoluminescence behavior of two substances was investigated in powder form and solutions of varying concentrations. After aggregation, one molecule displayed a redshifted luminescence spectrum, whereas another homolog showed a blueshift. Thus, density functional theory calculations were carried out to establish that introducing a terminal group allows modifying of the luminescence behavior by altering the molecular packing. Because of the non-planarity, intermolecular interactions, and tiny intermolecular distances within the dimers, the materials demonstrated a good emission quantum yield (Φem) in the solid state (ex. 25.6%). At high temperatures, the compounds also demonstrated a stable emission characteristic.

| S-EPMC9089344 | biostudies-literature

Conjugation of chemical handles and functional moieties to DNA during solid phase synthesis with sulfonyl azides.

Project description:Labelling of oligonucleotides with dyes, targeting ligands, and other moieties has become ever more essential in life-sciences. Conventionally, modifications are introduced to oligonucleotides during solid phase synthesis by special phosphoramidites functionalised with a chemical handle or the desired functional group. In this work, we present a facile and inexpensive method to introduce modifications to oligonucleotides without the need for special phosphoramidites. Sulfonyl azides are applied to react with one or more selected phosphite intermediates during solid phase synthesis. We have prepared 11 sulfonyl azides with different chemical handles such as amine, azide, alkyne, and thiol, and we have further introduced functionalities such as pyrene, other dyes, photo-switchable azobenzenes, and a steroid. The method is compatible with current phosphoramidite-based automated oligonucleotide synthesis and serves as a simple alternative to the unstable and expensive special phosphoramidites currently used for conjugation to oligonucleotides.

| S-EPMC9303310 | biostudies-literature

Solid-phase synthesis of peptoid-like oligomers containing diverse diketopiperazine units.

Project description:Diketopiperazine (DKP) units are found in many bioactive small molecules. Here we report facile chemistry for incorporating diverse DKP units within peptoid and peptoid-like libraries made by solid-phase split and pool synthesis.

| S-EPMC4148721 | biostudies-literature

Solid-phase synthesis of peptides containing aminoadipic semialdehyde moiety and their cyclisations.

Project description:Pathological levels of oxidative stress (OS) have been implicated in many diseases including diabetes mellitus, neurodegenerative diseases, inflammatory diseases, atherosclerosis, and cancer. Studies of oxidative stress are however complicated by the low concentration of oxidation products. To resolve this problem, we tested a new derivative of aminoadipic semialdehyde (Fmoc-Aea-OH) in the solid-phase synthesis of carbonylated peptides. We prepared a series of peptides with free and acetylated N-terminal amino groups using the Fmoc-Aea-OH reagent. LC-MS, ESI-MS, and MS/MS spectra confirmed the sequences of the modified peptides, although the LC-MS and ESI-MS spectra were dominated by signals corresponding to dehydration products. NMR studies of acetylated products revealed that the dominant product formed in this reaction contains a 1,2,3,4-tetrahydropyridine-2-carboxylic acid residue. Another side reaction in this system was the cleavage of the amide bond between the Aea residue and the amino acid moiety preceding it resulting in the formation of a side product with a six-membered ring at the N-terminus (2,3,4,5-tetrahydropyridine-2-carboxylic acid residue). We found that, depending on the peptide sequence, one of those side products is predominant. Our work suggests new methods for the solid-state synthesis of peptides containing unnatural amino acids.

| S-EPMC6041278 | 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