Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Stereospecific synthesis of phosphatidylglycerol using a cyanoethyl phosphoramidite precursor.

ABSTRACT: Phosphatidylglycerols (PG) are a family of naturally occurring phospholipids that are responsible for critical operations within cells. PG are characterized by an (R) configuration in the diacyl glycerol backbone and an (S) configuration in the phosphoglycerol head group. Herein, we report a synthetic route to provide control over the PG stereocenters as well as control of the acyl chain identity.

SUBMITTER: Struzik ZJ

PROVIDER: S-EPMC7484214 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Synthesis of comb-shaped DNA using a non-nucleosidic branching phosphoramidite.

Project description:Branched DNAs (bDNAs) having comb-like structures have found wide utility in molecular diagnostics and DNA nanotechnology. bDNAs can be generated either by designing and assembling linear DNA molecules into rigid non-covalent structures or by using an orthogonally protected branching unit to synthesize covalently linked structures. Despite the advantages of the covalently linked structures, use of this motif has been hampered by the challenging synthesis of appropriately protected branching monomers. We report the facile synthesis of a branching monomer having orthogonal DMT and Lev protecting groups using readily available ?-velarolactone and 1,3-diaminopropan-2-ol. Using this branching monomer, a comb-shaped bDNA was synthesized having three different DNA arms. The synthesis and hybridization capability of the bDNA was assessed by fluorescence microscopy using fluorescently labeled complementary and mismatched DNA probes. Convenient access to an orthogonally protected branching monomer is anticipated to accelerate applications of bDNAs in applications including diagnostics, biosensing, gene-profiling, DNA computing, multicolor imaging, and nanotechnology.

| S-EPMC6021227 | biostudies-literature

Synthesis and structural characterization of stable branched DNA g-quadruplexes using the trebler phosphoramidite.

Project description:Guanine (G)-rich sequences can form a noncanonical four-stranded structure known as the G-quadruplex. G-quadruplex structures are interesting because of their potential biological properties and use in nanosciences. Here, we describe a method to prepare highly stable G-quadruplexes by linking four G-rich DNA strands to form a monomolecular G-quadruplex. In this method, one strand is synthesized first, and then a trebler molecule is added to simultaneously assemble the remaining three strands. This approach allows the introduction of specific modifications in only one of the strands. As a proof of concept, we prepared a quadruplex where one of the chains includes a change in polarity. A hybrid quadruplex is observed in ammonium acetate solutions, whereas in the presence of sodium or potassium, a parallel G-quadruplex structure is formed. In addition to the expected monomolecular quadruplexes, we observed the presence of dimeric G-quadruplex structures. We also applied the method to prepare G-quadruplexes containing a single 8-aminoguanine substitution and found that this single base stabilizes the G-quadruplex structure when located at an internal position.

| S-EPMC3922461 | biostudies-literature

Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides.

Project description:The use of CuAAC chemistry to crosslink and stabilize oligonucleotides has been limited by the incompatibility of azides with the phosphoramidites used in automated oligonucleotide synthesis. Herein we report optimized reaction conditions to synthesize azide derivatives of thymidine and cytidine phosphoramidites. Investigation of the stability of the novel phosphoramidites using 31P NMR at room temperature showed less than 10% degradation after 6 hours. The azide modified thymidine was successfully utilized as an internal modifier in the standard phosphoramidite synthesis of a DNA sequence. The synthesized azide and alkyne derivatives of pyrimidines will allow efficient incorporation of azide and alkyne click pairs into nucleic acids, thus widening the applicability of click chemistry in investigating the chemistry of nucleic acids.

| S-EPMC6386463 | biostudies-literature

Stereospecific total synthesis of somocystinamide A.

Project description:The first total synthesis of somocystinamide A, a disulfide dimer with extremely labile enamide functional groups, was accomplished in a concise and stereospecific manner. Somocystinamide A is reported to possess exceptionally potent antiangiogenic and tumoricidal activities. The current work should enable further pharmacological investigation of this important natural product.

| S-EPMC3227555 | biostudies-literature

Facile synthesis of a 3-deazaadenosine phosphoramidite for RNA solid-phase synthesis.

Project description:Access to 3-deazaadenosine (c3A) building blocks for RNA solid-phase synthesis represents a severe bottleneck in modern RNA research, in particular for atomic mutagenesis experiments to explore mechanistic aspects of ribozyme catalysis. Here, we report the 5-step synthesis of a c3A phosphoramidite from cost-affordable starting materials. The key reaction is a silyl-Hilbert-Johnson nucleosidation using unprotected 6-amino-3-deazapurine and benzoyl-protected 1-O-acetylribose. The novel path is superior to previously described syntheses in terms of efficacy and ease of laboratory handling.

| S-EPMC5238537 | biostudies-other

Phosphoramidite gold(I)-catalyzed diastereo- and enantioselective synthesis of 3,4-substituted pyrrolidines.

Project description:In this article the utility of phosphoramidite ligands in enantioselective Au(I) catalysis was explored in the development of highly diastereo- and enantioselective Au(I)-catalyzed cycloadditions of allenenes. A Au(I)-catalyzed synthesis of 3,4-disubstituted pyrrolidines and γ-lactams is described. This reaction proceeds through the enantioselective Au(I)-catalyzed cyclization of allenenes to form a carbocationic intermediate that is trapped by an exogenous nucleophile, resulting in the highly diastereoselective construction of three contiguous stereogenic centers. A computational study (DFT) was also performed to gain some insight into the underlying mechanisms of these cycloadditions. The utility of this new methodology was demonstrated through the formal synthesis of (-)-isocynometrine.

| S-EPMC3071892 | biostudies-literature

Synthesis of a Morpholino Nucleic Acid (MNA)-Uridine Phosphoramidite, and Exon Skipping Using MNA/2'-O-Methyl Mixmer Antisense Oligonucleotide.

Project description:In this study, we synthesised a morpholino nucleoside-uridine (MNA-U) phosphoramidite and evaluated the potential of a MNA-modified antisense oligonucleotide (AO) sequences to induce exon 23 skipping in mdx mouse myotubes in vitro towards extending the applicability of morpholino chemistry with other nucleotide monomers. We designed, synthesised, and compared exon skipping efficiencies of 20 mer MNA-modified 2'-O-methyl RNA mixmer AO on a phosphorothioate backbone (MNA/2'-OMePS) to the corresponding fully modified 2'-O-methyl RNA AO (2'-OMePS) as a control. Our results showed that the MNA/2'-OMePS efficiently induced exon 23 skipping. As expected, the 2'-OMePS AO control yielded efficient exon 23 skipping. Under the applied conditions, both the AOs showed minor products corresponding to exon 22/23 dual exon skipping in low yield. As these are very preliminary data, more detailed studies are necessary; however, based on the preliminary results, MNA nucleotides might be useful in constructing antisense oligonucleotides.

| S-EPMC6274534 | biostudies-literature

Solution synthesis of germanium nanowires using a Ge2+ alkoxide precursor.

Project description:A simple solution synthesis of germanium (Ge0) nanowires under mild conditions (<400 degrees C and 1 atm) was demonstrated using germanium 2,6-dibutylphenoxide, Ge(DBP)2 (1), as the precursor where DBP = 2,6-OC6H3(C(CH3)3)2. Compound 1, synthesized from Ge(NR2)2 where R = SiMe3 and 2 equiv of DBP-H, was characterized as a mononuclear species by single-crystal X-ray diffraction. Dissolution of 1 in oleylamine, followed by rapid injection into a 1-octadecene solution heated to 300 degrees C under an atmosphere of Ar, led to the formation of Ge0 nanowires. The Ge0 nanowires were characterized by transmission electron microscopy (TEM), X-ray diffraction analysis, and Fourier transform infrared spectroscopy. These characterizations revealed that the nanowires are single crystalline in the cubic phase and coated with oleylamine surfactant. We also observed that the nanowire length (0.1-10 microm) increases with increasing temperature (285-315 degrees C) and time (5-60 min). Two growth mechanisms are proposed based on the TEM images intermittently taken during the growth process as a function of time: (1) self-seeding mechanism where one of two overlapping nanowires serves as a seed, while the other continues to grow as a wire; and (2) self-assembly mechanism where an aggregate of small rods (<50 nm in diameter) recrystallizes on the tip of a longer wire, extending its length.

| S-EPMC2538547 | biostudies-literature

Solid-Phase Synthesis of Fluorinated Analogues of Glycosyl 1-Phosphate Repeating Structures from Leishmania using the Phosphoramidite Method.

Project description:Bacterial and protozoan sugar chains contain glycosyl 1-phosphate repeating structures; these repeating structures have been studied for vaccine development. The fluorinated analogues of [?-Gal-(1?4)-?-Man-(1?6)-P-] n , which are glycosyl 1-phosphate repeating structures found in Leishmania, were synthesised using the solid-phase phosphoramidite method. This method has been less extensively studied for the synthesis of glycosyl 1-phosphate units than H-phosphonate chemistry. A stepwise synthesis of a compound containing five such repeating units has been conducted using the phosphoramidite method herein, which is the longest glycosyl 1-phosphate structures to be chemically constructed in a stepwise manner.

| S-EPMC5987806 | biostudies-other

Synthesis of the 5'-Se-thymidine phosphoramidite and convenient labeling of DNA oligonucleotide.

Project description:The synthesis of the 5'-Se-derivatized thymidine and phosphoramidite is reported, and the Se-phosphoramidite was incorporated into DNA. Because of its high nucleophilicity, this 5'-Se-moiety permits convenient postsynthetic modification of oligonucleotides. The proof of principle was successfully demonstrated by incorporating fluorescein into DNA. It was also found that the 5'-dye-labeled Se-DNA can be recognized by DNA polymerase as an efficient primer. This novel strategy opens a new avenue for nucleic acid probe preparation and detection.

| S-EPMC3241971 | 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