Browse
Submit Data
Databases
API
Help

Dataset Information

23 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Study on Synthesis and Upscaling of 2'-O-AECM-5-methyl Pyrimidine Phosphoramidites for Oligonucleotide Synthesis.

ABSTRACT: 2'-O-(N-(Aminoethyl)carbamoyl)methyl-modified 5-methyluridine (AECM-MeU) and 5-methylcytidine (AECM-MeC) phosphoramidites are reported for the first time and prepared in multigram quantities. The syntheses of AECM-MeU and AECM-MeC nucleosides are designed for larger scales (approx. 20 g up until phosphoramidite preparation steps) using low-cost reagents and minimizing chromatographic purifications. Several steps were screened for best conditions, focusing on the most crucial steps such as N³ and/or 2'-OH alkylations, which were improved for larger scale synthesis using phase transfer catalysis (PTC). Moreover, the need of chromatographic purifications was substantially reduced by employing one-pot synthesis and improved work-up strategies.

SUBMITTER: Karale K

PROVIDER: S-EPMC8619030 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Tandem oligonucleotide synthesis using linker phosphoramidites.

Project description:Multiple oligonucleotides of the same or different sequence, linked end-to-end in tandem can be synthesized in a single automated synthesis. A linker phosphoramidite [R. T. Pon and S. Yu (2004) Nucleic Acids Res., 32, 623-631] is added to the 5'-terminal OH end of a support-bound oligonucleotide to introduce a cleavable linkage (succinic acid plus sulfonyldiethanol) and the 3'-terminal base of the new sequence. Conventional phosphoramidites are then used for the rest of the sequence. After synthesis, treatment with ammonium hydroxide releases the oligonucleotides from the support and cleaves the linkages between each sequence. Mixtures of one oligonucleotide with both 5'- and 3'-terminal OH ends and other oligonucleotides with 5'-phosphorylated and 3'-OH ends are produced, which are deprotected and worked up as a single product. Tandem synthesis can be used to make pairs of PCR primers, sets of cooperative oligonucleotides or multiple copies of the same sequence. When tandem synthesis is used to make two self-complementary sequences, double-stranded structures spontaneously form after deprotection. Tandem synthesis of oligonucleotide chains containing up to six consecutive 20mer (120 bases total), various trinucleotide codons and primer pairs for PCR, or self-complementary strands for in situ formation of double-stranded DNA fragments has been demonstrated.

| S-EPMC1074720 | biostudies-literature

On-demand synthesis of phosphoramidites.

Project description:Automated chemical synthesis of oligonucleotides is of fundamental importance for the production of primers for the polymerase chain reaction (PCR), for oligonucleotide-based drugs, and for numerous other medical and biotechnological applications. The highly optimised automised chemical oligonucleotide synthesis relies upon phosphoramidites as the phosphate precursors and one of the drawbacks of this technology is the poor bench stability of phosphoramidites. Here, we report on the development of an on-demand flow synthesis of phosphoramidites from their corresponding alcohols, which is accomplished with short reaction times, near-quantitative yields and without the need of purification before being submitted directly to automated oligonucleotide synthesis. Sterically hindered as well as redox unstable phosphoramidites are synthesised using this methodology and the subsequent couplings are near-quantitative for all substrates. The vision for this technology is direct integration into DNA synthesisers thereby omitting manual synthesis and storage of phosphoramidites.

| S-EPMC8101336 | biostudies-literature

Synthesis of 5'-Thio-3'-O-ribonucleoside Phosphoramidites.

Project description:The chemical synthesis of phosphoramidite derivatives of all four 5'-deoxy-5'-thioribonucleosides is described. These phosphoramidites contained trityl (A, G, C, and U), dimethoxytrityl (A and G), or tert-butyldisulfanyl (G) as the 5'-S-protecting group. The application of several of these phosphoramidites for solid-phase synthesis of oligoribonucleotides containing a 2'-O-photocaged 5'-S-phosphorothiolate linkage or 5'-thiol-labeled RNAs is also further investigated.

| S-EPMC6557410 | biostudies-literature

2-Methyl-4,6-bis-(1-methyl-hydrazino)pyrimidine.

Project description:In the title compound, C(7)H(14)N(6), the amine groups of the two methyl-hydrazino substituents are orientated in the opposite direction to the methyl substituent at the 2-position of the pyrimidine ring. The mol-ecule is almost planar with only the two amine N atoms lying substanti-ally out of the mean plane of the pyrimidine ring [by 0.1430?(2) and 0.3092?(2)?Å]. The H atoms on these amine groups point inwards towards the aromatic ring, such that the lone pair of electrons points outwards from the mol-ecule. Each mol-ecule is linked to two others through N-H?N hydrogen bonds between the two amino groups, forming a one-dimensional chain in the [010] direction. Offset face-to-face ?-? stacking inter-actions between the pyrimidine rings organize these chains into a two-dimensional array [centroid-centroid distance = 3.789?(2)?Å].

| S-EPMC2969452 | biostudies-literature

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid.

Project description:IsoGNA, an isomer of glycerol nucleic acid GNA, is a flexible (acyclic) nucleic acid with bases directly attached to its linear backbone. IsoGNA exhibits (limited) base-pairing properties which are unique compared to other known flexible nucleic acids. Herein, we report on the details of the preparation of isoGNA phosphoramidites and an alternative route for the synthesis of the adenine derivative. The synthetic improvements described here enable an easy access to isoGNA and allows for the further exploration of this structural unit in oligonucleotide chemistry thereby spurring investigations of its usefulness and applicability.

| S-EPMC4168771 | biostudies-literature

Development of High-Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches.

Project description:Nucleosidic and oligonucleotidic diarylethenes (DAEs) are an emerging class of photochromes with high application potential. However, their further development is hampered by the poor understanding of how the chemical structure modulates the photochromic properties. Here we synthesized 26 systematically varied deoxyuridine- and deoxycytidine-derived DAEs and analyzed reaction quantum yields, composition of the photostationary states, thermal and photochemical stability, and reversibility. This analysis identified two high-performance photoswitches with near-quantitative, fully reversible back-and-forth switching and no detectable thermal or photochemical deterioration. When incorporated into an oligonucleotide with the sequence of a promotor, the nucleotides maintained their photochromism and allowed the modulation of the transcription activity of T7 RNA polymerase with an up to 2.4-fold turn-off factor, demonstrating the potential for optochemical control of biological processes.

| S-EPMC8049081 | biostudies-literature

Synthesis of <i>N</i> <sup>4</sup>-acetylated 3-methylcytidine phosphoramidites for RNA solid-phase synthesis.

Project description:The growing interest in 3-methylcytidine (m3C) originates from the recent discoveries of m3C modified tRNAs in humans as well as its intensively debated occurrence in mRNA. Moreover, m3C formation can be catalyzed by RNA without the assistance of proteins as has been demonstrated for a naturally occurring riboswitch fold using the methylated form of its cognate ligand as cofactor. Additionally, new RNA sequencing methods have been developed to detect this modification in transcriptome-wide manner. For all these reasons, an increasing demand for synthetic m3C containing oligoribonucleotides is emerging. Their chemical synthesis relies on RNA solid-phase synthesis using phosphoramidite building blocks. Here, we describe a facile synthetic path towards N4-acetylated 2'-O-TBDMS- and 2'-O-TOM m3C phosphoramidites to provide an optimal toolbox for solid-phase synthesis of m3C containing RNA.Graphical abstractSupplementary informationThe online version contains supplementary material available at 10.1007/s00706-022-02896-x.

| S-EPMC8948120 | biostudies-literature

4-Hydrazino-2-(methyl-sulfan-yl)-pyrimidine.

Project description:In the crystal of the title compound, C(5)H(8)N(4), centrosymmetric dimers are linked by pairs of N-H?N hydrogen bonds. Further N-H?N links result in a two-dimensional array whereby wave-like supra-molecular chains are inter-connected by R(2) (2)(8) ring motifs.

| S-EPMC2968169 | biostudies-literature

4-Hydrazino-1-methyl-pyrazolo[3,4-d]pyrimidine.

Project description:The title compound, C(6)H(8)N(6), crystallizes as an N-H?N hydrogen-bond-linked dimer of two almost identical mol-ecules in the asymmetric unit. Both of the mol-ecules are almost planar (rms deviations of 0.0186 and 0.0296?Å in the two molecules) and their hydrazino groups are turned towards the pyrazole rings. The dimers are arranged into chains via inter-molecular N-H?N hydrogen bonds between the hydrazino groups and the N atoms of the pyrimidine rings of both types of the mol-ecules, linking the mol-ecules into a C(7) graph-set motif along [100]. The methyl groups and the N atoms of the pyrazole rings form weak C-H?N hydrogen bonds, which connect chains of the dimers in a C(4) motif parallel to [100].

| S-EPMC2977168 | biostudies-literature

4-Methyl-2,6-bis-(pyrrolidin-1-yl)pyrimidine.

Project description:In the crystal of the title compound, C13H20N4, the mol-ecule is nearly planar, the dihedral angles between the pyrimidine and the two pyrrolidine rings being 4.71?(2) and 4.50?(2)°. The crystal features inversion-related dimers linked by pairs of C-H?N hydrogen bonds generating R2(2)(16) patterns. The dimeric units are further linked into C(6) chains via an additional C-H?N hydrogen bond.

| S-EPMC3589020 | 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