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Practical synthesis of N-(di-n-butylamino)methylene-protected 2-aminopurine riboside phosphoramidite for RNA solid-phase synthesis.

ABSTRACT: Graphic abstract Electronic supplementary materialThe online version of this article (10.1007/s00706-019-02502-7) contains supplementary material, which is available to authorized users.

SUBMITTER: Neuner E

PROVIDER: S-EPMC6936340 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Improved Synthesis of Phosphoramidite-Protected N6-Methyladenosine via BOP-Mediated SNAr Reaction.

Project description:N6-methyladenosine(m6A) is the most abundant modification in mRNA. Studies on proteins that introduce and bind m6A require the efficient synthesis of oligonucleotides containing m6A. We report an improved five-step synthesis of the m6A phosphoramidite starting from inosine, utilising a 1-H-benzotriazol-1-yloxytris(dimethylamino)phosphoniumhexafluorophosphate (BOP)-mediated SNAr reaction in the key step. The route manifests a substantial increase in overall yield compared to reported routes, and is useful for the synthesis of phosphoramidites of other adenosine derivatives, such as ethanoadenosine, an RNA analogue of the DNA adduct formed by the important anticancer drug Carmustine.

| S-EPMC7796277 | 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 building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA.

Project description:TEMPO spin labels protected with 2-nitrobenzyloxymethyl groups were attached to the amino residues of three different nucleosides: deoxycytidine, deoxyadenosine, and adenosine. The corresponding phosphoramidites could be incorporated by unmodified standard procedures into four different self-complementary DNA and two RNA oligonucleotides. After photochemical removal of the protective group, elimination of formic aldehyde and spontaneous air oxidation, the nitroxide radicals were regenerated in high yield. The resulting spin-labeled palindromic duplexes could be directly investigated by PELDOR spectroscopy without further purification steps. Spin-spin distances measured by PELDOR correspond well to the values obtained from molecular models.

| S-EPMC6036967 | biostudies-literature

Temperature-Controlled Conversion of Boc-Protected Methylene Blue: Advancing Solid-State Time-Temperature Indicators.

Project description:Cold-chain management is of high importance in preserving perishable products and in retaining quality. A visible marker on packages indicating complete maintenance of the cold chain assures safe consumption of products by end-users and assists in reducing waste. Time-temperature indicators (TTIs) are integrated markers that provide information about exposure of packages to adverse temperature and have been gaining increased attention by consumers. Here we present a methylene-blue-based derivative, N,N,N',N'-tetramethyl-N10 -Boc-phenothiazine-3,7-diamine (BocPTDA), that can be used as a solid-state organic TTI dye, exhibiting an irreversible change from colorless to blue green upon heating. The conversion properties, studied using a silicagel-coated plate, confirmed that BocPTDA undergoes a color change above 20 °C. At temperatures of 4 °C and below, no visible changes are exhibited, making BocPTDA a well-suited marker for monitoring abrupt temperature deviations indicating improper cold-chain management. Thus, application of BocPTDA-based TTI systems on packages could inform consumers about the cold-chain maintenance, assuring quality and safe consumption.

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The synthesis of 15N(7)-Hoogsteen face-labeled adenosine phosphoramidite for solid-phase RNA synthesis.

Project description:AbstractWe have developed an efficient route for the synthesis of 15N(7)-labeled adenosine as phosphoramidite building block for site- and atom-specific incorporation into RNA by automated solid-phase synthesis. Such labeled RNA is required for the evaluation of selected non-canonical base pair interactions in folded RNA using NMR spectroscopic methods.Graphical abstract

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Efficient access to N-trifluoroacetylated 2'-amino-2'-deoxyadenosine phosphoramidite for RNA solid-phase synthesis.

Project description:AbstractHere, we present a robust synthetic route to a 2'-amino-2'-deoxyadenosine phosphoramidite building block for automated RNA solid-phase synthesis. The thus accessible 2'-amino-modified RNA finds applications in the evaluation of hydrogen-bond networks in folded RNA, such as riboswitches or ribozymes. In this context, we previously implemented the here described 2'-amino-2'-deoxyadenosine building block in a comparative study on self-cleaving pistol ribozymes to shed light on structural versus catalytic roles of active-site 2'-OH groups in the reaction mechanism.Graphical abstract

| S-EPMC6534076 | biostudies-literature

Convenient Synthesis of Acetonide Protected 3,4-Dihydroxyphenylalanine (DOPA) for Fmoc Solid-Phase Peptide Synthesis.

Project description:We report a facile approach to the synthesis of acetonide and Fmoc protected 3,4-dihydroxyphenylalanine (DOPA), Fmoc-DOPA(acetonide)-OH. By protecting the amino group of DOPA with a phthaloyl group and the carboxyl group as a methyl ester, acetonide protection of the catechol of DOPA derivative was realized in the presence of p-toluenesulfonic acid. Following removal of protecting groups, the intermediate was converted to Fmoc-DOPA(acetonide)-OH, which was successfully incorporated into a short DOPA-containing peptide, derived from marine tubeworm cement proteins Pc1 and Pc2.

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Synthesis and solid-phase application of suitably protected gamma-hydroxyvaline building blocks.

Project description:Recently, an unexpected modified residue, gamma-hydroxy-D-valine (D-Hyv), was identified within ribosomally expressed polypeptide chains of four conopeptides from the venoms of Conus gladiator and Conus mus. To assemble Hyv-containing peptides, we have explored several routes for the synthesis of appropriately functionalized Hyv building blocks. D-Hyv was produced from D-Val by using a variation of the previously published K2PtCl4/CuCl2 oxidative method. Direct synthesis of Boc- or Cbz-D-Hyv lactone proceeded in low yield; additionally, the lactones are too unreactive for solid-phase applications. 9-Borabicyclononane or copper-complexed D-Hyv was prepared and treated with tert-butyldimethylsilyl trifluoromethanesulfonate (TBDMSOTf) to produce D-Hyv(O-TBDMS). The most efficient complex disruption was achieved by Chelex 110 resin (Na+ form) treatment of copper-complexed D-Hyv(O-TBDMS). Reaction of D-Hyv(O-TBDMS) with Fmoc-OSu produced Fmoc-D-Hyv(O-TBDMS) in 26% yield from D-Val. The Fmoc-D-Hyv(O-TBDMS) diastereomers were separated by preparative RP-HPLC in 13% yield from D-Val. Fmoc-D-Hyv(O-TBDMS) was used for the synthesis of the conopeptide gld-V* from Conus gladiator. The isolated synthetic and natural products had coincidental mass and NMR spectra. The methodology presented herein will greatly facilitate biological studies of Hyv-containing sequences, such as receptor responses to hydroxylated versus nonhydroxylated conopeptides and the relative susceptibility of proteins to modification by oxidative stress.

| S-EPMC2551766 | biostudies-literature

New chiral phosphoramidite complexes of iron as catalytic precursors in the oxidation of activated methylene groups.

Project description:New phosphoramidite complexes of iron were synthesized and structurally characterized. Reaction of the known chiral phosphoramidites (RO)2PNR'2 (R = binaphthyl, R' = CH3, 1a; R = binaphthyl, R' = benzyl, 1b) with [FeBr(Cp)(CO)2] afforded the title compounds [FeBr(Cp)(CO)(1a,b)] (4a,b) in 34 and 65 % isolated yields as mixtures of diastereomers, since both the metal and the ligand are stereogenic. Similarly, reaction of 1b with [Fe(Cp)I(CO)2] in the presence of catalytic [Fe(Cp)(CO)2]2 afforded [Fe(Cp)I(CO)(1b)] (5b) in 81% yield as a mixture of diastereomers. The molecular structures of 4a, 4b and 5 were determined, revealing a pseudo octahedral coordination geometry about the iron center. The new metal complexes are catalytically active in the oxidation of benzylic methylene groups to the corresponding ketones, utilizing t-BuOOH as oxidant (2 mol% catalyst, 36 h, room temperature, 31-80% yield).

| S-EPMC6257337 | 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 [β-Gal-(1→4)-α-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-literature

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