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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.

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

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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.

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An Improved Approach for Practical Synthesis of 5-Hydroxymethyl-2'-deoxycytidine (5hmdC) Phosphoramidite and Triphosphate.

Project description:5-Hydroxymethyl-2'-deoxycytidine (5hmdC) phosphoramidite and triphosphate are important building blocks in 5hmdC-containing DNA synthesis for epigenetic studies. However, efficient and practical methods for the synthesis of these compounds are still limited. The current research provides an intensively improved synthetic method that enables the preparation of commercially available cyanoethyl-protected 5hmdC phosphoramidite with an overall yield of 39% on 5 g scale. On the basis of facile and efficient accesses to cyanoethyl protected-5hmdU and 5hmdC intermediates, two efficient synthetic routes for 5hmdC triphosphate were also developed.

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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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Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates.

Project description:Oligonucleotide conjugates are versatile scaffolds that can be applied in DNA-based screening platforms and ligand display or as therapeutics. Several different chemical approaches are available for functionalizing oligonucleotides, which are often carried out on the 5' or 3' end. Modifying oligonucleotides in the middle of the sequence opens the possibility to ligate the conjugates and create DNA strands bearing multiple different ligands. Our goal was to establish a complete workflow that can be applied for such purposes from monomer synthesis to templated ligation. To achieve this, a monomer is required with an orthogonal functional group that can be incorporated internally into the oligonucleotide sequence. This is followed by conjugation with different molecules and ligation with the help of a complementary template. Here, we show the synthesis and the application of a thiol-modified thymidine nucleoside phosphoramidite to prepare ligatable oligonucleotide conjugates. The conjugations were performed both in solution and on solid phase, resulting in conjugates that can be assembled into multivalent oligonucleotides decorated with tissue-targeting peptides using templated ligation.

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Efficient access to <i>N</i>-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

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

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Practical Synthesis of Quinoline-Protected Morpholino Oligomers for Light-Triggered Regulation of Gene Function.

Project description:Photoactivatable cyclic caged morpholino oligomers (ccMOs) represent a promising tool to selectively regulate gene expression with spatiotemporal control. Nevertheless, some challenges associated with the preparation of these reagents have limited their broader use in biological settings. We describe a novel ccMO design that overcomes many of the challenges and considerably expedites the synthetic preparation. The key factor is the introduction of an ethynyl function on the photocleavable linker to facilitate the use of a Huisgen 1,3-dipolar cycloaddition for the coupling reaction with the oligonucleotide. Compared to previous strategies, this modification reduces the number of synthetic steps and significantly improves the total yield and the stability of the linker. We used the alkynyl-functionalized linker for the preparation of two different ccMOs targeting the mRNA of the glutamic acid decarboxylase genes, gad1 and gad2. HPLC analysis confirms that the caging strategy successfully inhibits the DNA binding ability, and the activity can be restored by brief illumination with 405-nm light. Overall, the straightforward preparation together with the clean and fast photochemistry make these caged antisense reagents excellent tools to modulate gene function in-vivo with spatial and temporal precision.

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