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Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides.

ABSTRACT: 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.

SUBMITTER: Lingala S

PROVIDER: S-EPMC6386463 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides.

Lingala Suresh S Nordstrøm Lars Ulrik LU Mallikaratchy Prabodhika R PR

Tetrahedron letters 20181208 3

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 <sup>31</sup>P NMR at room temperature showed less than 10% degradation after 6 hours. The azide modified thymidine wa ...[more]

PMID: 30804607

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Project description:Copper(I) [Cu2(μ-Br)2(tBuImCH2pyCH2L)] n (L = OMe, NEt2, NHtBu) compounds supported by flexible functionalized NHC-based polydentate ligands have been prepared in a one-pot procedure by reacting the corresponding imidazolium salt with an excess of copper powder and Ag2O. An X-ray diffraction analysis has revealed that [Cu2(μ-Br)2(tBuImCH2pyCH2NEt2)] n is a linear coordination polymer formed by bimetallic [Cu(μ-Br)]2 units linked by the lutidine-based NHC-py-NEt2 ligand, which acts as a heteroditopic ligand with a 1κC-2κ2 N,N' coordination mode. We propose that the polymeric compounds break down in the solution into more compact tetranuclear [Cu2(μ-Br)2(tBuImCH2pyCH2L)]2 compounds with a coordination mode identical to the functionalized NHC ligands. These compounds have been found to exhibit high catalytic activity in the Cu-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. In particular, [Cu2(μ-Br)2(tBuImCH2pyCH2NEt2)]2 efficiently catalyzes the click reaction of a range of azides and alkynes, under an inert atmosphere at room temperature in neat conditions at a very low catalyst loading, to quantitatively afford the corresponding 1,4-disubstituted 1,2,3-triazole derivatives in a few minutes. The cycloaddition reaction of benzyl azide to phenylacetylene can be performed at 25-50 ppm catalyst loading by increasing the reaction time and/or temperature. Reactivity studies have shown that the activation of the polynuclear catalyst precursor involves the alkyne deprotonation by the NHC moiety of the polydentate ligand to afford a copper(I)-alkynyl species bearing a functionalized imidazolium ligand. DFT calculations support the participation of the dinuclear species [(CuBr)2(μ-tBuImCH2pyCH2NEt2)], resulting from the fragmentation of the tetranuclear compound, as the catalytically active species. The proposed reaction pathway proceeds through zwitterionic dinuclear intermediates and entails the active participation of both copper atoms, as well as the NHC moiety as an internal base, which activates the reacting alkyne via deprotonation.

Project description:Protein prenylation is a post-translational modification that involves the addition of one or two isoprenoid groups to the C-terminus of selected proteins using either farnesyl diphosphate or geranylgeranyl diphosphate. Three crucial enzymatic steps are involved in the processing of prenylated proteins to yield the final mature product. The farnesylated dodecapeptide, a-factor, is particularly useful for studies of protein prenylation because it requires the identical three-step process to generate the same C-terminal farnesylated cysteine methyl ester substructure present in larger farnesylated proteins. Recently, several groups have developed isoprenoid analogs bearing azide and alkyne groups that can be used in metabolic labeling experiments. Those compounds have proven useful for profiling prenylated proteins and also show great promise as tools to study how the levels of prenylated proteins vary in different disease models. Herein, we describe the preparation and use of prenylated a-factor analogs, and precursor peptides, to investigate two key questions. First, a-factor analogues containing modified isoprenoids were prepared to evaluate whether the non-natural lipid group interferes with the biological activity of the a-factor. Second, a-factor-derived precursor peptides were synthesized to evaluate whether they can be efficiently processed by the yeast proteases Rce1 and Ste24 as well as the yeast methyltransferase Ste14 to yield mature a-factor analogues. Taken together, the results reported here indicate that metabolic labeling experiments with azide- and alkyne-functionalized isoprenoids can yield prenylated products that are fully processed and biologically functional. Overall, these observations suggest that the isoprenoids studied here that incorporate bio-orthogonal functionality can be used in metabolic labeling experiments without concern that they will induce undesired physiological changes that may complicate data interpretation.

Dataset Information

Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides.

Publications

Synthesis of stable azide and alkyne functionalized phosphoramidite nucleosides.

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