An efficient approach for conversion of 5-substituted 2-thiouridines built in RNA oligomers into corresponding desulfured 4-pyrimidinone products

Chwialkowska, Anna; Wielgus, Ewelina; Leszczyńska, Grażyna; Sobczak, Milena; Mikołajczyk, Barbara; Sochacka, Elżbieta; Nawrot, Barbara

doi:10.1016/j.bmcl.2015.06.019

Cited by 5 publications

(6 citation statements)

References 16 publications

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“…Under slightly acidic conditions (pH 6.6), S2U was mainly converted into H2U, whereas uridine was the major product at pH 7.6. Using oxone (KHSO 5 ) instead of H 2 O 2 , we were able to convert several 5‐substituted 2‐thiouridines present within an RNA chain (R5S2U‐RNA) exclusively into the corresponding 4‐pyrimidinone nucleoside containing RNAs, which were further used for biological and biophysical studies . The DSC (differential scanning calorimetry) and UV‐melting measurements of complexes of S2U‐, U‐, or H2U‐RNA with complementary RNA containing either A (A‐RNA) or G (G‐RNA) opposite to the modification site showed that H2U‐RNA binds preferentially to G‐RNA, whereas S2U‐RNA forms a stable duplex with A‐RNA.…”

Section: Introductionmentioning

confidence: 99%

Cytochrome cCatalyzes the Hydrogen Peroxide‐Assisted Oxidative Desulfuration of 2‐Thiouridines in Transfer RNAs

et al. 2018

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The 5-substituted 2-thiouridines (R5S2Us) present in the first (wobble) position of the anticodon of transfer RNAs (tRNAs) contribute to accuracy in reading mRNA codons and tuning protein synthesis. Previously, we showed that, under oxidative stress conditions in vitro, R5S2Us were sensitive to hydrogen peroxide (H O ) and that their oxidative desulfuration produced 5-substituted uridines (R5Us) and 4-pyrimidinone nucleosides (R5H2Us) at a ratio that depended on the pH and an R5 substituent. Here, we demonstrate that the desulfuration of 2-thiouridines, either alone or within an RNA/tRNA chain, is catalyzed by cytochrome c (cyt c). Its kinetics are similar to those of Fenton-type catalytic 2-thiouridine (S2U) desulfuration. Cyt c/H O - and Fe -mediated reactions deliver predominantly 4-pyrimidinone nucleoside (H2U)-type products. The pathway of the cyt c/H O -peroxidase-mediated S2U→H2U transformation through uridine sulfenic (U-SOH), sulfinic (U-SO H), and sulfonic (U-SO H) intermediates is confirmed by LC-MS. The cyt c/H O -mediated oxidative damage of S2U-tRNA may have biological relevance through alteration of the cellular functions of transfer RNA.

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Section: Introductionmentioning

confidence: 99%

Cytochrome cCatalyzes the Hydrogen Peroxide‐Assisted Oxidative Desulfuration of 2‐Thiouridines in Transfer RNAs

et al. 2018

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“…[77] To address this, Nawrot et al developed a method for efficient synthesis of RNA containing U H2 using post-synthetic modification in solution (Scheme 17a). [78] The treatment of RNA 17b). [79] This geranylation can also be applied as solid-phase modification.…”

Section: Modification At the 2-or 3-positionmentioning

confidence: 99%

Synthesis of Nucleobase‐Modified Oligonucleotides by Post‐Synthetic Modification in Solution

Ito

Hari

2022

The Chemical Record

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Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.

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“…The post-synthetic strategy of RNA modification has several important advantages in comparison to the classical modified monomer approach. Firstly, one single modified precursor oligoribonucleotide can provide several sequentially homologous, variously modified RNA fragments [ 60 , 61 , 62 ]. Such a strategy significantly reduces the cost of synthesis compared to preparing each modified monomeric unit separately.…”

Section: Post-synthetic Strategy For Nucleobase Rna Modificationsmentioning

confidence: 99%

“…A thiocarbonyl group in 2-thiouridines (s 2 Us) was found to be a reactive site for two post-synthetic RNA conversions. The first strategy was based on the oxidative desulfuration of s 2 U-containing oligomers leading to the formation of 4-pyrimidinone nucleosides (H 2 U) [ 61 ]. The second approach involved the reaction of a nucleophilic substitution between alkyl halide and an s 2 U-oligomer where the sulfur atom acts as a nucleophile agent, providing S -alkylated analogs of 2-thiouridine [ 12 ].…”

Section: Post-synthetic Strategy For Nucleobase Rna Modificationsmentioning

confidence: 99%

“…The attempt to incorporate an H 2 U phosphoramidite into the RNA chain turned out to be not straightforward by the classical approach because of H 2 U-RNA instability under alkaline conditions [ 104 ]. In 2015, Chwialkowska and co-workers published a selective post-synthetic transformation of oligomers modified with 2-thiouridine and 5-substituted 2-thiouridines (R 5 s 2 U-RNA, 98a – f ) exclusively to the 4-pyrimidinone-containing derivatives (R 5 H 2 U-RNA, 99a – f , Scheme 24 ) [ 61 ]. Six types of R 5 s 2 U modifications were selected to show the generality of the method: 2-thiouridine (s 2 U, R 2 = H), 2′- O -methyl-2-thiouridine (s 2 Um, R 1 = OMe, R 2 = H), 5-methyl-2-thiouridine (m 5 s 2 U, R 2 = -CH 3 ), 5-metoxycarbonylmethyl-2-thiouridine, mcm 5 s 2 U, R 2 = CH 2 COOMe), 5-methylaminomethyl-2-thiouridine (mnm 5 s 2 U, R 2 = CH 2 NHCH 3 ), and 5-taurinomethyl-2-thiouridine (τm 5 s 2 U, R 2 = CH 2 NHCH 2 CH 2 SO 3 H).…”

Section: Post-synthetic Strategy For Nucleobase Rna Modificationsmentioning

confidence: 99%

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Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach

et al. 2020

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The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers providing the oligonucleotide-based therapeutic agents in the antisense and siRNA technologies. The important sites of RNA modification/functionalization are the nucleobase residues. Standard phosphoramidite RNA chemistry allows the site-specific incorporation of a large number of functional groups to the nucleobase structure if the building blocks are synthetically obtainable and stable under the conditions of oligonucleotide chemistry and work-up. Otherwise, the chemically modified RNAs are produced by post-synthetic oligoribonucleotide functionalization. This review highlights the post-synthetic RNA modification approach as a convenient and valuable method to introduce a wide variety of nucleobase modifications, including recently discovered native hypermodified functional groups, fluorescent dyes, photoreactive groups, disulfide crosslinks, and nitroxide spin labels.

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An efficient approach for conversion of 5-substituted 2-thiouridines built in RNA oligomers into corresponding desulfured 4-pyrimidinone products

Cited by 5 publications

References 16 publications

Cytochrome cCatalyzes the Hydrogen Peroxide‐Assisted Oxidative Desulfuration of 2‐Thiouridines in Transfer RNAs

Cytochrome cCatalyzes the Hydrogen Peroxide‐Assisted Oxidative Desulfuration of 2‐Thiouridines in Transfer RNAs

Synthesis of Nucleobase‐Modified Oligonucleotides by Post‐Synthetic Modification in Solution

Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach

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