Chemistry of installing epitranscriptomic 5-modified cytidines in RNA oligomers.

Studies of 5-hydroxymethylcytidine (hmC), 5-formylcytidine (fC) and 5-carboxycytidine (caC) modifications as products of the 5-methylcytidine (mC) oxidative demethylation pathway in cellular mRNAs constitute an important element of the new epitranscriptomic field of research. The dynamic process of mC conversion and final turnover to the parent cytidine is considered a post-transcriptional layer of gene-expression regulation. However, the regulatory mechanism associated with epitranscriptomic cytidine modifications remains largely unknown.

Protection-Free, Two-step Synthesis of C5-C Functionalized Pyrimidine Nucleosides.

A simple, reliable, and efficient method for the gram-scale chemical synthesis of pyrimidine nucleosides functionalized with C5-carboxyl, nitrile, ester, amide, or amidine, starting from unprotected uridine and cytidine, is described. The protocol involves the synthesis of 5-trifluoromethyluridine and 5-trifluoromethylcytidine with Langlois reagent (CF SO Na) in the presence of tert-butyl hydroperoxide and subsequent transformation of the CF group to the C5-C 'carbon substituents' under alkaline conditions. © 2024 Wiley Periodicals LLC.

Two-step conversion of uridine and cytidine to variously C5-C functionalized analogs.

C5-substituted pyrimidine nucleosides are an important class of molecules that have practical use as biological probes and pharmaceuticals. Herein we report an operationally simple protocol for C5-functionalization of uridine and cytidine transformation of underexploited 5-trifluoromethyluridine or 5-trifluoromethylcytidine, respectively. The unique reactivity of the CF group in the aromatic ring allowed the direct incorporation of several distinct C5-C "carbon substituents": carboxyl, nitrile, ester, amide, and amidine.

Synthesis and properties of the anticodon stem-loop of human mitochondrial tRNA containing the disease-related G or mG nucleosides at position 37.

A single point mutation (A4435G) in the human mitochondrial tRNA (hmt-tRNA) gene causes severe mitochondrial disorders associated with hypertension, type 2 diabetes and LHON. This mutation leads to the exchange of A in the anticodon loop of hmt-tRNA for G and 1-methylguanosine (mG). Here we present the first synthesis and structural/biophysical studies of the anticodon stem and loop of pathogenic hmt-tRNAs.

Iron-sulfur biology invades tRNA modification: the case of U34 sulfuration.

Sulfuration of uridine 34 in the anticodon of tRNAs is conserved in the three domains of life, guaranteeing fidelity of protein translation. In eubacteria, it is catalyzed by MnmA-type enzymes, which were previously concluded not to depend on an iron-sulfur [Fe-S] cluster. However, we report here spectroscopic and iron/sulfur analysis, as well as in vitro catalytic assays and site-directed mutagenesis studies unambiguously showing that MnmA from Escherichia coli can bind a [4Fe-4S] cluster, which is essential for sulfuration of U34-tRNA.

Chemical Synthesis of Oligoribonucleotide (ASL of tRNA T. brucei) Containing a Recently Discovered Cyclic Form of 2-Methylthio-N -threonylcarbamoyladenosine (ms ct A).

The synthesis of the protected form of 2-methylthio-N -threonylcarbamoyl adenosine (ms t A) was developed starting from adenosine or guanosine by using the optimized carbamate method and, for the first time, an isocyanate route. The hypermodified nucleoside was subsequently transformed into the protected ms t A-phosphoramidite monomer and used in a large-scale synthesis of the precursor 17nt ms t A-oligonucleotide (the anticodon stem and loop fragment of tRNA from T. brucei).