Oxidative stress is known to be highly deleterious in the maintenance of genetic information. Sugar radicals and related species have been shown to be involved in oxidative events involving RNA. The characterization of RNA degradation products has lagged when compared to the DNA field and requires further investigation. Our lab previously utilized the site selective, photocleavable radical moiety, pivaloyl, to study 5'-radical degradation in uridine and pseudouridine nucleosides. It is our aim to introduce such radical precursors into biologically relevant oligonucleotide sequences using reverse RNA synthesis and study the impact 5'-radicals have on RNA within the context of primary and secondary structures. Prior to integration into oligonucleotide sequences, the impact of the presence of the pivaloyl moiety on nucleoside conformation must be fully characterized. We have synthesized 5'-pivaloyl pseudouridine and characterized the base orientation and sugar pucker conformation. Our results allow us to understand more completely the degradation products of the nucleoside and anticipate the outcome of radical induction in the context of oligonucleotide sequences.

Synthesis and structural analysis of 5'-pivaloyl pseudouridine, a site-selective radical nucleoside precursor

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