Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles

Abstract

Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.

Diastereoselective Synthesis of Pyridone ribo‐C‐Nucleosides via Heck Reaction and Oxidation

“…Targets 9 a-d were chosen as precursors of inhibitors of the RNA-dependant RNA polymerase (RdRp) of RNA viruses. The choice of pyridones as nucleobase analogs [10,13,32,33] was made to cover a range of pairing strengths with adenine in template strands. An ethynyl group was one of the substituents chosen for the 6-position of the pyridone, as it known to assist strong pairing with adenine.…”

“…Thus far, our synthetic efforts in the field of pyridone C ‐nucleosides had been focused on 2’‐deoxynucleosides [13,31,32,33] . Target molecules, such as deoxynucleoside E (Figure 1) were synthesized via Heck reaction, desilylation and diastereoselective reduction, to produce the desired β‐anomers.…”

“…Thus far, our synthetic efforts in the field of pyridone Cnucleosides had been focused on 2'-deoxynucleosides. [13,31,32,33] Target molecules, such as deoxynucleoside E (Figure 1) were synthesized via Heck reaction, desilylation and diastereoselective reduction, to produce the desired β-anomers. We therefore sought a method that would produce ribonucleosides, starting from the silyl enol ether as substrate for oxidation reactions, possibly in the form of an epoxidation or dihydroxylation.…”