Synthesis of Oligonucleotides and Thermal Stability of Duplexes Containing the β-C-Nucleoside Analogue of Fapy·dG

The formamidopyrimidine lesions (Fapy·dA, Fapy·dG) are formed in significant amounts when DNA is exposed to oxidative stress. These lesions are unusual in that they readily epimerize in solution. The distribution of configurational isomers in DNA is unknown. Nonepimerizable, nonhydrolyzable analogues are useful probes for investigating the configuration of Fapy lesions in DNA and as potential enzyme inhibitors. The β-C-nucleoside of Fapy·dG has been prepared and introduced sight-specifically into oligonucleotides via its respective β-cyanoethyl phosphoramidite. The phosphoramidite was prepared via a Wittig reaction between a protected form of deoxyribose and a suitably functionalized pyrimidine. The pyrimidine contained methyl and 2-propyl groups at the O4 and O2 positions, respectively, to differentiate between them following C-nucleoside formation. The formamide was derived from a nitro group at C5. The phosphoramidite coupled in 80% yield via a single 15-min coupling using tetrazole as activator. Oligonucleotides as long as 36 nucleotides were prepared and characterized by ESI-MS.