Oligonucleotides containing 6-aza-2'-deoxyuridine: synthesis, nucleobase protection, pH-dependent duplex stability,...

Oligodeoxyribonucleotides containing the nucleoside 6-aza-2'-deoxyuridine z6Ud (1a) were prepared by using solid-phase synthesis. As the pKa value of this nucleoside is 6.8, unwanted side reactions are observed. Consequently, nitrogen-3 was protected (o-anisoyl protection). The phosphoramidite of 1a prepared on this route was as efficient as the building blocks of canonical nucleosides in allowing multiple incorporations into oligonucleotides. Oligonucleotide duplexes containing 1a show a pH dependence of the Tm value. This is caused by nucleobase deprotonation occurring on compound 1a already under neutral conditions. Metal (M)-DNA formation was studied in the presence of Zn+2 ions. It is demonstrated that 6-azauracil-modified duplexes form M-DNA already in neutral medium while alkaline conditions (above pH 8.5) are required for natural DNA. The conformational analysis of the sugar moiety of the nucleoside 1a and its anisoyl derivative 5a shows a preferred N-conformation in solution while an S-conformation for compound 1a was obtained in the solid state (single-crystal X-ray analysis).