2 `-deoxyuridine and 2 `-deoxyisocytidine as constituents of DNA with parallel chain orientation: The stabilization of the iC(d)center dot Gd base pair by the 5-methyl group

Abstract

Parallel-stranded oligonucleotides containing 2'-deoxyuridine (2) and 2'-deoxyisocytidine (4) were synthesized. The phosphoramidite 11 employed in the solid-phase synthesis carries a (dimethylamino)methylidene residue as amino-protecting group. This group stabilizes the acid-labile glycosylic bond of 4 and enables the base-catalyzed deprotection of oligonucleotides without degrading the nucleoside 4 residues. Oligonucleotide duplexes incorporating the 5-Me derivatives of 2 (--> 2'-deoxythymidine) and 4 (--> 2'-deoxy-5methylisocytidine), which are more stable than those containing the unmethylated nucleosides, were also compared. Depending on the nearest-neighbor environment, Me groups provide an additional stabilization through Me/Me contacts or Me/backbone interactions.