The N-8-(2 `-deoxyribofuranoside) of 8-aza-7-deazaadenine : a universal nucleoside forming specific hydrogen bonds with the four canonical DNA constituents

Abstract

The 8-aza-7-deazaadenine (pyrazolo[3,4-d]pyrimidin-4-amine) N-8-(2'-deoxyribonucleoside) (2) which has an unusual glycosylation position was introduced as a universal nucleoside in oligonucleotide duplexes. These oligonucleotides were prepared by solid-phase synthesis employing phosphoramidite chemistry. Oligonucleotides incorporating the universal nucleoside 2 are capable of forming base pairs with the four normal DNA nucleosides without significant structural discrimination. The thermal stabilities of those duplexes are very similar and are only moderately reduced compared to those with regular Watson-Crick base pairs, The universal nucleoside 2 belongs to a new class of compounds that form bidentate base pairs with all four natural DMA constituents through hydrogen bonding. The base pair motifs follow the Watson-Crick or the Hoogsteen mode. Also an uncommon motif is suggested for the base pair of 2 and dG. All of the new base pairs have a different shape compared to those of the natural DNA but fit well into the DNA duplex as the distance of the anomeric carbons approximates those of the common DNA base pairs.