5-aza-7-deaza-2 `-deoxyguanosine: Oligonucleotide duplexes with novel base pairs, parallel chain orientation and protonation sites in the core of a double helix

Abstract

Oligonucleotides containing 5-aza-7-deaza-2'-deoxyguanosine (1) were synthesized. Solid-phase synthesis was performed with the phosphonate 15 or the phosphoramidite 5. The amino-unprotected phosphonate 4 was also employed. Hybridization studies of oligonucleotides containing 1 resulted in new base pairs leading to duplexes with parallel tps) or antiparallel taps) chain orientation. Among those with parallel chains a stable ``purine-purine'' base pair was observed between 5-aza-7-deazaguanine and guanine or 7-deazaguanine. Antiparallel stranded duplexes are formed when 5-aza-7-deazaguanine pairs with cytosine. This base pair has only two hydrogen bonds under neutral conditions but is stabilized by a third one in acidic medium. A new base pair is also detected between the base of 1 and isoguanine (neutral medium).