Purine-Purine Base Pairs in Parallel DNA: beta-D Anomeric 8-Aza-7-deazaisoguanine and 7-Functionalized Conjugates Form Stable Base Pairs with alpha-D 5-Aza-7-deaza-2 `-deoxyguanosine

Abstract

Anomeric purine-purine DNA represents a new recognition system with strands in parallel orientation. This work investigates the new heterochiral system and the positional impact of nucleobase functionalization. Tracts of anomeric isoguanine/8-aza-7-deazaisoguanine base pairs with 5-aza-7-deazaguanine were embedded in anomeric Watson-Crick DNA. It was discovered that stable purine-purine base pairs are formed in anomeric DNA. Nucleobase functionalization of the novel base pair system with short ethynyl and bulky octadiynyl chains showed that the position of functionalization is critical. From T-m values and thermodynamic data, it is disclosed that side chains at 7-position of the beta-D 8-aza-7-deaza-2'-deoxyisoguanosine-alpha-D 5-aza-7-deaza-2'-deoxyguanosine purine-purine pair are well accommodated in this new heterochiral DNA, whereas functionalization at 8-position of isoguanine hinders base pair formation. The new DNA base pair system has the potential to be applied in chemical biology, bioconjugation, and nanobiotechnology.