Oligodeoxyribonucleotides containing 4-aminobenzimidazole in place of adenine: Solid-phase synthesis and base pairing

Article abstract of DOI:10.1002/hlca.19950780405

Oligonucleotides containing 4-aminobenzimidazole 2'-deoxyribofuranoside (1,3-dideaza-2'-deoxyadenosine; c¹c³A(d), 1) were synthesized. For this purpose, various NH₂-protecting groups were investigated, and the [(9H-fluoren-9-yl)methoxy]carbonyl group was selected for phosphoramidite protection (→4c). Apart from the phosphoramidite 3, the phosphonate 2 was prepared. Compound 1 was incorporated in a homooligonucleotide as well as in oligomers containing naturally occurring nucleosides. The T(m) values and the thermodynamic data of various duplexes (11.10, 17.10, 18.10) containing 4-aminobenzimidazole were determined. Although d[(c¹c³A)₂₀] (11) does not form a Hoogsteen duplex with d(T₂₀) (10) as observed with d[(c¹A)₂₀], it destabilizes the Watson-Crick duplexes to a much smaller extent than it was expected from a bulged loop structure. Apparently, 4-aminobenzimidazole interacts with regular nucleoside residues within a Watson-Crick duplex structure, most likely by vertical stacking. According to the low basicity of the amino group, only weak H-bonding is expected.