Oligodeoxyribonucleotides Containing 4-Aminobenzimidazole in Place of Adenine: Solid-phase synthesis and base pairing

Authors

  • Frank Seela,

    Corresponding author
    1. Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, D–49069 Osnabrück
    • Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, D–49069 Osnabrück
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  • Thomas Wenzel

    1. Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie, Universität Osnabrück, Barbarastrasse 7, D–49069 Osnabrück
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Abstract

Oligonucleotides containing 4-aminobenzimidazole 2′-deoxyribofuranoside (1,3-dideaza-2′-deoxyadenosine; c1c3Ad, 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 homooligonuclectide as well as in oligomers containing naturally occurring nucleosides. The Tm 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-aminobenz-imidazole 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.

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