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Oligodeoxyribonucleotides Containing 4‐Aminobenzimidazole in Place of Adenine: Solid‐phase synthesis and base pairing
Author(s) -
Seela Frank,
Wenzel Thomas
Publication year - 1995
Publication title -
helvetica chimica acta
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.74
H-Index - 82
eISSN - 1522-2675
pISSN - 0018-019X
DOI - 10.1002/hlca.19950780405
Subject(s) - chemistry , phosphoramidite , duplex (building) , stacking , oligonucleotide , stereochemistry , nucleoside , phosphonate , deoxyadenosine , base pair , crystallography , oligonucleotide synthesis , molecule , dna , organic chemistry , biochemistry
Oligonucleotides containing 4‐aminobenzimidazole 2′‐deoxyribofuranoside (1,3‐dideaza‐2′‐deoxyadenosine; c 1 c 3 A d , 1 ) were synthesized. For this purpose, various NH 2 ‐protecting groups were investigated, and the [(9 H ‐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 T m values and the thermodynamic data of various duplexes ( 11 · 10 , 17 · 10 , 18 · 10 ) containing 4‐aminobenzimidazole were determined. Although d[(c 1 c 3 A) 20 ] ( 11 ) does not form a Hoogsteen duplex with d(T 20 ) ( 10 ) as observed with d[(c 1 A) 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.