Bending of oligonucleotides containing an isosteric nucleobase: 7-deaza-2'-deoxyadenosine replacing dA within d(A)6 tracts

Publisher Website
Google Scholar
Abstract
Decanucleotide duplexes of the parent sequence d(GGCA6C).cntdot.d(CCGT6G) containing various numbers of 2''-deoxytubercidin (c7Ad) in place of 2''-deoxyadenosine have been synthesized. Phosphoramidites of protected c7Ad (3a,b) were used in automated solid-phase synthesis together with those of regular nucleosides. Upon enzymic 5''-phosphorylation and ligation, multimers of 5 and 7-11 were analyzed by polyacrylamide gel electrophoresis and compared with regard to intrinsic, sequence-directed bending. Replacement of dA by C7Ad within the oligomers decreased bending, but the extent depends strongly on the position of incorporation: strong bending was still observed if the 3''- and 5''-terminal dA residues of the dA tract were replaced while the interruption of the d(A)6 tract by c7Ad reduced bending strongly.