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

• Published in: Biochemistry (Easton) 1989-07, Vol.28 (15), p.6193-6198
• Main Authors: Seela, Frank, Berg, Heike, Rosemeyer, Helmut
• Format: Article
• Language: English
• Subjects: Aminoglycosides; Analytical, structural and metabolic biochemistry; Anti-Bacterial Agents - analogs & derivatives; Base Sequence; Biological and medical sciences; Deoxyadenosines; Fundamental and applied biological sciences. Psychology; Indicators and Reagents; Magnetic Resonance Spectroscopy; Molecular Sequence Data; Nucleic Acid Conformation; Nucleic acids; Nucleic bases, nucleotides; Oligodeoxyribonucleotides - chemical synthesis; Spectrophotometry, Ultraviolet; Tubercidin - analogs & derivatives
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi00441a010

Decanucleotide duplexes of the parent sequence d(GGCA6C).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.