Sequence Preference for Strand Cleavage of Gapped Duplexes by Dynemicin A: Possible Mechanism of Sequence-Dependent Double-Stranded Breaks

• Published in: Biochemistry (Easton) Vol. 34; no. 31; pp. 9944 - 9950
• Main Authors: Kusakabe, Tetsuya, Uesugi, Motonari, Sugiura, Yukio
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 08-08-1995
• Subjects: Alkenes; Anthraquinones - metabolism; Anthraquinones - pharmacology; Antibiotics, Antineoplastic - metabolism; Antibiotics, Antineoplastic - pharmacology; Base Sequence; DNA - drug effects; DNA Damage; DNA, Superhelical - drug effects; Enediynes; Intercalating Agents - pharmacology; Models, Chemical; Molecular Sequence Data; Oligodeoxyribonucleotides; Thioglycolates
• DOI: 10.1021/bi00031a017
• EISSN: 1520-4995
• ISSN: 0006-2960

A double-stranded DNA cleavage mechanism by a novel enediyne type antitumor antibiotic, dynemicin A, has been investigated through sequence-dependent strand breakage of a series of duplexes containing a single nucleotide gap. We found that (1) dynemicin A breaks specifically at the 3'-shifted position by one base opposite the gap, (2) the strong cleavage is detected at 5'-Pu_Pu/3'-PyPuPy sequences, and (3) dynemicin H (aromatized form of dynemicin A) gives only a small inhibition effect (20%) on the cleavage of gapped duplex by dynemicin A. The long half-life of aromatization of dynemicin A (118 min, in the presence of DNA) obtained from HPLC analysis provides enough time for the second cleavage. The present results strongly indicate a two-step mechanism for the double-stranded DNA scission of dynemicin A. Namely, this double-stranded break is caused by two drug molecules, each of which cuts one DNA strand.