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Nucleic Acids Research, 1994, Vol. 22, No. 8 1342-1345
© 1994

CHEMISTRY

DNA sequence specificity of mitoxantrone

Con Panousis and Don R. Phillips*

Department of Biochemistry, La Trobe University Bundoora, Victoria 3083, Australia

*To whom correspondence should be addressed

Received March 9, 1994. Accepted March 16, 1994.

An in vitro transcription assay was used to determine the sequence specificity of binding of mitoxantrone to a 497 bp fragment of DNA containing the lac UV5 promoter. Transcriptlonal blockages of the E.coli RNA polymerase were observed domlnantly prior to 5'-CpA sequences (64% occurrence), and to a lesser extent 5'-CpG sequences (29%). Overall, 93% of all blockage sites were prior to pyrimldine (3'-5') purine sequences. An effect of flanking sequences was evident since the blockage sites contained an A/T base pair 5' prior to the consensus CpA and CpG intercalation sites. The consensus sequences for the preferred mitoxantrone intercalation sites are therefore 5'-(A/T)CA and 5'-(A/T)CG. The location of transcriptlonal blockages one base pair prior to the intercalation site is consistent with the fact that the mitoxantrone side chains lie in the major groove.


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