BINDING OF DISTAMYCIN AND CHROMOMYCIN TO HUMAN IMMUNODEFICIENCY TYPE-1 VIRUS-DNA - A NONRADIOACTIVE AUTOMATED FOOTPRINTING STUDY

Sequence-selectivity of DNA-binding drugs was recently reported in a n umber of studies employing footprinting and gel retardation approaches . In this paper we studied sequence-selectivity of the binding of chro momycin and distamycin to DNA by performing DNase I footprinting and a nalysis of the cleaved fragments by the Pharmacia ALF(TM) DNA Sequenci ng System. As a model system we employed the long terminal repeat of t he human immunodeficiency type 1 virus. The main conclusion of our exp eriments is that automated analysis of DNase I footprinting is a fast and reliable technique to study drugs-DNA interactions. The results ob tained suggest that distamycin and chromomycin differentially interact with the long terminal repeat of the human immunodeficiency type 1 vi rus; this differential binding depends upon the DNA sequences recogniz ed. The data presented are consistent with a preferential binding of d istamycin to DNA sequences of the binding sites of nuclear factor kapp a B and transcription factor IID. By contrast, distamycin exhibits onl y weak binding to DNA sequences recognized by the promoter-specific tr anscription factor Sp1. Unlike distamycin, chromomycin preferentially interacts with the binding sites of the promoter-specific transcriptio n factor Sp1.