Effect of DNA-binding drugs on early growth response factor-1 and TATA box-binding protein complex formation with the herpes simplex virus latency promoter

Adjacent binding sites for early growth response factor-1 (EGR1) and TATA box-binding protein (TBP) were identified on the herpes simplex virus latency promoter in previous work. The binding of EGR1 to the GC-rich region prevented TBP binding to the AT-rich region. With the simultaneous addition of both EGR1 and TBP, the intercalator nogalamycin prevented EGR1 complex formation, resulting in a dose-dependent increase of the TBP DNA complex. The minor groove binder chromomycin A(3) inhibited EGR1 complex formation but resulted in a smaller increase of the TBP complex. In contrast, an alkylating intercalator hedamycin strongly inhibited binding of both proteins. The ability of these GC-binding drugs to prevent EGR1 DNA complex formation was in the following order: hedamycin > nogalamycin > chro momycin A(3), and the specificity was nogalamycin > chromomycin A(3) > hedamycin, With transcription factor IIA (TFIIA) in the assay, TBP was able to bind the promoter whereas formation of the EGR1 DNA complex was reduced. An AT minor groove-binding drug, distamycin A(3) disrupted the TBP TFIIA DNA complex and restored the EGR1 DNA complex. We conclude that the binding motif and sequence preference of DNA-interactive drugs are manifested in their ability to inhibit the transcription factor-DNA complexes.