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 > chromomycin 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, 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.