Effect of drug-DNA interactions upon transcription initiation at the lac promoter

We have examined the effects of six DNA binding drugs upon initiation at the lac UV5 promoter by Escherichia coli RNA polymerase. Experiments were directed at determining the influence of added drug on open complex formation, open complex stability, initiation from the open complex, and stability of the resulting initiated complex. The narrow groove binding drugs distamycin and 4',6-diamidino-2-phenylindole dihydrochloride were more effective in inhibiting initiation through their effect on the first three of these factors than were the intercalators ethidium bromide, daunomycin, and actinomycin. The bisintercalator bis(daunomycin) inhibited open complex formation better than its parent daunomycin. With the possible exception of actinomycin, the drugs tested were not able to disrupt preformed initiated complex, in contrast to their destabilizing effect upon the open complex. Combined with other results, the data suggest that the antitumor activity of daunomycin is unlikely to result from its effect on transcription. We compare the relative effectiveness of the drugs with the known physical properties of the corresponding drug-DNA interactions. The rate of open complex formation seems to be influenced by both the on and off rates of the drug, probably due to the relative slowness of open complex formation. This is in contrast to elongation, a much quicker process, which seems to be limited by the drug off rate alone; these considerations may possibly rationalize the difference in relative effect of particular drugs upon initiation and elongation. All drugs were able actively to disrupt open complex, although to substantially different extents; some possible mechanisms for this disruption, and the insensitivity of the initiated complex, are discussed.