In vitro effects of acridine intercalation on RNA polymerase interactions with supercoiled DNA

In vitro transcription of supercoiled DNA by purified E. coli RNA polymerase was inhibited by Acridine Orange in a bimodal manner while N-10 benzyl substituted Acridine Orange is about one-third as inhibitory and effects monophasic inhibition. The inhibition correlates with the supercoil unwinding abilities of these two intercalators with Acridine Orange unwinding supercoiled DNA at 1/3 the concentration required for the substituted acridine orange. Direct visualization of DNA-RNA polymerase complex on agarose gels showed that these intercalators directly interfere with this association and the more effective the drug is in unwinding DNA supercoils the more effective it is in interfering with the DNA-enzyme complex. In addition, specific intercalators differentially affect the stability of DNA-RNA polymerase-RNA ternary complexes.