THE FUNDAMENTAL RIBOSOMAL-RNA TRANSCRIPTION INITIATION FACTOR-IB (TIF-IB, SL1, FACTOR-D) BINDS TO THE RIBOSOMAL-RNA CORE PROMOTER PRIMARILYBY MINOR-GROOVE CONTACTS

Acanthamoeba castellanii transcription initiation factor-IB (TIF-IB) i s the TATA-binding protein containing transcription factor that binds the rRNA promoter to form the committed complex. Minor groove-specific drugs inhibit TIF-IB binding, with higher concentrations needed to di srupt preformed complexes because of drug exclusion by bound TIF-IB. T IF-IB/DNA interactions were mapped by hydroxyl radical and uranyl nitr ate footprinting. TIF-IB contacts four minor grooves in its binding si te. TIF-IB and DNA wrap around each other in a right-handed superhelix of high pitch, so the upstream and downstream contacts are on opposit e faces of the helix. Dimethyl sulfate protection assays revealed limi ted contact with a few guanines in the major groove. This detailed ana lysis suggests significant DNA conformation dependence of the interact ion.