MODEL PROKARYOTIC PROMOTER .5. FOOTPRINTING OF ESCHERICHIA-COLI RNA-POLYMERASE COMPLEXES WITH CONSTRUCTS CONTAINING REPEATED PRIBNOW BOXES

Permanganate footprinting was used to study complex formation in vitro and in vivo between Escherichia coli RNA polymerase and DNA construct s containing synthetic palindromic inserts with a varied copy number o f the TATAATg consensus (Pribnow box, PB) of the prokaryotic promoter -10 region. The entire insert proved to be susceptible to permanganate in vitro; the relatively symmetrical distribution of modified bases i n both strands regardless of the repeat number testified to the presen ce of various open complexes involving practically all PB-containing s tructures. In contrast, interaction of the constructs with RNA polymer ase in vivo was asymmetrical, which indirectly supported the earlier d ata that all the structures had a single active transcription start si gnal. The differences in the location of permanganate-sensitive bases in the presence and in the absence of rifampicin indicated that the en zyme could halt at the palindromic structure in an open, abortive and/ or paused transcription complex.