A model prokaryotic promoter. V. Footprinting E. coli RNA polymerase complex with constructs containing Pribnow sequence repeats
Koroleva, O.N.; Drutsa, V.L.; Basbi, S.J.
Molekuliarnaia Biologiia 31(1): 49-58
1997
ISSN/ISBN: 0026-8984 PMID: 9173246 Document Number: 472221
Footprinting by means of potassium permanganate was used to study in vivo and in vitro complex formation of E. coli RNA-polymerase with constructions containing palindromic synthetic DNA fragments with varying number of the repeats of the consensus structure of the prokaryotic promoter TATAATg (Pribnow box) 10th nucleotide area. It was shown that in vitro, the entire area of synthetic insertion was subjected to the effect of permanganate. Relatively symmetrical distribution of modified bases in both chains, regardless of the number of repeats, points to the presence in a solution of various open complexes that are formed with the participation of practically all Pribnow box-containing structures. On the other hand, the interaction of RNA-polymerase with these structures in vivo was of asymmetrical nature. This fact indirectly confirms obtained earlier data on the presence of only one active signal of transcription initiation in all structures. Differences in the localization of bases sensitive to the effect of permanganate in the presence or absence of permanganate show that the enzyme is able to remain in the palindromic structure area in open, initiator and/or elongation complexes.