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Employing a newly developed uranyl photofootprinting technique (Nielsen et al. (1988) FEBS Lett. 235, 122), we have analyzed the structure of the E. coli RNA polymerase deoP1 promoter open complex. The results show strong polymerase DNA backbone contacts in the -40, -10, and most notably in the +10 region. These results suggest that unwinding of the -12 to +3 region of the promoter in the open complex is mediated through polymerase DNA backbone contacts on both sides of this region. The pattern of bases that are hyperreactive towards KMnO4 or uranyl within the -12 to +3 region furthermore argues against a model in which this region is simply unwound and/or single stranded. The results indicate specific protein contacts and/or a fixed DNA conformation within the -12 to +3 region.

nucleic acids research

Uranyl mediated photofootprinting reveals strong<i>E.coli</i>RNA polymerase-DNA backbone contacts in the +10 region of the<i>Deo</i>P1 promoter open complex

Uranyl mediated photofootprinting reveals strongE.coliRNA polymerase-DNA backbone contacts in the +10 region of theDeoP1 promoter open complex