[Specificiety of DNA-protein interactions within transcription complexes of Escherichia coli].

Current requirement for description of each new promoter assumes identification of all DNA-protein and protein-protein contacts important for transcription complex formation. Experimental approaches allow estimating which one of seven alternative sigma-subunits is employed for RNA synthesis and verifying transcription dependence on known regulatory proteins. Promoter sequence by itself also contains this information.

[Levels in the structural organization of Escherichia coli promoter DNA].

A number of additional structural elements were identified by statistic analysis of nucleotide sequences in promoters recognized by Escherichia coli RNA polymerase. Together with canonical hexanucleotides, these elements characterize different levels in the structural organization of promoter DNA. Sequence motifs exhibiting the highest statistical significance, which dominate in the contact regions with RNA polymerase alpha and sigma subunits, are considered as targets for specific interaction with RNA polymerase.

[Sequence-determined conformational changes in the coding region of the promoter DNA on transcription complex formation].

Chemical footprinting was used to study the spatial structure of bacteriophage T7 promoter D upon formation of the transcriptionally active complex with Escherichia coli RNA polymerase. Enzyme binding was shown to induce conformational changes in sites located at positions 43 and 57, several helix turns away from the transcription start. This was the first finding of a structural deformation induced by assembly of the transcription complex.