The Fourier spectra of more then 400 E.coli DNA promoter sequences have been obtained with the aid of Matrix Fourier analysis [Makeev & Tumanyan, 1996] using the computer program PERF. The typical and individual properties of these spectra were analyzed. We observed wide diversity in the Fourier spectra of different promoters. The Fourier spectra of promoter sequences were compared with that of adjacent to them regions of DNA. We observed differences between Fourier spectrum of a given promoter sequence and Fourier spectra of adjacent to it DNA regions.
The relation between promoter nucleotide sequence periodicities and promoter efficiency has been established.
We found also periodicities in the RNA polymerase contacts on the promoters lacUV5, tetR, T7 A3, RNA1, trp S.t., lambda cinand lambda c17 on the basis of the results of protection and premodification experiments from [Chenchick et al., 1981, Duval-Valentin et al., 1986]. The comparison of periodicities in contacts of core RNA polymerase on the lacUV5 promoter and that of holoenzyme on the basis of experimental data from [Chenchick et al., 1981] revealed more prominent 7-fold periodicity in Fourier-spectrum of the holoenzyme contacts. Comparison of the Fourier spectra of the RNA polymerase contacts on seven different promoters revealed that despite of diversity of these spectra, they share some common features. It is possible that RNA polymerase recognizes specific periodic pattern in the promoter structure.
This work was supported by Russian Foundation for Basic Research grant