Distribution of electrostatic potential around nucleotide sequences is one of fundamental characteristics of DNA contributing to its recognition by DNA-binding proteins. Using original method (1, 2), calculation of electrostatic potential distribution was performed for complete nucleotide sequence of E. coli genome containing 4639221 base pairs.

The results obtained representing the profile of electrostatic potential distribution around the complete genome are in our database (lptolik@icb.psn.ru).

The possibility of extracting some functional information from the electrostatic map of E. coli genome can be demonstrated by the example provided by a large-scale analysis of electrostatic patterns of promoter and nonpromoter DNA sites. Electrostatic profiles of 425 σ⁷⁰-specific promoters and of their nearby coding sequences were analyzed by the presence of peaks and valleys as well as by their arrangement and values. It is found that coding regions are characterized by more homogeneous distribution of electrostatic potential, whereas local inhomogeneities with the most positive and negative areas correspond to promoter sites. It should be noted that individual promoters vary in the design of their electrostatic profiles but all of them, in contrast to coding regions, are characterized by inhomogeneous complex-shaped patterns. These characteristic variations of electrostatic potential of DNA may be related to RNA polymerase-promoter recognition in genome.

Acknowledgement

This work was supported by Russian Foundation for Basic Research (grant RFBR-naukograd 04-04-97275).

References and Footnotes

1. Kamzolova S. G., Sivozhelezov V. S., Sorokin A. A., Dzhelyadin T. R., Ivanova N. N., and Polozov R. V. J. Biomol. Struct. Dyn. 18, 325-334 (2000).
2. Sorokin A. A. Functional Analysis of E. coli Promoter Sequences. New Promoter Determinants. Ph. D. Thesis. Pushchino, Institute of Theoretical and Experimental Biophysics RAS. 2001.