Book of Abstracts: Albany 2003

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Conversation 13
Abstract Book
June 17-21 2003

Electrostatic Properties of Promoter DNA. Approach to Classification Analysis.

Electrostatic interactions between promoter DNA and E.coli RNA polymerase have recently been shown to be of considerable importance in regulating promoter function (1, 2). Electrostatic characteristics of promoter DNA has been suggested to be a new promoter determinant marked by its relative independence from promoter nucleotide sequence (1, 2).

Using original method (3), distribution of electrostatic potential around 359 DNA fragments (500bp) containing individual promoters from E.coli, T4 and T7 phages was calculated. DNA electrostatic profiles of different promoters were analyzed for the presence of some characteristic elements in two domains: the first one is from ?90 to +1bp containing core promoter and near upstream region; the second one is from ?140 to ?50bp involving near upstream and far upstream regions.

Some groups of promoters with similar patterns of electrostatic potential in each of the DNA domains were revealed. The presence of specific elements in DNA electrostatic profiles of promoters belonging to the same group may be considered as an indication of a common mechanism in their functioning. In this connection it is interesting to note that T4 ?early? promoters possessing very similar nucleotide sequences but differing in their functional response to ADP-ribosylation of RNA polymerase alpha-subunit belong to different electrostatic promoter groups while T4 ?early? promoters with similar response to the enzyme modification fall in the same group. These groups were shown to be characterized by their specific electrostatic elements in far upstream region of promoter DNA, which are involved in RNA polymerase-promoter recognition by acting through electrostatic interactions with alpha-CTD of the enzyme (1). So, a direct correlation between electrostatic characteristics of promoter DNA and its functional behavior was observed in this case.

Thus, theoretical analysis of electrostatic potential of promoter DNA and classification of promoters by their electrostatic characteristics appeared to be a valuable method for identification of some new, potentially important ptomoter elements.

A. A. Sorokin1
T. R. Dzhelyadin1
N. N. Ivanova1
R. V. Polozov2
S. G. Kamzolova1

1Institute of Cell Biophysics of RAS
Pushchino, Moscow region
142290, Russia
2Institute of Theoretical and Experimental Biophysics of RAS
Pushchino, Moscow region
142290, Russia
Phone: 7(0967)739352

References and Footnotes
  1. Kamzolova S. G., Sorokin A. A., Dzhelyadin T. R., Ivanova N. N., Sivozhelezov V. S., Polozov R. V., J. Biomolec. Struct. Dyn. 18, 325-334 (2000).
  2. Sorokin A. A., Dzhelyadin T. R., Ivanova N. N., Polozov R. V., Kamzolova S. G., J. Biomolec. Struct. Dyn. 18, 1020 (2001).
  3. Polozov R. V., Dzhelyadin T. R., Sorokin A. A., Ivanova N. N., Sivozhelezov V. S., Kamzolova S. G, J. Biomolec. Struct. Dyn. 16, 1135-1143 (1999).