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Book of Abstracts: Albany 2009

category image Albany 2009
Conversation 16
June 16-20 2009
© Adenine Press (2008)

Electrostatic Properties of Promoter and Nonpromoter Sites in T7 Bacteriophage Genome

The entire T7 bacteriophage genome contains 39937 base pairs (Database NCBI RefSeq N1001604). Here, electrostatic potential distribution around double ? helical T7 DNA was calculated by Coulomb method (1) using the computer program of Sorokin A.A. (lptolik@icb.psn.ru). Electrostatic profiles of 17 promoters recognized by T7 phage specific RNA-polymerase were localized on T7 DNA electrostatic map.

Comparative analysis of electrostatic properties of T7 DNA promoter and nonpromoter sites was carried out. Electrostatic profiles of all T7 RNA-polymerase specific promoters are shown in Figure 1. Although electrostatic profiles of the individual promoters differ by their details, they have some common features. When superimposed, they reveal a well-defined wave-shaped design with minimum at ? 10bp and a higher potential at the start point of transcription. By contrast, no common specific elements were found in electrostatic profiles of T7 DNA nonpromoter sites (Fig. 2). Electrostatic pattern of superimposed profiles of these sites can be characterized by a rather homogeneous distribution of electrostatic potential.

It is interesting that electrostatic profiles of promoters recognized by E. coli or T7 phage specific RNA-polymerases differ in their size and design. Electrostatic profile of E. coli RNA-polymerase specific promoters embraces 200 base pairs (-150 - +50) (2). The most noticeable electrostatic signals involved in recognition of this enzyme were found in far upstream region of promoter DNA(-70 ? -120) (3, 4). By contrast, there are no specific electrostatic elements in this region of T7 RNA-polymerase specific promoters. All electrostatic signals recognized by T7 RNA-polymerase are located in the region from -35 bp to + 15 bp of promoter DNA (Fig. 1).

Thus, electrostatic potential distribution around DNA provides an effective means for identification of promoter sites in genome and their differentiation by different RNA-polymerases.



Figure 1: Distribution of electrostatic potential around T7 RNA-polymerase specific promoters.




Figure 2: Distribution of electrostatic potential around T7 DNA nonpromoter sites (random sequences).

References and Footnotes
  1. Polozov, R. V., Dzhelyadin, T. R., Sorokin, A. A., Ivanova, N. N., Sivozhelezov, V. S., Kamzolova, S. G. J Biomol Struct Dyn 16, 1135-1143 (1999).
  2. Kamzolova, S. G., Sorokin, A. A., Dzhelyadin, T. D., Beskaravainy, P. M., Osypov, A. A. J Biomol Struct Dyn 23, 341-346 (2005).
  3. Kamzolova, S. G., Sivozhelezov, V. S., Sorokin, A. A.,. Dzhelyadin, T. R, Ivanova, N. N., Polozov, R. V. J Biomol Struct Dyn 18, 325-334 (2000).
  4. Sorokin, A. A., Osypov, A. A., Dzhelyadin, T. R., Beskaravainy, P. M., Kamzolova, S. G. J Bioinform Comput Biol 4, 455-467 (2006).

S. G. Kamzolova1
P. M. Beskaravainy1*
A. A. Sorokin1,2

1Inst of Cell Biophysics of RAS
Pushchino Moscow Region 142290
Russia
2The Univ of Edinburgh
Kings Buildings
Edinburgh, EH93JR
UK

*beskaravainy@gmail.com asorokin@inf.ed.ac.uk