Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Comparative Analysis of Electrostatic and Functional Properties of Some Synthetic A-Tracts Containing Promoters

Analysis of electrostatic properties of promoter DNA is a promising source for yielding information about promoter recognizable elements and their functioning.

Here were studied electrostatic properties of three synthetic consensus-like promoters Ps1, Ps2, Ps3, and the Ps1 derivatives Ps1/A3-40, Ps1/A3-44, and Ps1/A3-48, containing three A-tracts at different positions in upstream region of Ps1. All these promoters have been earlier characterized in details in comparative experiments by their interaction with RNA polymerase at different steps of complex formation and transcription initiation (1, 2). The choice of these promoters for our study was motivated by their unusual functional characteristics differing from ?consensus sequence rule? behavior; thus, stimulating a search of new promoter determinants.

Electrostatic potential distribution around double-helical DNA of the promoters was calculated by the Coulomb method (3) using the computer program of Sorokin A.A.

The insertion of A-tracts in upstream region of Ps1 strongly influences electrostatic properties of the promoter introducing many changes in its electrostatic pattern. That changes cover many sequences including those that are very far apart: in core sequences and downstream from the transcriptional start as well as in the far upstream region. The data show that there is no direct correlation between nucleotide sequence and its electrostatic pattern; thus, confirming independent character of promoter determinants based on electrostatic characteristics of promoter DNA and its structure.

The results obtained indicate that electrostatic characteristics of promoter DNA can be responsible for the interaction with RNA polymerase acting at early steps of complex formation.

Specific electrostatic motifs found in the upstream region of A-tracts containing promoters were shown to be involved as signal elements in differential recognition of the promoters by RNA polymerase alpha-subunit.


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

References and Footnotes
  1. Ellinger, T., Behnke, D., Bujard, H., Gralla, J.D. J Mol Biol 239, 455-465 (1994a).
  2. Ellinger, T., Behnke, D., Knaus, R., Bujard, H., Gralla, J. D. J Mol Biol 239, 466-475 (1994b).
  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. Kamzolova, S. G., Sorokin, A. A., Dzhelyadin, T. D., Beskaravainy, P. M., Osypov, A. A. J Biomol Struct Dyn 23, 341-346 (2005).

Anatoly A. Sorokin1, 2, *
Alexander A. Osypov2
Svetlana G. Kamzolova2

1The University of Edinburgh
Kings Buildings
Edinburgh, EH9 3JR, UK
2Institute of Cell Biophysics of RAS
Pushchino, Moscow region, Russia

*Phone: : +44 131 650 8282
Fax: +44 131 650 6513
Email: asorokin@inf.ed.ac.uk