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Book of Abstracts: Albany 2011

category image Albany 2011
Conversation 17
June 14-18 2011
©Adenine Press (2010)

Electrostatic Properties of T7 RNA Polymerase Specific Promoters

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

Here, electrostatic properties of 17 T7 RNA-polymerase specific promoters where studied, , and this has been recently reported to play an important role in protein-nucleic acid recognition (1, 2). These promoters may be classified into three groups according to their expression time and functional characteristics of the corresponding genes: class ”early” (subgroup of class II), class II and class III (1). All the promoters have been erlier characterized in detail by their interaction with RNA-polymerase and transcription initiation (3, 4). Their sequences are characterized by comparatively extended consensus sequence (23 bp) with a high level of homology for all promoters but, despite their considerable sequence similarity, the different promoter classes differ by their strengths and by many other biochemical properties (3, 4). Thus, the choice of these promoters for our study was motivated by their unusual functional characteristics differing from ”consensus sequence rule” behavior.

Electrostatic potential distribution around duble-helical DNA of the promoters was calculated by the Coulombic method (5) using a new computer program (6).

Electrostatic profiles of the individual promoters were combined into three corresponding groups and the averaged electrostatic profiles of these separate groups were calculated as indicated in (6). The data obtained are shown in figure 1. The profiles of the promoters can be characterized by the presence of particular electrostatic elements in the region from -25 bp to + 20 bp wich is known to be involved in contacts with T7 RNA-polymerase. These electrostatic elements are specific for the different promoter groups. The promoters belonging to class II are characterized by two valleys at ~ -18 bp to ~ -5 bp and a more positive flanking site at +5 bp. In contrast, the promoters belonging to class III has the only most expressed negative fall at ~ -18 bp and two peaks downstream at ~ + 5 bp and ~ +20 bp. The promoters belonging to the ”early” group are characterized a more smoothed profile. They are located within coding region transcribed by the host E. coli RNA-polymerase. This can account for a more smoothed profile of this group since the variation of average electrostatic potential is more homogeneous in nonpromoter DNA.

Thus, electrostatic patterns of T7 DNA promoters are distinguished owing to specific motifs wich may be involved as signal elements in differential recognition of T7 RNA-polymerase specific promoters by the enzyme.

P.M. Beskaravainy1,2*
A.A. Osypov1
G.G. Krutinin1
E.A. Krutinina1
S.G. Kamzolova1

1Institute of Biophysics RAS Pushchino Moscow Region 142290 Russia
2Institute of Theoretical and Experimental Biophysics RAS Pushchino Moscow Region 142290 Russia

beskaravainy@gmail.com


Fig. 1. The averaged profiles of electrostatic potential distribution around T7 RNA-polymerase specific promoters belonging to different functional group.

References
  1. S.M. West, R. Rohs, R. S. Mann, B. Honig, J Biomol Struct Dyn 27, 861-866 (2010)
  2. D. Wang, N. B. Ulyanov, V. B. Zhurkin, J Biomol Struct Dyn 27, 843-859 (2010)
  3. J. J. Dunn , F. W. Studier, Proc Natl Acad Sci USA. 70, 1559-63 (1973).
  4. W. T. McAllister, C. Morris, A. H. Rosenberg, F. W. Studier, J Mo Biol 153, 527-44 (1981).
  5. R. V. Polozov, T. R. Dzhelyadin, A. A. Sorokin, N. N. Ivanova, V. S. Sivozhelezov, S. G. Kamzolova, J Biomol Struct Dyn 16, 1135-43 (1999)
  6. A. A. Osypov, G. G. Krutinin, S. G. Kamzolova, J Bioinf Comp Biol 8, 413-25 (2010).