SUNY at Albany
June 19-23, 2001
The quest for new forms of promoter determinants. Relationship of promoter nucleotide sequences to their electrostatic potential distribution
Using original method , calculation of electrostatic potential distribution was performed for some native promoters of T4 DNA as well as for three synthetic promoters pS1, pS2, and pS3 and their derivatives containing phased A-tracts located at different positions upstream of the ?35 hexamer ? A3-40, A3-42, A3-44, A3-46 and A3-48 constructions . In the case of pS1, pS2 and pS3 promoters, differences in their nucleotide sequences result in local changes in the corresponding region of their profiles of electrostatic potential distribution. In contrast, local difference in nucleotide sequences of A3-44 and A3-48 promoters (position ?35 to -39) causes long-range changes located much further upstream in the profiles of electrostatic potential distribution, thus indicating the presence of hypersensitive electrostatic sites in some promoters (fig. 1a).
Fig 1. Profiles of electrostatic potential distributions for three synthetic promoters (a, left)) and for two T4 DNA promoters (b, right). X axis is nucleotide position relatively to transcription start, Y axis is electrostatic potential, in arbitrary scale.
It is interesting that topologies of electrostatic potential distribution for P12.8 and P54.4 native promoters of T4 phage match almost exactly (fig 1b), although they essentially differ in nucleotide sequences. On the other hand, promoters P54.4 and P164.5 belonging to the same class by their nucleotide sequences are characterized by different types of electrostatic potential distribution. In all cases functional behavior of these promoters correlates well with their electrostatic characteristics. The data indicate that electrostatic characteristics of promoter DNA can be one of new promoter determinants marked by its relative independence from promoter nucleotide sequences. This work was supported by the Russian Foundation for Basic Research (grant 99-04-48177).
* A.A. Sorokin(1), T.R. Dzhelyadin(1), N.N. Ivanova(1), R.V. Polozov(2), S.G. Kamzolova(1)
(1)Institute of Cell Biophysics of RAS,