Electrostatic Potentials of DNA. Comparative Analysis of Promoter and Nonpromoter Nucleotide Sequences

Abstract

Distribution of electrostatic potential of DNA fragments was evaluated. A method for calculation of electrostatic potential distribution based on Coulomb's law is proposed for long DNA fragments (approximately 1000 nucleotide pairs). For short DNA sequences, this technique provides a good correlation with the results obtained using Poisson-Boltzmann equation thus justifying its application in comparative studies for long DNA fragments. Calculation was performed for several DNA fragments from E. coli and bacteriophage T7 genomes containing promoter and nonpromoter regions. The results obtained indicate that coding regions are characterized by more homogeneous distribution of electrostatic potential whereas local inhomogeneity of DNA electrostatic profile is typical for promoter regions. The possible role of electrostatic interactions in RNA polymerase-promoter recognition is discussed.

Deppdb — Dna Electrostatic Potential Properties Database: Electrostatic Properties of Genome Dna Elements

“…Though the method cannot be applied for rigorous treatment, it is quite suitable for qualitative analysis of electrostatic map of natural DNA molecule and for comparative studies of its di®erent parts. 7 For further analysis, the two-dimensional distribution of the potential was averaged along the azimuthal angle to yield a one-dimensional pro¯le.…”

“…We have suggested and used an approach to this problem based on the analysis of electrostatic properties of promoter DNA. Using the developed method for the whole-genome calculation of electrostatic potential distribution, 7 we revealed the general properties of genome DNA electrostatic potential pro¯le 7À10 and principles of its formation, 8 and explored the electrostatic properties of some genomes and the role of electrostatics in their functioning. 7À14 Studies of the general properties of genome DNA electrostatic potential pro¯le found that it correlates with the GC content, although it does not correspond to it exactly, and strongly depends on both the sequence arrangement and its context (°anking regions).…”

Salerno's Model of DNA Re-Analysed: Could Breather Solitons have Biological Significance?

“…The protein effectively slides, onedimensionally, along the groove through a series of nonspecific binding events. The translocation mechanism for the nonspecific complex is not known, but is ATP-independent [25] and widely assumed to be driven by thermal motion. Other possible diffusion modes include "hopping", where a nonspecifically bound protein dissociates and re-associates within the same DNA domain.…”

“…Finally the role of counterions in determining DNA structure such as bending and groove width [24] and affinity for such tracts is not yet fully understood. Sequence-dependent variations in the electrostatic surface of DNA may also present a unique "signature" in promoter regions [25].…”

70 Electrostatic properties of bacterial DNA and promoter predictions

“…Electrostatic potential distribution (EPD) around a DNA molecule seems to be the only physical property that could be recognized by other molecules from a distance. More than 10 years ago, a method for simple and fast calculation of EPD was proposed in our laboratory (Polozov et al, 1999). It is based on Coulomb formula and allows us to estimate the main EPD patterns for DNA sequences of a size of a whole prokaryotic genome.…”