Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences.
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.
Polozov
R V
RV
Institute of Theoretical and Experimental Biophysics of RAS, Pushchino Moscow region, Russia. polozov@venus.iteb.serpukhov.su
Dzhelyadin
T R
TR
Sorokin
A A
AA
Ivanova
N N
NN
Sivozhelezov
V S
VS
Kamzolova
S G
SG
D027321:Anion Transport Proteins; D001426:Bacterial Proteins / Q000235:genetics; D017123:Bacteriophage T7 / Q000235:genetics; D001483:Base Sequence; D004269:DNA, Bacterial; D004279:DNA, Viral; D004926:Escherichia coli / Q000235:genetics; D029968:Escherichia coli Proteins; D008565:Membrane Proteins / Q000235:genetics; D008780:Methyltransferases / Q000235:genetics; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D055672:Static Electricity; D014764:Viral Proteins / Q000235:genetics
C041424:0.3 protein, Enterobacteria phage T7; D027321:Anion Transport Proteins; D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004279:DNA, Viral; D029968:Escherichia coli Proteins; D008565:Membrane Proteins; C088104:NirC protein, Bacteria; C490243:NirC protein, E coli; D014764:Viral Proteins; D008780:Methyltransferases; C060508:uroporphyrin-III C-methyltransferase