Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences.

Distribution of electrostatic potential of DNA fragments was evaluated. A m ethod for calculation of electrostatic potential distribution based on Coul omb's law is proposed for long DNA fragments (similar to 1000 nucleotide pa irs). For short DNA sequences, this technique provides a,good correlation w ith the results obtained using Poisson-Boltzmann equation thus justifying i ts application in comparative studies for long DNA fragments. Calculation w as performed for several DNA fragments from E. coli and bacteriophage T7 ge nomes containing promoter and nonpromoter regions. The results obtained ind icate that coding regions are characterized by more homogeneous distributio n of electrostatic potential whereas local inhomogeneity of DNA electrostat ic profile is typical for promoter regions. The possible role of electrosta tic interactions in RNA polymerase-promoter recognition is discussed.