Polozov RV, Dzhelyadin TR, Sorokin AA, Ivanova NN, Sivozhelezov VS, Kamzolova SG. Electrostatic potentials of DNA. Comparative analysis of promoter and nonpromoter nucleotide sequences.
J Biomol Struct Dyn 1999;
16:1135-43. [PMID:
10447198 DOI:
10.1080/07391102.1999.10508322]
[Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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.
Collapse