title: Effect of DNA structural flexibility on promoter strength--molecular dynamics studies of E. coli promoter sequences.
abstract: To study possible correlations between promoter activity and the structural flexibility of the DNA helix, we have carried out unrestrained molecular dynamics simulations of the -10 consensus region sequence and five variants forming the -10 region of various Escherichia coli promoter sequences. Analyses of the trajectories obtained from the simulations show that the consensus sequence has a pattern of two structurally flexible nucleotide steps sandwiched between two stiff steps. In the other sequences, this pattern varies in consonance with the change in the sequence. The variations in the patterns show correlation with the promoter strength.
authors.affiliation: Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu 600 025, India.
authors.forename: S
authors.initials: S
authors.lastname: Thiyagarajan
authors.forename: S S
authors.initials: SS
authors.lastname: Rajan
authors.forename: N
authors.initials: N
authors.lastname: Gautham
mesh_terms: D001483:Base Sequence; D019295:Computational Biology; D003198:Computer Simulation; D004269:DNA, Bacterial / Q000737:chemistry*; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D005798:Genes, Bacterial / Q000235:genetics; D008957:Models, Genetic; D008968:Molecular Conformation; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic
chemical_list: D004269:DNA, Bacterial