title: The DNA secondary structure of the Bacillus subtilis genome.
abstract: The entire genomic DNA sequence of the Gram-positive bacterium Bacillus subtilis reported in the SubtiList database has been subjected in this work to a complete bioinformatic analysis of the potential formation of secondary DNA structures such as hairpins and bending. The most significant of these structures have been mapped with respect to their genomic location and compared to those structures already known to have a physiological role, such as the rho-independent transcription terminators. The distribution of these structures along the bacterial chromosome shows two major features: (i). the concentration of the most curved DNA in the intergenic regions rather than within the ORFs, and (ii). a decreasing gradient of large hairpins from the origin towards the terC end of chromosomal DNA replication. Given the increasing biological relevance of secondary DNA structures, these findings should facilitate further studies on the evolution, dynamics and expression of the genetic information stored in bacterial genomes.
authors.affiliation: Microbiology Group, International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34012, Trieste, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Tosato
authors.forename: Kresimir
authors.initials: K
authors.lastname: Gjuracic
authors.forename: Kristian
authors.initials: K
authors.lastname: Vlahovicek
authors.forename: Sandor
authors.initials: S
authors.lastname: Pongor
authors.forename: Antoine
authors.initials: A
authors.lastname: Danchin
authors.forename: Carlo V
authors.initials: CV
authors.lastname: Bruschi
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry*; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames / Q000235:genetics
chemical_list: D004269:DNA, Bacterial