title: Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content.
abstract: BACKGROUND
  Periodic spacing of A-tracts (short runs of A or T) with the DNA helical period of ~10-11 bp is characteristic of intrinsically bent DNA. In eukaryotes, the DNA bending is related to chromatin structure and nucleosome positioning. However, the physiological role of strong sequence periodicity detected in many prokaryotic genomes is not clear.
  
  
  RESULTS
  We developed measures of intensity and persistency of DNA curvature-related sequence periodicity and applied them to prokaryotic chromosomes and phages. The results indicate that strong periodic signals present in chromosomes are generally absent in phage genomes. Moreover, chromosomes containing prophages are less likely to possess a persistent periodic signal than chromosomes with no prophages.
  
  
  CONCLUSIONS
  Absence of DNA curvature-related sequence periodicity in phages could arise from constraints associated with DNA packaging in the viral capsid. Lack of prophages in chromosomes with persistent periodic signal suggests that the sequence periodicity and concomitant DNA curvature could play a role in protecting the chromosomes from integration of phage DNA.
authors.affiliation: Department of Microbiology, University of Georgia, Athens, GA 30602, USA.
authors.forename: Jacob
authors.initials: J
authors.lastname: Abel
authors.forename: Jan
authors.initials: J
authors.lastname: Mrázek
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000821:virology; D001483:Base Sequence; D002876:Chromosomes, Bacterial / Q000235:genetics*; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics*; D009690:Nucleic Acid Conformation; D011387:Prokaryotic Cells / Q000378:metabolism*; D039002:Prophages / Q000235:genetics*; D016662:Virus Integration / Q000235:genetics
chemical_list: D004269:DNA, Bacterial