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Open Access Research article

Differences in DNA curvature-related sequence periodicity between prokaryotic chromosomes and phages, and relationship to chromosomal prophage content

Jacob Abel13 and Jan Mrázek12*

Author Affiliations

1 Department of Microbiology, University of Georgia, Athens, GA, 30602, USA

2 Institute of Bioinformatics, University of Georgia, Athens, GA, 30602, USA

3 Present address: School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA

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BMC Genomics 2012, 13:188  doi:10.1186/1471-2164-13-188

Published: 15 May 2012

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.

Keywords:
Prokaryotic genome; DNA bending; Nucleoid structure; Prophage integration; Virus; DNA packaging