Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA

Abstract

Motivation: The phenomenon of strand symmetry, which may provide clues to genome evolution, exists in all prokaryotic and eukaryotic genomes studied. Several possible mechanisms for its origins have been proposed, including: no strand biases for mutation and selection, strand inversion and selection of stem-loop structures. However, the relative contributions of these mechanisms to strand symmetry are not clear. In this article, we studied specifically the role of stem-loop potential of single-stranded DNA in strand symmetry. Results: We analyzed the complete genomes of 90 prokaryotes. We found that most oligonucleotides (pentanucleotides and higher) do not have a reverse complement in close proximity in the genomic sequences. Combined with further analysis, we conclude that the contribution of the widespread stem-loop potential of single-stranded genomic DNA to the formation and maintenance of strand symmetry would be very limited, at least for higherorder oligonucleotides. Therefore, other possible causes for strand symmetry must be taken into account to a deeper degree. Contacts: lsszsh@mail.sysu.edu.cn, molevol@mail.sysu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. © The Author 2009. Published by Oxford University Press.