Journal Article

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

Shang-Hong Zhang and Ya-Zhi Huang

in Bioinformatics

Volume 26, issue 4, pages 478-485
Published in print February 2010 | ISSN: 1367-4803
Published online December 2009 | e-ISSN: 1460-2059 | DOI:
Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA

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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 higher-order oligonucleotides. Therefore, other possible causes for strand symmetry must be taken into account to a deeper degree.


Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  6760 words. 

Subjects: Bioinformatics and Computational Biology

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