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

• Published in: Bioinformatics 2010-02, Vol.26 (4), p.478-485
• Main Authors: Zhang, Shang-Hong, Huang, Ya-Zhi
• Format: Article
• Language: English
• Subjects: Biological and medical sciences; Computational Biology - methods; DNA, Single-Stranded - chemistry; Fundamental and applied biological sciences. Psychology; General aspects; Genes, Bacterial; Genome, Bacterial; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Nucleic Acid Conformation; Oligodeoxyribonucleotides - chemistry
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btp703

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. Contacts: [e-mail]; [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.