Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA.
BACKGROUND
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.
Zhang
Shang-Hong
SH
The Key Laboratory of Gene Engineering of Ministry of Education, and Biotechnology Research Center, Sun Yat-sen University, Guangzhou 510275, China. lsszsh@mail.sysu.edu.cn
Huang
Ya-Zhi
YZ
D019295:Computational Biology / Q000379:methods*; D004277:DNA, Single-Stranded / Q000737:chemistry*; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry
D004277:DNA, Single-Stranded; D009838:Oligodeoxyribonucleotides