The Key Laboratory of Gene Engineering of Ministry of Education, and Biotechnology Research Center, Sun Yat-sen University, Guangzhou 510275, China.
Bioinformatics. 2010 Feb 15;26(4):478-85. doi: 10.1093/bioinformatics/btp703. Epub 2009 Dec 22.
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.
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.
链对称性现象存在于所有已研究的原核生物和真核生物基因组中，这可能为基因组进化提供线索。已经提出了几种可能的起源机制，包括：突变和选择没有链偏向性、链反转和茎环结构的选择。然而，这些机制对链对称性的相对贡献尚不清楚。在本文中，我们专门研究了单链 DNA 茎环结构的潜力在链对称性中的作用。
我们分析了 90 个原核生物的完整基因组。我们发现大多数寡核苷酸（五核苷酸及更高）在基因组序列中没有紧密互补的反向互补物。结合进一步的分析，我们得出结论，单链基因组 DNA 的广泛茎环结构的潜力对链对称性的形成和维持的贡献将是非常有限的，至少对于高阶寡核苷酸是如此。因此，必须更深入地考虑链对称性的其他可能原因。
