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Updated: Jun 17, 2026

Studying DNA Looping by Single-Molecule FRET
Published on: June 28, 2014
Limited contribution of stem-loop potential to symmetry of single-stranded genomic DNA
Shang-Hong Zhang1, Ya-Zhi Huang
1The 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
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.
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