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Background: Strand symmetry, a ubiquitous phenomenon existing in all cellular genomes studied, is the marked similarity of the frequencies of oligonucleotides to those of their respective reverse complements within single strands of sufficiently long genomic sequences.It is one of the major causes for the existence of two common profiles for genomic oligonuc[eotide frequencies (Zhang and Wang, Genomics 2011, 97:330-331).However, the riddle of strand symmetry is far from being unraveled.One of the hypotheses for its origin is the selection of stem-loop structures in single-stranded genomic DNA.Though our previous work has indicated that stem-loop potential of single-stranded genomic DNA would contribute little to strand symmetry for higher-order oligonucleotides (Zhang and Huang, Bioinformatics 2010, 26: 478-485), its contribution to lower-order strand symmetry is not clear.Methods: We analyzed 90 representative prokaryotic genomes (including archaea and bacteria and with a wide range of GC content).Fragments of genomic sequences were obtained by a sliding window of various lengths (200 bp, 500 bp, 1000 bp and 5000 bp, respectively).We evaluated the stem-loop potential of fragnents of genomic sequences in terms of folding energies (dG in kcal/mol) and calculated the symmetry indexes of the corresponding fragments for correlation analysis.Results: There is not an overall correlation pattern for the folding energies and symmetry indexes.The coefficients of correlation may be positive or negative, and may be significant or nonsignificant.In addition, while symmetry indexes increase with the lengths of fragments of genomic sequences, their correlations with the corresponding folding energies usually decrease, especially for lower-order oligonucleotides.Results of the correlation analysis are in contradiction with the assumption of the stem-loop hypothesis.Conclusions: The contribution of local stem-loop potential of single-stranded genomic DNA to the formation and maintenance of strand symmetry would be very limited, not only for higher-order oligonucleotides, but also for mono-, di-, tri-and tetranucleotides.Therefore, other hypotheses for the origin of the phenomenon of strand symmetry must be considered further .