Trends in Genetics
Genome AnalysisStrand misalignments lead to quasipalindrome correction
Section snippets
Frequency of quasipalindromes within complete genomes
One would expect that correction of quasipalindromes over a period of time should result in an increase in the frequency of perfect palindromes within the bacterial genome. The repetitiveness of genomes has been investigated before [8], as well as frequencies of specific repeats in single genomes 9, 10. Here we test sequenced bacterial genomes for the frequencies of quasipalindromes and perfect palindromes, and compare them with expected values. In Fig. 3, we show that the relative frequencies
Cruciform atlases for localization of palindromes with genomes
Palindromes are not homogeneously distributed throughout the chromosome, and the localization of quasipalindromes and perfect palindromes can be plotted in a ‘DNA atlas’ format, as described previously 13, 14, 15. Figure 5 shows a cruciform atlas for Bacillus anthracis plasmid pX01 [16]. The left-hand side of the figure has a higher fraction of palindromes than the rest of the genome. This region contains a 44 800-bp pathogenicity island, located between the two IS1627 insertion sequence (IS)
Potential for DNA directed mutational change at quasipalindrome
Quasipalindrome correction mutations constitute one class of mutation hotspot. The DNA symmetry elements allow the formation of DNA secondary structures that promote mutation. In addition, the inverted repeat nature of the sequence provides the opportunity that during leading strand replication of the quasipalindrome, a second complementary copy of the template exists in single stranded form in the lagging strand template, which might also contribute to the high frequency of mutation at
Acknowledgements
Support for research on quasipalindrome corrections mutations was provided by grant ES 05508 from the National Institute of Environmental Health Sciences, National Institutes of Health to R.R.S. D.W.U. and P.W. are supported by a grant from the Danish Research Foundation. Work in the W.A.R. laboratory is supported by a grant from the Bovaird Center for Studies in Molecular Biology and Biotechnology. The authors thank Hans Henrik Stærfeldt, Lars Juhl Jensen and Jacob L. Reimers for their help.
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