Palindromy is eliminated through a structure-specific recombination process in rodent cells

Higher eukaryotes are proficient at remodeling palindromic DNA. As shown here, a fully palindromic 15.4 kb circular DNA can be introduced into rodent cells with the novel result that the molecule is reproducibly and site-specifically converted to a monomeric circle. The dimer-to-monomer conversion has not been described previously, and in particular is undetectable in Escherichia coli. Comparative DNA sequence analyses of the new junctions found within the monomer circles suggest that the resolution process involves formation of hairpin DNA structures followed by the introduction of single-strand nicks near their termini. By extension, hairpin nicking combined with non-homologous end-joining may be important as a general mechanism for the main-tenance of genomic stability in mammalian cells. It is suggested that the absence of a comparable strategy for coping with palindrome-induced structure in E.coli and other unicellular organisms underlies a fundamental difference in DNA sequence organiz-ation in the genomes of prokaryotes versus higher eukaryotes.