Stability of DNA repeats in Escherichia coli dam mutant strains indicates a Dam methylation-dependent DNA deletion process

In this study we report on the stabilization of short direct repetitive DNA elements. We arranged a 20 bp SK-primer element in a direct repeat manner within the cloning vector pBluescript KS (+). This resulted in an array of 27 direct repeats consisting of 24 bp units. We show that this plasmid coul d only be propagated without deletion of repeats in dam mutant Escherichia coli hosts, whereas all efforts to use strains that were defective in the m ethylation-dependent restriction system and the recA- or the mismatch repai r-dependent deletion system failed. The deletions always affected whole rep eat units and not parts of them, leading to an unpredictable reduction of t he unit number down to a range of between 12 and two during propagation. We conclude that a Dam methylation-dependent, but recA- and mismatch repair-i ndependent, deletion mechanism caused the DNA rearrangements without an obv ious involvement of the known methylated-DNA restriction systems. (C) 2000 Elsevier Science B.V. All rights reserved.