Direct repeats at nuclear matrix-associated DNA regions and their putative control function in the replicating eukaryotic genome.

Short DNA regions, known to contain replication origins, were isolated from 2 M NaCl resistant nuclear structures of Physarum polycephalum after predigestion with DNase. Regions of 100 bp average length were cloned and sequenced. About 25% of the clones contained direct repeats of 12 to 16 bp and variable base sequences, that have been shown to possess the potential of playing a crucial role in the control of DNA replication. In one of the two alternative three-dimensional configurations such repeats expose single-stranded loops that can function as sites for the initiation of new DNA strands. As these regions are converted into full-length duplexes by their own replication, reinitiation at the same site is excluded. Restoration of the initiationable configuration is considered to be coupled to structural rearrangements involved in the transient condensation of chromosomes in mitosis. This mechanisms ensures that any part of the entire eukaryotic genome is reproduced just a single time during one cell cycle.