Distribution of Inverted Repeat Sequences in Nuclear DNA from Physarum polycephalum

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Abstract
Inverted repeat sequences, capable of forming stable intra‐chain foldback duplexes, are shown using electron microscopy to be located in over 90% of fragments of nuclear DNA from Physarum polycephalum. A statistical treatment of the data indicates that, on average, foldback sequence foci are spaced every 7000 nucleotides and that they are distributed uniformly amongst the DNA chains. The majority of inverted repeat sequences give rise to the simple types of foldback structure observed in DNA from other eukaryotic species, but a significant proportion of the DNA fragments also contain novel foldback structures with a more complex appearance, referred to as ‘bubbld’ hairpins. The latter structures appear to be formed by the annealing of several distinct segments of homologous inverted repeat sequence, each separated by interspersed non‐foldback sequences of variable sizes up to 15000 nucleotides in length. The size, both of the foldback duplexes and of the intervening single‐chain segments of DNA, are not random. Instead, they appear to forma regular, arithmetic series of lengths. These obsevations suggest that the different segments of Physarum DNA from which foldback structures are derived contain nucleotide sequences that share a highly ordered and uniform pattern of structural organisation. These regular units of organisation in Physarum DNA in some cases cases extend over distances up to 50000 nucleotides in length.