S1 nuclease removes DNA from eukaryotic metaphase chromosomes: cytological evidence

Fixed and unfixed human chromosomes, as well as fixed rye chromosomes were treated with S1 nuclease, which specifically cleaves single stranded DNA. Subsequent staining with either acridine orange, ethidium bromide or Giemsa revealed that, contrary to what has previously been reported, S1 digestion extensively altered chromosomal morphology and staining intensity, although the alteration was more pronounced in fixed as compared to unfixed metaphases. A number of mechanisms, which may account for our findings, have been invoked: a) the presence in metaphase chromatin of B-DNA/Z-DNA transitional junctions, b) the induction, by alcohol: acid fixation procedure, of nicks within regular B-DNA conformation and c) the induction of sites available to S1 by torsional stress due to metaphase high condensation degree.