Persistence of cruciform structure and preferential location of nucleosomes on some regions of pBR322 and ColE 1 DNAs.

Inverted repeats of pBR322 and ColE 1 DNAs have been analyzed for the presence of cruciform structures upon formation of nucleosomes, using S1, P1 and restriction enzyme analysis. In both cases the fraction of molecules showing nuclease-sensitive sites is unaffected by the DNA relaxation, owing to the formation of nucleosomes. A kinetic mechanism, based on the freezing of cruciform structures on the nucleosome surface or nearby, is proposed. This hypothesis is supported by a preferential location of nucleosomes at the DNA sequences containing the nuclease-sensitive sites, as indicated by restriction enzyme analysis and electron microscopy visualization after psoralen cross-linking.