DNA conformation at the 5' end of the chicken adult beta-globin gene.

We have examined the conformation of DNA cloned from the hypersensitive region 5' of the chicken adult beta-globin gene, in order to determine whether the unusual sensitivity to nucleases is related to altered secondary structure of the DNA. The region contains a large number of sites for methylation; we have studied the effect of methylation at HpaII sites on the topological properties of a small plasmid containing the region. We find that methylation does not alter the supercoiling properties of the plasmid under a wide variety of conditions; we find no evidence for conversion of any measurable segment of DNA to the Z conformation, even at high superhelix densities. We have also devised a protocol for mapping precisely the sites sensitive to S1 nuclease. The data are not consistent with the presence of cruciform structures. They reveal, however, a major cutting site located within a tract of 16 consecutive deoxyguanosine residues in the center of the hypersensitive region. Susceptibility to cutting is dependent upon supercoiling, but methylation at HpaII sequences has no effect on the S1 cutting pattern.